Starting phenix.real_space_refine on Sun Aug 24 02:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s94_40236/08_2025/8s94_40236.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s94_40236/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8s94_40236/08_2025/8s94_40236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s94_40236/08_2025/8s94_40236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s94_40236/08_2025/8s94_40236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s94_40236/08_2025/8s94_40236.map" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.97, per 1000 atoms: 0.24 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: 1.35 Conformation dependent library (CDL) restraints added in 757.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.32 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: 2.42 Time building geometry restraints manager: 1.75 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: 0.01 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: 3.890 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG D 650 TYR 0.016 0.001 TYR E 294 PHE 0.011 0.001 PHE E 504 TRP 0.008 0.001 TRP D 519 HIS 0.002 0.000 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00271 (16551) covalent geometry : angle 0.74872 (22407) hydrogen bonds : bond 0.22177 ( 531) hydrogen bonds : angle 6.28106 ( 1500) *********************** 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 : 0.593 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: 0.1194 time to fit residues: 41.6099 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 : 0.397 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 699 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.167132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129837 restraints weight = 21323.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125976 restraints weight = 22422.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126526 restraints weight = 24613.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127289 restraints weight = 23309.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127260 restraints weight = 22006.828| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16551 Z= 0.109 Angle : 0.657 16.235 22407 Z= 0.309 Chirality : 0.040 0.189 2613 Planarity : 0.004 0.039 2856 Dihedral : 5.663 55.015 2316 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.27 % Favored : 90.19 % Rotamer: Outliers : 2.21 % Allowed : 15.62 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.19), residues: 2049 helix: -0.19 (0.19), residues: 921 sheet: -0.65 (0.36), residues: 210 loop : -2.40 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 371 TYR 0.012 0.001 TYR E 294 PHE 0.010 0.001 PHE E 504 TRP 0.008 0.001 TRP D 519 HIS 0.003 0.000 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00232 (16551) covalent geometry : angle 0.65718 (22407) hydrogen bonds : bond 0.03833 ( 531) hydrogen bonds : angle 4.46423 ( 1500) *********************** 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 275 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.397 Fit side-chains REVERT: A 394 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 512 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: A 534 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: A 668 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8302 (ttpt) REVERT: A 736 ASP cc_start: 0.8355 (m-30) cc_final: 0.8141 (m-30) REVERT: D 375 THR cc_start: 0.8867 (t) cc_final: 0.8663 (p) REVERT: D 600 MET cc_start: 0.8272 (tpp) cc_final: 0.7983 (tpt) REVERT: C 394 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7886 (tm-30) REVERT: C 408 ASN cc_start: 0.8026 (t0) cc_final: 0.7749 (t0) REVERT: C 599 GLU cc_start: 0.7155 (tp30) cc_final: 0.6813 (tp30) REVERT: C 664 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7794 (tm-30) REVERT: F 449 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8584 (t) REVERT: F 622 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6614 (tm-30) REVERT: F 637 GLU cc_start: 0.7745 (tt0) cc_final: 0.7380 (tt0) REVERT: E 600 MET cc_start: 0.8044 (tpt) cc_final: 0.7738 (tpp) REVERT: E 639 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6669 (pp) outliers start: 39 outliers final: 22 residues processed: 258 average time/residue: 0.1135 time to fit residues: 43.9443 Evaluate side-chains 246 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 534 MET 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 373 VAL Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 519 TRP 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 749 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 473 ILE Chi-restraints excluded: chain E residue 639 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 199 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 GLN ** 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 = 0.3796 r_free = 0.3796 target = 0.164445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127889 restraints weight = 21648.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125286 restraints weight = 25869.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126112 restraints weight = 28970.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126291 restraints weight = 24710.