Starting phenix.real_space_refine on Sun May 18 01:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.map" model { file = "/net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s94_40236/05_2025/8s94_40236.cif" } resolution = 3.94 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= -0.001 sd= 0.038 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 12 5.49 5 Mg 6 5.21 5 S 81 5.16 5 C 10230 2.51 5 N 2841 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16305 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "D" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "F" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 2 Chain: "E" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2844 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 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} Chain: "D" 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: "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: "F" 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: "E" 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: 10.25, per 1000 atoms: 0.63 Number of scatterers: 16305 At special positions: 0 Unit cell: (150.96, 149.85, 69.93, 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 81 16.00 P 12 15.00 Mg 6 11.99 O 3135 8.00 N 2841 7.00 C 10230 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: 3.80 Conformation dependent library (CDL) restraints added in 2.0 seconds 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 48.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.854A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.566A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 530 through 537 removed outlier: 3.574A pdb=" N GLU A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.818A pdb=" N LEU A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 3.815A pdb=" N ARG A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.794A pdb=" N LYS A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 701 removed outlier: 4.123A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.572A pdb=" N GLU A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 738 through 743 removed outlier: 4.026A pdb=" N GLU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 4.104A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.720A pdb=" N TYR D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 removed outlier: 4.516A pdb=" N GLY D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.873A pdb=" N ALA D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 330 " --> pdb=" O MET D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.809A pdb=" N LYS D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR D 369 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 3.787A pdb=" N LEU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 4.048A pdb=" N ASP D 407 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.735A pdb=" N GLU D 432 " --> pdb=" O HIS D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 468 through 473 removed outlier: 3.602A pdb=" N ASN D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 Processing helix chain 'D' and resid 520 through 531 Processing helix chain 'D' and resid 539 through 554 removed outlier: 3.868A pdb=" N ASN D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN D 544 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 569 Processing helix chain 'D' and resid 573 through 580 Processing helix chain 'D' and resid 589 through 604 removed outlier: 3.888A pdb=" N SER D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 removed outlier: 3.931A pdb=" N GLN D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS D 638 " --> pdb=" O LEU D 634 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 639 " --> pdb=" O ILE D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 654 removed outlier: 3.813A pdb=" N LEU D 645 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 646 " --> pdb=" O GLN D 642 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.508A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.668A pdb=" N LYS C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.602A pdb=" N ALA C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 537 removed outlier: 3.577A pdb=" N GLN C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.604A pdb=" N GLU C 607 " --> pdb=" O HIS C 603 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 613 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 674 removed outlier: 3.702A pdb=" N LYS C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 669 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY C 671 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR C 672 " --> pdb=" O LYS C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 701 removed outlier: 4.030A pdb=" N ARG C 687 " --> pdb=" O THR C 683 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 723 removed outlier: 3.662A pdb=" N GLU C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 748 through 753 removed outlier: 4.309A pdb=" N SER C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.620A pdb=" N TYR F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 309 removed outlier: 3.958A pdb=" N ARG F 303 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 309 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 330 removed outlier: 4.211A pdb=" N ALA F 325 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 369 removed outlier: 3.729A pdb=" N PHE F 361 " --> pdb=" O GLY F 357 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR F 369 