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126301 restraints weight = 23404.799| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1166 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= 0.105 Angle : 0.632 15.080 22407 Z= 0.295 Chirality : 0.039 0.178 2613 Planarity : 0.004 0.040 2856 Dihedral : 5.566 54.865 2314 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.03 % Favored : 90.43 % Rotamer: Outliers : 2.55 % Allowed : 17.49 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.19), residues: 2049 helix: -0.06 (0.19), residues: 924 sheet: -0.77 (0.35), residues: 216 loop : -2.38 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 371 TYR 0.010 0.001 TYR A 669 PHE 0.010 0.001 PHE E 504 TRP 0.007 0.001 TRP F 519 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00230 (16551) covalent geometry : angle 0.63162 (22407) hydrogen bonds : bond 0.03362 ( 531) hydrogen bonds : angle 4.15848 ( 1500) *********************** 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 256 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.560 Fit side-chains REVERT: A 394 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 534 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7429 (mtp) REVERT: A 736 ASP cc_start: 0.8359 (m-30) cc_final: 0.8124 (m-30) REVERT: D 375 THR cc_start: 0.8800 (t) cc_final: 0.8594 (p) REVERT: D 600 MET cc_start: 0.8420 (tpp) cc_final: 0.8155 (tpt) REVERT: D 650 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7557 (mtp85) REVERT: C 394 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 407 VAL cc_start: 0.8974 (p) cc_final: 0.8765 (p) REVERT: C 408 ASN cc_start: 0.8264 (t0) cc_final: 0.7749 (t0) REVERT: F 449 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8396 (t) REVERT: F 622 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6704 (tm-30) REVERT: F 650 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7440 (mtp85) REVERT: B 528 GLN cc_start: 0.8279 (tt0) cc_final: 0.8059 (tt0) REVERT: B 736 ASP cc_start: 0.8347 (m-30) cc_final: 0.8027 (m-30) REVERT: E 371 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6888 (ttm170) REVERT: E 374 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7659 (tp) REVERT: E 600 MET cc_start: 0.8108 (tpt) cc_final: 0.7801 (tpp) outliers start: 45 outliers final: 31 residues processed: 235 average time/residue: 0.1054 time to fit residues: 37.5739 Evaluate side-chains 234 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 ILE 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 373 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 449 THR 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 554 THR Chi-restraints excluded: chain C residue 612 ILE 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 519 TRP 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 661 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain E residue 326 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 608 HIS F 433 GLN B 536 GLN B 576 ASN B 701 GLN ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117594 restraints weight = 21738.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117564 restraints weight = 26258.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118716 restraints weight = 23889.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118461 restraints weight = 19845.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118466 restraints weight = 19613.438| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16551 Z= 0.174 Angle : 0.695 15.675 22407 Z= 0.328 Chirality : 0.042 0.191 2613 Planarity : 0.004 0.042 2856 Dihedral : 5.828 56.568 2314 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.59 % Favored : 88.92 % Rotamer: Outliers : 3.45 % Allowed : 17.66 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.19), residues: 2049 helix: -0.28 (0.18), residues: 942 sheet: -0.83 (0.35), residues: 216 loop : -2.47 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 711 TYR 0.018 0.001 TYR A 669 PHE 0.012 0.002 PHE B 429 TRP 0.008 0.002 TRP D 292 HIS 0.003 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00417 (16551) covalent geometry : angle 0.69480 (22407) hydrogen bonds : bond 0.04474 ( 531) hydrogen bonds : angle 4.37180 ( 1500) *********************** 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 265 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.491 Fit side-chains REVERT: A 394 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 713 LEU cc_start: 0.8625 (tp) cc_final: 0.8423 (tp) REVERT: D 600 MET cc_start: 0.8432 (tpp) cc_final: 0.8139 (tpt) REVERT: D 650 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7594 (mtp85) REVERT: C 394 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7937 (tm-30) REVERT: C 736 ASP cc_start: 0.8403 (m-30) cc_final: 0.8109 (m-30) REVERT: F 449 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8503 (t) REVERT: F 622 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6810 (tm-30) REVERT: F 650 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7388 (mtp85) REVERT: B 442 ILE cc_start: 0.8671 (mm) cc_final: 0.8216 (mm) REVERT: B 455 ASP cc_start: 0.8442 (m-30) cc_final: 0.8111 (m-30) REVERT: B 736 ASP cc_start: 0.8491 (m-30) cc_final: 0.8169 (m-30) REVERT: E 374 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7954 (tp) REVERT: E 424 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7708 (tmm-80) outliers start: 61 outliers final: 41 residues processed: 240 average time/residue: 0.1057 time to fit residues: 38.4434 Evaluate side-chains 239 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 447 ASP 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 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 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 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 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 477 VAL Chi-restraints excluded: chain B residue 554 THR 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 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 Chi-restraints excluded: chain E residue 594 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 155 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 GLN D 433 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 701 GLN ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121877 restraints weight = 21637.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119379 restraints weight = 25402.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119983 restraints weight = 29407.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120467 restraints weight = 25979.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120683 restraints weight = 22804.081| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16551 Z= 0.125 Angle : 0.651 15.218 22407 Z= 0.305 Chirality : 0.040 0.190 2613 Planarity : 0.004 0.037 2856 Dihedral : 5.716 54.267 2314 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.27 % Favored : 90.24 % Rotamer: Outliers : 4.24 % Allowed : 18.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.19), residues: 2049 helix: -0.15 (0.19), residues: 939 sheet: -0.83 (0.35), residues: 216 loop : -2.51 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 371 TYR 0.013 0.001 TYR D 294 PHE 0.011 0.001 PHE E 504 TRP 0.007 0.001 TRP D 292 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00289 (16551) covalent geometry : angle 0.65081 (22407) hydrogen bonds : bond 0.03497 ( 531) hydrogen bonds : angle 4.12549 ( 1500) *********************** 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 280 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 0.627 Fit side-chains REVERT: A 389 ASP cc_start: 0.7895 (m-30) cc_final: 0.7139 (m-30) REVERT: A 394 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 668 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8275 (ttpt) REVERT: D 345 GLU cc_start: 0.7923 (mp0) cc_final: 0.7660 (mp0) REVERT: D 600 MET cc_start: 0.8486 (tpp) cc_final: 0.8192 (tpt) REVERT: C 389 ASP cc_start: 0.7730 (m-30) cc_final: 0.7483 (m-30) REVERT: C 394 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 512 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: C 530 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8307 (pp) REVERT: C 664 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7725 (tp40) REVERT: C 668 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8455 (ttmm) REVERT: C 736 ASP cc_start: 0.8308 (m-30) cc_final: 0.8025 (m-30) REVERT: F 371 ARG cc_start: 0.7383 (ttm110) cc_final: 0.7102 (ttm170) REVERT: F 622 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6813 (tm-30) REVERT: F 650 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7410 (mtp85) REVERT: B 442 ILE cc_start: 0.8709 (mm) cc_final: 0.8290 (mm) REVERT: B 736 ASP cc_start: 0.8349 (m-30) cc_final: 0.8149 (m-30) REVERT: E 371 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7094 (ttm170) REVERT: E 374 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7770 (tp) REVERT: E 424 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7763 (tmm-80) outliers start: 75 outliers final: 47 residues processed: 254 average time/residue: 0.1147 time to fit residues: 44.2153 Evaluate side-chains 257 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 554 THR 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 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 584 PHE Chi-restraints excluded: chain F residue 636 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 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 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 520 SER 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 141 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 overall best weight: 1.0762 ------------------------------------------------------------------------------- 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 701 GLN E 333 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 = 0.3719 r_free = 0.3719 target = 0.157450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118009 restraints weight = 21896.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118208 restraints weight = 28976.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118099 restraints weight = 22853.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117783 restraints weight = 20904.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117750 restraints weight = 20327.230| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16551 Z= 0.150 Angle : 0.680 15.510 22407 Z= 0.319 Chirality : 0.041 0.196 2613 Planarity : 0.004 0.039 2856 Dihedral : 5.756 53.841 2314 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.15 % Favored : 89.41 % Rotamer: Outliers : 4.02 % Allowed : 19.02 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.19), residues: 2049 helix: -0.18 (0.18), residues: 942 sheet: -0.90 (0.35), residues: 216 loop : -2.51 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 371 TYR 0.014 0.001 TYR A 669 PHE 0.011 0.001 PHE E 504 TRP 0.008 0.001 TRP D 292 HIS 0.002 0.001 HIS E 579 Details of bonding type rmsd covalent geometry : bond 0.00355 (16551) covalent geometry : angle 0.68026 (22407) hydrogen bonds : bond 0.03968 ( 531) hydrogen bonds : angle 4.15449 ( 1500) *********************** 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 280 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 0.610 Fit side-chains REVERT: A 394 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 668 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: A 713 LEU cc_start: 0.8624 (tp) cc_final: 0.8397 (tp) REVERT: D 345 GLU cc_start: 0.7974 (mp0) cc_final: 0.7658 (mp0) REVERT: D 600 MET cc_start: 0.8319 (tpp) cc_final: 0.8021 (tpt) REVERT: C 389 ASP cc_start: 0.7817 (m-30) cc_final: 0.7587 (m-30) REVERT: C 394 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 442 ILE cc_start: 0.8419 (mm) cc_final: 0.8178 (mm) REVERT: C 512 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: C 668 