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.698A pdb=" N LEU F 385 " --> pdb=" O THR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.738A pdb=" N ASP F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 427 through 433 removed outlier: 3.534A pdb=" N GLU F 432 " --> pdb=" O HIS F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 468 through 473 removed outlier: 3.584A pdb=" N ASN F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.829A pdb=" N SER F 481 " --> pdb=" O PRO F 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG F 482 " --> pdb=" O LEU F 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 478 through 482' Processing helix chain 'F' and resid 496 through 508 removed outlier: 3.509A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 531 Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.878A pdb=" N ASN F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL F 545 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 569 Processing helix chain 'F' and resid 571 through 577 removed outlier: 3.682A pdb=" N ALA F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 604 removed outlier: 3.506A pdb=" N MET F 604 " --> pdb=" O MET F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 639 removed outlier: 4.099A pdb=" N GLN F 627 " --> pdb=" O ASN F 623 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 637 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS F 638 " --> pdb=" O LEU F 634 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 654 removed outlier: 3.714A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER F 646 " --> pdb=" O GLN F 642 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU F 647 " --> pdb=" O SER F 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.636A pdb=" N LYS B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.586A pdb=" N GLU B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 613 removed outlier: 3.528A pdb=" N GLU B 607 " --> pdb=" O HIS B 603 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 613 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.730A pdb=" N LYS B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 671 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 701 removed outlier: 4.048A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 removed outlier: 3.607A pdb=" N GLU B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 748 through 753 removed outlier: 4.077A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.717A pdb=" N TYR E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 310 removed outlier: 4.480A pdb=" N GLY E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG E 303 " --> pdb=" O PRO E 299 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 330 removed outlier: 3.564A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY E 330 " --> pdb=" O MET E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.764A pdb=" N LYS E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.653A pdb=" N LEU E 385 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.814A pdb=" N ASP E 407 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 426 Processing helix chain 'E' and resid 427 through 433 removed outlier: 3.799A pdb=" N GLU E 432 " --> pdb=" O HIS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 468 through 473 removed outlier: 3.515A pdb=" N ASN E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 507 Processing helix chain 'E' and resid 520 through 531 Processing helix chain 'E' and resid 539 through 554 removed outlier: 3.872A pdb=" N ASN E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL E 545 " --> pdb=" O VAL E 541 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 569 Processing helix chain 'E' and resid 575 through 583 removed outlier: 3.507A pdb=" N ALA E 580 " --> pdb=" O ALA E 576 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG E 581 " --> pdb=" O GLU E 577 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET E 583 " --> pdb=" O HIS E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 604 removed outlier: 3.821A pdb=" N SER E 598 " --> pdb=" O ILE E 594 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 599 " --> pdb=" O THR E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 639 removed outlier: 3.905A pdb=" N GLN E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 654 removed outlier: 3.727A pdb=" N LEU E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E 646 " --> pdb=" O GLN E 642 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU E 647 " --> pdb=" O SER E 643 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.691A pdb=" N GLY A 454 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA3, first strand: chain 'D' and resid 334 through 335 removed outlier: 4.493A pdb=" N ARG D 334 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.909A pdb=" N VAL D 373 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS D 412 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 375 " --> pdb=" O CYS D 412 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D 414 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 452 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 454 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 456 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 348 " --> pdb=" O ALA D 455 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR D 457 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 350 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU D 349 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU D 489 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 