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8473 (ttmm) REVERT: C 736 ASP cc_start: 0.8397 (m-30) cc_final: 0.8157 (m-30) REVERT: F 371 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7277 (ttm170) REVERT: F 622 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6834 (tm-30) REVERT: F 650 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7406 (mtp85) REVERT: B 442 ILE cc_start: 0.8742 (mm) cc_final: 0.8343 (mm) REVERT: B 528 GLN cc_start: 0.8365 (tt0) cc_final: 0.8137 (tt0) REVERT: B 584 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8835 (tp) REVERT: B 736 ASP cc_start: 0.8418 (m-30) cc_final: 0.8207 (m-30) REVERT: E 371 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7240 (ttm170) REVERT: E 374 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7966 (tp) REVERT: E 424 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7662 (tmm-80) outliers start: 71 outliers final: 55 residues processed: 255 average time/residue: 0.1234 time to fit residues: 47.0198 Evaluate side-chains 263 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 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 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 335 THR 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 470 SER Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 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 477 VAL 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 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 520 SER 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 148 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 333 GLN ** F 434 GLN ** 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 = 0.3751 r_free = 0.3751 target = 0.160291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119327 restraints weight = 21674.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118993 restraints weight = 28432.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120700 restraints weight = 24345.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120028 restraints weight = 20616.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119931 restraints weight = 21072.469| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16551 Z= 0.113 Angle : 0.651 14.855 22407 Z= 0.305 Chirality : 0.040 0.179 2613 Planarity : 0.003 0.038 2856 Dihedral : 5.588 51.411 2314 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.98 % Favored : 90.58 % Rotamer: Outliers : 3.90 % Allowed : 19.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.19), residues: 2049 helix: -0.00 (0.19), residues: 942 sheet: -0.86 (0.35), residues: 216 loop : -2.44 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 341 TYR 0.017 0.001 TYR E 294 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP D 292 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00257 (16551) covalent geometry : angle 0.65097 (22407) hydrogen bonds : bond 0.03118 ( 531) hydrogen bonds : angle 3.89171 ( 1500) *********************** 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 277 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 0.655 Fit side-chains REVERT: A 394 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7757 (tm-30) REVERT: D 345 GLU cc_start: 0.7953 (mp0) cc_final: 0.7684 (mp0) REVERT: D 600 MET cc_start: 0.8279 (tpp) cc_final: 0.7964 (tpt) REVERT: C 394 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 442 ILE cc_start: 0.8457 (mm) cc_final: 0.8207 (mm) REVERT: C 512 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: C 530 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8086 (pp) REVERT: C 668 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8502 (ttpt) REVERT: C 736 ASP cc_start: 0.8379 (m-30) cc_final: 0.8114 (m-30) REVERT: F 622 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6782 (tm-30) REVERT: F 650 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7386 (mtp85) REVERT: B 442 ILE cc_start: 0.8687 (mm) cc_final: 0.8297 (mm) REVERT: B 464 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8252 (tt) REVERT: B 528 GLN cc_start: 0.8368 (tt0) cc_final: 0.8121 (tt0) REVERT: B 584 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8797 (tp) REVERT: B 736 ASP cc_start: 0.8431 (m-30) cc_final: 0.8193 (m-30) REVERT: E 374 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7902 (tp) REVERT: E 424 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7556 (tmm-80) outliers start: 69 outliers final: 52 residues processed: 252 average time/residue: 0.1305 time to fit residues: 49.9870 Evaluate side-chains 259 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 661 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 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 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 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 449 THR Chi-restraints excluded: chain F residue 584 PHE Chi-restraints excluded: chain F residue 636 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 464 LEU 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 657 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 726 LEU 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 520 SER 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 2 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 0.0770 chunk 115 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 9 optimal weight: 0.0870 overall best weight: 0.2054 ------------------------------------------------------------------------------- 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 F 434 GLN B 701 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.164023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124485 restraints weight = 21649.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125020 restraints weight = 26929.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.124494 restraints weight = 21925.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124018 restraints weight = 20246.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123979 restraints weight = 19966.691| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2009 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= 0.096 Angle : 0.643 13.530 22407 Z= 0.300 Chirality : 0.039 0.178 2613 Planarity : 0.003 0.039 2856 Dihedral : 5.320 47.402 2314 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.69 % Favored : 90.87 % Rotamer: Outliers : 3.06 % Allowed : 20.66 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.20), residues: 2049 helix: 0.24 (0.19), residues: 936 sheet: -0.79 (0.33), residues: 255 loop : -2.24 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 341 TYR 0.017 0.001 TYR E 294 PHE 0.010 0.001 PHE E 504 TRP 0.008 0.001 TRP D 519 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00206 (16551) covalent geometry : angle 0.64335 (22407) hydrogen bonds : bond 0.02352 ( 531) hydrogen bonds : angle 3.64450 ( 1500) *********************** 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 266 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.626 Fit side-chains REVERT: A 394 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 345 GLU cc_start: 0.7955 (mp0) cc_final: 0.7685 (mp0) REVERT: D 521 MET cc_start: 0.7983 (mmp) cc_final: 0.7680 (mmt) REVERT: D 600 MET cc_start: 0.8283 (tpp) cc_final: 0.7993 (tpt) REVERT: C 394 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 442 ILE cc_start: 0.8408 (mm) cc_final: 0.8137 (mm) REVERT: C 530 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8112 (pp) REVERT: C 668 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8396 (ttmt) REVERT: C 736 ASP cc_start: 0.8311 (m-30) cc_final: 0.8045 (m-30) REVERT: F 286 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8515 (ttpt) REVERT: F 449 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8410 (t) REVERT: F 521 MET cc_start: 0.7781 (mmp) cc_final: 0.7460 (mmt) REVERT: F 622 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6844 (tm-30) REVERT: F 650 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7433 (mtp85) REVERT: B 442 ILE cc_start: 0.8649 (mm) cc_final: 0.8260 (mm) REVERT: B 464 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8127 (tt) REVERT: B 579 MET cc_start: 0.7628 (mtt) cc_final: 0.7348 (mtt) REVERT: B 584 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8771 (tp) REVERT: B 736 ASP cc_start: 0.8225 (m-30) cc_final: 0.7958 (m-30) outliers start: 54 outliers final: 41 residues processed: 245 average time/residue: 0.1333 time to fit residues: 49.6046 Evaluate side-chains 250 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 412 CYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 519 TRP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 530 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 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 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 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 464 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 661 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 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 44 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 29 optimal weight: 0.7980 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.161423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120557 restraints weight = 21780.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119557 restraints weight = 26807.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121033 restraints weight = 26093.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121058 restraints weight = 21781.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121119 restraints weight = 20768.307| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2042 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= 0.119 Angle : 0.670 13.562 22407 Z= 0.311 Chirality : 0.040 0.164 2613 Planarity : 0.004 0.044 2856 Dihedral : 5.337 47.362 2314 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.32 % Favored : 90.24 % Rotamer: Outliers : 3.00 % Allowed : 20.83 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.20), residues: 2049 helix: 0.26 (0.19), residues: 936 sheet: -0.78 (0.33), residues: 255 loop : -2.24 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 371 TYR 0.015 0.001 TYR F 294 PHE 0.009 0.001 PHE E 504 TRP 0.007 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00277 (16551) covalent geometry : angle 0.66973 (22407) hydrogen bonds : bond 0.03034 ( 531) hydrogen bonds : angle 3.69917 ( 1500) *********************** 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 258 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.813 Fit side-chains REVERT: A 394 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 296 LYS cc_start: 0.8724 (tppt) cc_final: 0.8499 (ttpp) REVERT: D 345 GLU cc_start: 0.7984 (mp0) cc_final: 0.7764 (mp0) REVERT: D 600 MET cc_start: 0.8314 (tpp) cc_final: 0.8013 (tpt) REVERT: C 394 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 442 ILE cc_start: 0.8451 (mm) cc_final: 0.8188 (mm) REVERT: C 512 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: C 530 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7947 (pp) REVERT: C 668 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8414 (ttmt) REVERT: C 736 ASP cc_start: 0.8380 (m-30) cc_final: 0.8085 (m-30) REVERT: F 449 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8440 (t) REVERT: F 622 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6836 (tm-30) REVERT: F 650 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7423 (mtp85) REVERT: B 