351 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 435 through 438 removed outlier: 3.758A pdb=" N LEU D 447 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 438 " --> pdb=" O CYS D 445 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 477 through 478 removed outlier: 7.203A pdb=" N VAL C 477 " --> pdb=" O ASP C 518 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 559 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 454 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'F' and resid 334 through 335 removed outlier: 4.537A pdb=" N ARG F 334 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 342 " --> pdb=" O ARG F 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 409 through 414 removed outlier: 3.813A pdb=" N THR F 452 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 454 " --> pdb=" O CYS F 411 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 456 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY F 352 " --> pdb=" O THR F 457 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 349 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU F 489 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL F 351 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 435 through 438 removed outlier: 3.806A pdb=" N LEU F 447 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 438 " --> pdb=" O CYS F 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.522A pdb=" N ALA B 559 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 454 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB4, first strand: chain 'E' and resid 372 through 374 removed outlier: 3.777A pdb=" N VAL E 373 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS E 412 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E 452 " --> pdb=" O GLY E 409 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 454 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 456 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY E 352 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 349 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU E 489 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL E 351 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 435 through 438 removed outlier: 3.803A pdb=" N LEU E 447 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 438 " --> pdb=" O CYS E 445 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5439 1.34 - 1.46: 3343 1.46 - 1.58: 7625 1.58 - 1.70: 18 1.70 - 1.82: 126 Bond restraints: 16551 Sorted by residual: bond pdb=" CB LYS A 578 " pdb=" CG LYS A 578 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS F 460 " pdb=" CG LYS F 460 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CB GLN B 394 " pdb=" CG GLN B 394 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" CG LYS F 460 " pdb=" CD LYS F 460 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CA LEU E 480 " pdb=" CB LEU E 480 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.31e-02 5.83e+03 1.30e+00 ... (remaining 16546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 22022 2.53 - 5.06: 317 5.06 - 7.59: 59 7.59 - 10.12: 5 10.12 - 12.65: 4 Bond angle restraints: 22407 Sorted by residual: angle pdb=" N VAL F 541 " pdb=" CA VAL F 541 " pdb=" C VAL F 541 " ideal model delta sigma weight residual 112.98 106.45 6.53 1.25e+00 6.40e-01 2.73e+01 angle pdb=" N VAL E 541 " pdb=" CA VAL E 541 " pdb=" C VAL E 541 " ideal model delta sigma weight residual 112.98 106.60 6.38 1.25e+00 6.40e-01 2.61e+01 angle pdb=" N VAL D 541 " pdb=" CA VAL D 541 " pdb=" C VAL D 541 " ideal model delta sigma weight residual 112.98 106.86 6.12 1.25e+00 6.40e-01 2.40e+01 angle pdb=" N SER E 481 " pdb=" CA SER E 481 " pdb=" C SER E 481 " ideal model delta sigma weight residual 114.62 109.34 5.28 1.14e+00 7.69e-01 2.14e+01 angle pdb=" CB LYS F 460 " pdb=" CG LYS F 460 " pdb=" CD LYS F 460 " ideal model delta sigma weight residual 111.30 120.81 -9.51 2.30e+00 1.89e-01 1.71e+01 ... (remaining 22402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8714 17.90 - 35.80: 1077 35.80 - 53.71: 244 53.71 - 71.61: 41 71.61 - 89.51: 28 Dihedral angle restraints: 10104 sinusoidal: 4101 harmonic: 6003 Sorted by residual: dihedral pdb=" CA LEU D 639 " pdb=" C LEU D 639 " pdb=" N GLU D 640 " pdb=" CA GLU D 640 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU F 639 " pdb=" C LEU F 639 " pdb=" N GLU F 640 " pdb=" CA GLU F 640 " ideal model delta harmonic sigma weight residual -180.00 -156.47 -23.53 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU E 518 " pdb=" C LEU E 518 " pdb=" N TRP E 519 " pdb=" CA TRP E 519 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1985 0.044 - 0.087: 495 0.087 - 0.131: 115 0.131 - 0.175: 15 0.175 - 0.218: 3 Chirality restraints: 2613 Sorted by residual: chirality pdb=" CB ILE C 658 " pdb=" CA ILE C 658 " pdb=" CG1 ILE C 658 " pdb=" CG2 ILE C 658 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE B 658 " pdb=" CA ILE B 658 " pdb=" CG1 ILE B 658 " pdb=" CG2 ILE B 658 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU D 639 " pdb=" CB LEU D 639 " pdb=" CD1 LEU D 639 " pdb=" CD2 LEU D 639 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 2610 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 408 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C ASN C 408 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN C 408 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 409 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 564 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C THR D 564 " -0.030 2.00e-02 2.50e+03 pdb=" O THR D 564 " 0.011 2.00e-02 2.50e+03 pdb=" N THR D 565 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 369 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO E 370 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 370 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 370 " -0.024 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 992 2.73 - 3.28: 16003 3.28 - 3.82: 23406 3.82 - 4.36: 26332 4.36 - 4.90: 47483 Nonbonded interactions: 114216 Sorted by model distance: nonbonded pdb=" OD1 ASP D 484 " pdb=" OG SER D 571 " model vdw 2.192 3.040 nonbonded pdb=" OD1 ASP E 484 " pdb=" OG SER E 571 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP C 588 " pdb=" OG SER C 715 " model vdw 2.222 3.040 nonbonded pdb=" N GLN F 285 " pdb=" OE1 GLN F 285 " model vdw 2.242 3.120 nonbonded pdb=" O SER D 380 " pdb=" NZ LYS D 420 " model vdw 2.259 3.120 ... (remaining 114211 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.010 Find NCS groups from input model: 0.790 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.043 16551 Z= 0.134 Angle : 0.749 12.654 22407 Z= 0.384 Chirality : 0.041 0.218 2613 Planarity : 0.004 0.043 2856 Dihedral : 16.597 89.511 6228 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.32 % Favored : 90.14 % Rotamer: Outliers : 0.11 % Allowed : 15.85 % Favored : 84.04 % 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: -2.07 (0.19), residues: 2049 helix: -0.47 (0.19), residues: 906 sheet: -0.49 (0.39), residues: 177 loop : -2.48 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 519 HIS 0.002 0.000 HIS E 579 PHE 0.011 0.001 PHE E 504 TYR 0.016 0.001 TYR E 294 ARG 0.005 0.000 ARG D 650 Details of bonding type rmsd hydrogen bonds : bond 0.22177 ( 531) hydrogen bonds : angle 6.28106 ( 1500) covalent geometry : bond 0.00271 (16551) covalent geometry : angle 0.74872 (22407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: D 650 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7675 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 234 average time/residue: 0.2815 time to fit residues: 97.9142 Evaluate side-chains 228 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain B residue 661 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** C 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN B 528 GLN B 536 GLN B 608 HIS ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.160538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119612 restraints weight = 21557.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120774 restraints weight = 25646.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121064 restraints weight = 20979.947| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16551 Z= 0.151 Angle : 0.695 17.083 22407 Z= 0.329 Chirality : 0.042 0.191 2613 Planarity : 0.004 0.041 2856 Dihedral : 5.858 56.468 2316 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.25 % Favored : 89.21 % Rotamer: Outliers : 2.89 % Allowed : 15.79 % Favored : 81.32 % 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: -1.98 (0.19), residues: 2049 helix: -0.34 (0.19), residues: 918 sheet: -0.76 (0.35), residues: 210 loop : -2.49 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 292 HIS 0.003 0.001 HIS C 527 PHE 0.011 0.001 PHE E 504 TYR 0.016 0.001 TYR A 669 ARG 0.006 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 531) hydrogen bonds : angle 4.57193 ( 1500) covalent geometry : bond 0.00349 (16551) covalent geometry : angle 0.69530 (22407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 1.722 Fit side-chains REVERT: A 389 ASP cc_start: 0.7674 (m-30) cc_final: 0.7162 (m-30) REVERT: A 394 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 512 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: A 668 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8227 (ttpt) REVERT: A 736 ASP cc_start: 0.8446 (m-30) cc_final: 0.8165 (m-30) REVERT: D 375 THR cc_start: 0.8997 (t) cc_final: 0.8738 (p) REVERT: C 394 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 599 GLU cc_start: 0.7488 (tp30) cc_final: 0.7185 (tp30) REVERT: C 664 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7871 (tm-30) REVERT: F 371 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7114 (ttm170) REVERT: F 449 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 455 ASP cc_start: 0.8546 (m-30) cc_final: 0.8261 (m-30) REVERT: E 374 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7871 (tp) REVERT: E 600 MET cc_start: 0.7993 (tpt) cc_final: 0.7739 (tpp) outliers start: 51 outliers final: 31 residues processed: 246 average time/residue: 0.2618 time to fit residues: 97.0260 Evaluate side-chains 239 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 520 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 184 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 57 optimal weight: 0.0040 chunk 52 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124177 restraints weight = 21540.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121029 restraints weight = 24218.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121636 restraints weight = 27243.479| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16551 Z= 0.117 Angle : 0.644 14.019 22407 Z= 0.303 Chirality : 0.040 0.177 2613 Planarity : 0.004 0.038 2856 Dihedral : 5.724 55.377 2314 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.42 % Favored : 90.04 % Rotamer: Outliers : 2.94 % Allowed : 17.43 % Favored : 79.63 % 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: -1.87 (0.19), residues: 2049 helix: -0.24 (0.19), residues: 930 sheet: -0.85 (0.35), residues: 216 loop : -2.45 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 292 HIS 0.002 0.000 HIS E 347 PHE 0.011 0.001 PHE E 504 TYR 0.012 0.001 TYR A 669 ARG 0.006 0.000 ARG E 371 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 531) hydrogen bonds : angle 4.26079 ( 1500) covalent geometry : bond 0.00265 (16551) covalent geometry : angle 0.64396 (22407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 1.774 Fit side-chains REVERT: A 389 ASP cc_start: 0.7913 (m-30) cc_final: 0.7099 (m-30) REVERT: A 394 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 512 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: A 668 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8223 (mtpt) REVERT: D 375 THR cc_start: 0.8929 (t) cc_final: 0.8653 (p) REVERT: D 600 MET cc_start: 0.8438 (tpp) cc_final: 0.8168 (tpt) REVERT: D 650 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7569 (mtp85) REVERT: C 394 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 599 GLU cc_start: 0.7370 (tp30) cc_final: 0.7117 (tp30) REVERT: C 736 ASP cc_start: 0.8284 (m-30) cc_final: 0.8010 (m-30) REVERT: F 449 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8388 (t) REVERT: F 650 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7482 (mtp85) REVERT: B 455 ASP cc_start: 0.8430 (m-30) cc_final: 0.8116 (m-30) REVERT: E 371 ARG cc_start: 0.7569 (ttm110) cc_final: 0.7000 (ttm170) REVERT: E 374 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7698 (tp) REVERT: E 424 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7787 (tmm-80) outliers start: 52 outliers final: 35 residues processed: 244 average time/residue: 0.2700 time to fit residues: 98.0743 Evaluate side-chains 240 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 584 PHE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125652 restraints weight = 21382.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121669 restraints weight = 22516.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122206 restraints weight = 24138.428| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16551 Z= 0.115 Angle : 0.633 13.356 22407 Z= 0.298 Chirality : 0.040 0.193 2613 Planarity : 0.003 0.037 2856 Dihedral : 5.650 54.541 2314 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.52 % Favored : 90.00 % Rotamer: Outliers : 3.40 % Allowed : 18.28 % Favored : 78.32 % 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: -1.80 (0.19), residues: 2049 helix: -0.13 (0.19), residues: 939 sheet: -0.82 (0.35), residues: 216 loop : -2.48 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.012 0.001 TYR F 294 ARG 0.007 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 531) hydrogen bonds : angle 4.07901 ( 1500) covalent geometry : bond 0.00261 (16551) covalent geometry : angle 0.63296 (22407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 1.764 Fit side-chains REVERT: A 394 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7730 (tm-30) REVERT: D 600 MET cc_start: 0.8356 (tpp) cc_final: 0.8076 (tpt) REVERT: D 650 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7558 (mtp85) REVERT: C 394 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 599 GLU cc_start: 0.7362 (tp30) cc_final: 0.7090 (tp30) REVERT: C 664 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7801 (tp40) REVERT: C 736 ASP cc_start: 0.8315 (m-30) cc_final: 0.8036 (m-30) REVERT: F 449 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8416 (t) REVERT: F 650 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7445 (mtp85) REVERT: B 442 ILE cc_start: 0.8652 (mm) cc_final: 0.8210 (mm) REVERT: E 371 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7063 (ttm170) REVERT: E 374 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7834 (tp) REVERT: E 639 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6805 (pp) outliers start: 60 outliers final: 41 residues processed: 247 average time/residue: 0.2576 time to fit residues: 96.7214 Evaluate side-chains 243 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 118 optimal weight: 0.0470 chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 180 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128218 restraints weight = 21536.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.125577 restraints weight = 21867.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125412 restraints weight = 24999.045| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16551 Z= 0.100 Angle : 0.625 14.663 22407 Z= 0.292 Chirality : 0.039 0.188 2613 Planarity : 0.003 0.040 2856 Dihedral : 5.524 52.800 2314 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.88 % Favored : 90.63 % Rotamer: Outliers : 3.85 % Allowed : 18.90 % Favored : 77.25 % 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: -1.66 (0.19), residues: 2049 helix: 0.00 (0.19), residues: 942 sheet: -0.81 (0.35), residues: 216 loop : -2.42 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.014 0.001 TYR E 294 ARG 0.006 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 531) hydrogen bonds : angle 3.86082 ( 1500) covalent geometry : bond 0.00217 (16551) covalent geometry : angle 0.62463 (22407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 1.899 Fit side-chains REVERT: A 389 ASP cc_start: 0.7665 (m-30) cc_final: 0.7030 (m-30) REVERT: A 394 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 668 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8317 (mtpt) REVERT: D 600 MET cc_start: 0.8345 (tpp) cc_final: 0.8080 (tpt) REVERT: C 394 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 442 ILE cc_start: 0.8366 (mm) cc_final: 0.8078 (mm) REVERT: C 512 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: C 530 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8235 (pp) REVERT: C 599 GLU cc_start: 0.7286 (tp30) cc_final: 0.6957 (tp30) REVERT: C 664 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7793 (tp40) REVERT: C 736 ASP cc_start: 0.8284 (m-30) cc_final: 0.7984 (m-30) REVERT: F 449 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8397 (t) REVERT: F 650 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7508 (mtp85) REVERT: B 442 ILE cc_start: 0.8614 (mm) cc_final: 0.8175 (mm) REVERT: B 579 MET cc_start: 0.7722 (mtt) cc_final: 0.7431 (mtt) REVERT: E 424 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7638 (tmm-80) outliers start: 68 outliers final: 47 residues processed: 259 average time/residue: 0.2576 time to fit residues: 101.2218 Evaluate side-chains 256 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 120 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.160539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120941 restraints weight = 21784.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119637 restraints weight = 27700.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120768 restraints weight = 26636.537| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16551 Z= 0.120 Angle : 0.655 14.613 22407 Z= 0.304 Chirality : 0.040 0.200 2613 Planarity : 0.003 0.038 2856 Dihedral : 5.530 52.780 2314 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.57 % Favored : 89.95 % Rotamer: Outliers : 4.13 % Allowed : 18.62 % Favored : 77.25 % 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: -1.62 (0.19), residues: 2049 helix: 0.07 (0.19), residues: 939 sheet: -0.84 (0.35), residues: 216 loop : -2.41 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE F 504 TYR 0.015 0.001 TYR E 294 ARG 0.004 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 531) hydrogen bonds : angle 3.88105 ( 1500) covalent geometry : bond 0.00277 (16551) covalent geometry : angle 0.65503 (22407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 1.771 Fit side-chains REVERT: A 389 ASP cc_start: 0.7727 (m-30) cc_final: 0.7171 (m-30) REVERT: A 394 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 668 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8213 (ttpt) REVERT: D 600 MET cc_start: 0.8385 (tpp) cc_final: 0.8070 (tpt) REVERT: C 394 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 442 ILE cc_start: 0.8379 (mm) cc_final: 0.8134 (mm) REVERT: C 512 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: C 530 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8227 (pp) REVERT: C 599 GLU cc_start: 0.7460 (tp30) cc_final: 0.7207 (tp30) REVERT: C 664 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7844 (tp40) REVERT: C 736 ASP cc_start: 0.8316 (m-30) cc_final: 0.7987 (m-30) REVERT: F 434 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: F 449 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (t) REVERT: F 650 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7504 (mtp85) REVERT: B 442 ILE cc_start: 0.8667 (mm) cc_final: 0.8256 (mm) REVERT: B 528 GLN cc_start: 0.8284 (tt0) cc_final: 0.8074 (tt0) REVERT: B 584 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8779 (tp) REVERT: E 374 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7862 (tp) REVERT: E 424 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7568 (tmm-80) outliers start: 73 outliers final: 53 residues processed: 256 average time/residue: 0.2537 time to fit residues: 98.6976 Evaluate side-chains 264 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 317 MET Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 197 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 194 optimal weight: 0.0970 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 0.0170 chunk 112 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123218 restraints weight = 21657.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121963 restraints weight = 27600.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123774 restraints weight = 27264.193| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16551 Z= 0.099 Angle : 0.633 14.068 22407 Z= 0.295 Chirality : 0.039 0.177 2613 Planarity : 0.003 0.046 2856 Dihedral : 5.393 50.610 2314 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.78 % Favored : 90.78 % Rotamer: Outliers : 3.62 % Allowed : 19.30 % Favored : 77.08 % 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: -1.47 (0.19), residues: 2049 helix: 0.22 (0.19), residues: 936 sheet: -0.88 (0.35), residues: 207 loop : -2.33 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.016 0.001 TYR E 294 ARG 0.011 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.02608 ( 531) hydrogen bonds : angle 3.69936 ( 1500) covalent geometry : bond 0.00218 (16551) covalent geometry : angle 0.63266 (22407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 1.767 Fit side-chains REVERT: A 389 ASP cc_start: 0.7702 (m-30) cc_final: 0.7320 (m-30) REVERT: A 394 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 668 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8206 (ttpt) REVERT: D 600 MET cc_start: 0.8332 (tpp) cc_final: 0.8016 (tpt) REVERT: C 394 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 442 ILE cc_start: 0.8453 (mm) cc_final: 0.8183 (mm) REVERT: C 512 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: C 530 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8219 (pp) REVERT: C 599 GLU cc_start: 0.7371 (tp30) cc_final: 0.7048 (tp30) REVERT: C 664 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7743 (tp40) REVERT: C 736 ASP cc_start: 0.8331 (m-30) cc_final: 0.8046 (m-30) REVERT: F 286 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8515 (ttpt) REVERT: F 449 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8386 (t) REVERT: F 650 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7542 (mtp85) REVERT: B 442 ILE cc_start: 0.8610 (mm) cc_final: 0.8194 (mm) REVERT: B 528 GLN cc_start: 0.8338 (tt0) cc_final: 0.8128 (tt0) REVERT: B 584 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8770 (tp) REVERT: E 424 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7574 (tmm-80) outliers start: 64 outliers final: 48 residues processed: 254 average time/residue: 0.2549 time to fit residues: 98.4935 Evaluate side-chains 257 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 39 optimal weight: 0.0000 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121200 restraints weight = 21593.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121011 restraints weight = 27493.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.121538 restraints weight = 22901.703| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16551 Z= 0.109 Angle : 0.646 14.021 22407 Z= 0.300 Chirality : 0.040 0.176 2613 Planarity : 0.003 0.043 2856 Dihedral : 5.376 49.877 2314 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.27 % Favored : 90.29 % Rotamer: Outliers : 3.57 % Allowed : 19.64 % Favored : 76.80 % 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: -1.39 (0.19), residues: 2049 helix: 0.29 (0.19), residues: 936 sheet: -0.78 (0.35), residues: 216 loop : -2.31 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 292 HIS 0.002 0.000 HIS E 579 PHE 0.010 0.001 PHE E 504 TYR 0.016 0.001 TYR E 294 ARG 0.009 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 531) hydrogen bonds : angle 3.69502 ( 1500) covalent geometry : bond 0.00247 (16551) covalent geometry : angle 0.64635 (22407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 1.787 Fit side-chains REVERT: A 389 ASP cc_start: 0.7722 (m-30) cc_final: 0.7368 (m-30) REVERT: A 394 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 668 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8193 (ttpt) REVERT: D 600 MET cc_start: 0.8305 (tpp) cc_final: 0.7990 (tpt) REVERT: C 394 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7843 (tm-30) REVERT: C 442 ILE cc_start: 0.8423 (mm) cc_final: 0.8155 (mm) REVERT: C 512 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: C 530 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8119 (pp) REVERT: C 599 GLU cc_start: 0.7444 (tp30) cc_final: 0.7122 (tp30) REVERT: C 664 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7833 (tp40) REVERT: C 736 ASP cc_start: 0.8354 (m-30) cc_final: 0.8065 (m-30) REVERT: F 434 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: F 449 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8354 (t) REVERT: F 650 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7527 (mtp85) REVERT: B 442 ILE cc_start: 0.8610 (mm) cc_final: 0.8210 (mm) REVERT: B 528 GLN cc_start: 0.8369 (tt0) cc_final: 0.8150 (tt0) REVERT: B 579 MET cc_start: 0.7802 (mtt) cc_final: 0.7511 (mtt) REVERT: B 584 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8776 (tp) REVERT: E 374 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7846 (tp) REVERT: E 424 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7481 (tmm-80) outliers start: 63 outliers final: 50 residues processed: 243 average time/residue: 0.2524 time to fit residues: 93.3462 Evaluate side-chains 256 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 0.0980 chunk 104 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 118 optimal weight: 0.0570 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 GLN ** B 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123405 restraints weight = 21604.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.122542 restraints weight = 26883.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.123677 restraints weight = 25921.334| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16551 Z= 0.101 Angle : 0.642 13.761 22407 Z= 0.298 Chirality : 0.039 0.168 2613 Planarity : 0.003 0.040 2856 Dihedral : 5.286 47.652 2314 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.93 % Favored : 90.63 % Rotamer: Outliers : 3.34 % Allowed : 19.92 % Favored : 76.74 % 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: -1.29 (0.20), residues: 2049 helix: 0.37 (0.19), residues: 936 sheet: -0.71 (0.35), residues: 216 loop : -2.27 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 519 HIS 0.002 0.000 HIS E 347 PHE 0.010 0.001 PHE E 504 TYR 0.018 0.001 TYR E 294 ARG 0.009 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.02610 ( 531) hydrogen bonds : angle 3.63106 ( 1500) covalent geometry : bond 0.00225 (16551) covalent geometry : angle 0.64196 (22407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 1.807 Fit side-chains REVERT: A 389 ASP cc_start: 0.7659 (m-30) cc_final: 0.7299 (m-30) REVERT: A 394 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 668 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8183 (ttpt) REVERT: D 521 MET cc_start: 0.7878 (mmp) cc_final: 0.7481 (mmt) REVERT: D 600 MET cc_start: 0.8347 (tpp) cc_final: 0.8035 (tpt) REVERT: C 394 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 442 ILE cc_start: 0.8462 (mm) cc_final: 0.8189 (mm) REVERT: C 512 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: C 530 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8189 (pp) REVERT: C 590 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 599 GLU cc_start: 0.7367 (tp30) cc_final: 0.7044 (tp30) REVERT: C 664 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7803 (tp40) REVERT: C 736 ASP cc_start: 0.8317 (m-30) cc_final: 0.8022 (m-30) REVERT: F 449 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (t) REVERT: F 650 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7546 (mtp85) REVERT: B 442 ILE cc_start: 0.8645 (mm) cc_final: 0.8247 (mm) REVERT: B 528 GLN cc_start: 0.8491 (tt0) cc_final: 0.8246 (tt0) REVERT: B 579 MET cc_start: 0.7664 (mtt) cc_final: 0.7373 (mtt) REVERT: B 584 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8747 (tp) REVERT: E 374 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (tp) REVERT: E 424 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6301 (ttm-80) outliers start: 59 outliers final: 47 residues processed: 245 average time/residue: 0.2689 time to fit residues: 100.7419 Evaluate side-chains 260 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 641 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 434 GLN B 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.157317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117212 restraints weight = 21907.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117035 restraints weight = 29091.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117389 restraints weight = 25409.351| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16551 Z= 0.157 Angle : 0.701 14.666 22407 Z= 0.329 Chirality : 0.041 0.165 2613 Planarity : 0.004 0.040 2856 Dihedral : 5.507 48.834 2314 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.76 % Favored : 89.85 % Rotamer: Outliers : 3.17 % Allowed : 20.37 % Favored : 76.46 % 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: -1.48 (0.19), residues: 2049 helix: 0.21 (0.19), residues: 936 sheet: -0.80 (0.35), residues: 207 loop : -2.35 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 292 HIS 0.002 0.000 HIS E 579 PHE 0.010 0.001 PHE F 504 TYR 0.014 0.001 TYR A 669 ARG 0.009 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 531) hydrogen bonds : angle 3.91309 ( 1500) covalent geometry : bond 0.00374 (16551) covalent geometry : angle 0.70148 (22407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4098 Ramachandran restraints generated. 2049 Oldfield, 0 Emsley, 2049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 1.792 Fit side-chains REVERT: A 394 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 296 LYS cc_start: 0.8748 (tppt) cc_final: 0.8491 (ttpp) REVERT: D 600 MET cc_start: 0.8351 (tpp) cc_final: 0.8029 (tpt) REVERT: C 394 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 442 ILE cc_start: 0.8490 (mm) cc_final: 0.8247 (mm) REVERT: C 512 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: C 530 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8046 (pp) REVERT: C 599 GLU cc_start: 0.7658 (tp30) cc_final: 0.7401 (tp30) REVERT: C 664 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7853 (tp40) REVERT: C 736 ASP cc_start: 0.8386 (m-30) cc_final: 0.8112 (m-30) REVERT: F 371 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7143 (ttm170) REVERT: F 449 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8481 (t) REVERT: F 650 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7534 (mtp85) REVERT: B 442 ILE cc_start: 0.8605 (mm) cc_final: 0.8222 (mm) REVERT: B 528 GLN cc_start: 0.8445 (tt0) cc_final: 0.8196 (tt0) REVERT: B 584 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8792 (tp) REVERT: E 374 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7970 (tp) REVERT: E 424 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6240 (ttm-80) outliers start: 56 outliers final: 43 residues processed: 239 average time/residue: 0.2754 time to fit residues: 98.7724 Evaluate side-chains 248 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 512 GLN Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 LEU Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain B residue 435 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 424 ARG Chi-restraints excluded: chain E residue 473 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 126 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.162035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122317 restraints weight = 21621.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122194 restraints weight = 26178.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123357 restraints weight = 24562.606| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16551 Z= 0.115 Angle : 0.669 14.360 22407 Z= 0.312 Chirality : 0.040 0.166 2613 Planarity : 0.004 0.040 2856 Dihedral : 5.417 46.680 2314 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.13 % Favored : 90.48 % Rotamer: Outliers : 3.17 % Allowed : 20.43 % Favored : 76.40 % 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: -1.33 (0.19), residues: 2049 helix: 0.31 (0.19), residues: 933 sheet: -0.84 (0.33), residues: 246 loop : -2.25 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 292 HIS 0.003 0.000 HIS F 579 PHE 0.010 0.001 PHE E 504 TYR 0.018 0.001 TYR E 294 ARG 0.008 0.000 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 531) hydrogen bonds : angle 3.75111 ( 1500) covalent geometry : bond 0.00264 (16551) covalent geometry : angle 0.66878 (22407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4408.14 seconds wall clock time: 78 minutes 15.68 seconds (4695.68 seconds total)