442 ILE cc_start: 0.8668 (mm) cc_final: 0.8283 (mm) REVERT: B 464 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8154 (tt) REVERT: B 584 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 736 ASP cc_start: 0.8259 (m-30) cc_final: 0.8045 (m-30) REVERT: B 748 MET cc_start: 0.5273 (tpp) cc_final: 0.5043 (mmp) outliers start: 53 outliers final: 44 residues processed: 240 average time/residue: 0.1263 time to fit residues: 46.6700 Evaluate side-chains 249 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 661 ILE 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 D residue 480 LEU 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 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 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 449 THR Chi-restraints excluded: chain F residue 519 TRP Chi-restraints excluded: chain F residue 584 PHE 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 464 LEU 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 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 473 ILE Chi-restraints excluded: chain E residue 519 TRP Chi-restraints excluded: chain E residue 520 SER 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 193 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114373 restraints weight = 21973.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113833 restraints weight = 27172.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113886 restraints weight = 25193.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113763 restraints weight = 21105.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113468 restraints weight = 21604.639| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16551 Z= 0.199 Angle : 0.753 16.284 22407 Z= 0.355 Chirality : 0.043 0.160 2613 Planarity : 0.004 0.055 2856 Dihedral : 5.830 49.934 2314 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.79 % Favored : 88.82 % Rotamer: Outliers : 3.06 % Allowed : 21.00 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.19), residues: 2049 helix: 0.02 (0.19), residues: 912 sheet: -0.87 (0.35), residues: 216 loop : -2.36 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 371 TYR 0.017 0.002 TYR A 669 PHE 0.013 0.002 PHE A 692 TRP 0.012 0.002 TRP F 292 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00481 (16551) covalent geometry : angle 0.75276 (22407) hydrogen bonds : bond 0.04824 ( 531) hydrogen bonds : angle 4.25070 ( 1500) ********************** 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 257 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.691 Fit side-chains REVERT: A 394 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7768 (tm-30) REVERT: A 442 ILE cc_start: 0.8610 (mm) cc_final: 0.8404 (mm) REVERT: A 713 LEU cc_start: 0.8732 (tp) cc_final: 0.8527 (tp) REVERT: A 736 ASP cc_start: 0.8438 (m-30) cc_final: 0.8073 (m-30) REVERT: D 283 GLU cc_start: 0.7440 (tp30) cc_final: 0.7146 (tp30) REVERT: D 600 MET cc_start: 0.8305 (tpp) cc_final: 0.7980 (tpt) REVERT: C 394 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 442 ILE cc_start: 0.8581 (mm) cc_final: 0.8373 (mm) REVERT: C 512 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: C 530 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 736 ASP cc_start: 0.8413 (m-30) cc_final: 0.8202 (m-30) REVERT: F 371 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7258 (ttm170) REVERT: F 622 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6928 (tm-30) REVERT: F 637 GLU cc_start: 0.7900 (tt0) cc_final: 0.7546 (tp30) REVERT: F 650 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7463 (mtp85) REVERT: B 442 ILE cc_start: 0.8728 (mm) cc_final: 0.8394 (mm) REVERT: B 464 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (tt) REVERT: B 584 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8844 (tp) REVERT: B 736 ASP cc_start: 0.8362 (m-30) cc_final: 0.8146 (m-30) REVERT: E 371 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7230 (ttm170) REVERT: E 374 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7990 (tp) outliers start: 54 outliers final: 42 residues processed: 238 average time/residue: 0.1276 time to fit residues: 46.3514 Evaluate side-chains 245 residues out of total 1767 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 661 ILE 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 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 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 449 THR Chi-restraints excluded: chain F residue 584 PHE 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 464 LEU 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 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 473 ILE Chi-restraints excluded: chain E residue 520 SER 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 201 optimal weight: 0.0570 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 169 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118218 restraints weight = 21770.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118821 restraints weight = 27311.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.118850 restraints weight = 22642.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118604 restraints weight = 21659.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118658 restraints weight = 20415.152| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16551 Z= 0.111 Angle : 0.686 14.628 22407 Z= 0.318 Chirality : 0.040 0.171 2613 Planarity : 0.004 0.054 2856 Dihedral : 5.497 45.548 2314 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.18 % Favored : 90.43 % Rotamer: Outliers : 2.72 % Allowed : 21.39 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.19), residues: 2049 helix: 0.21 (0.19), residues: 915 sheet: -0.81 (0.35), residues: 216 loop : -2.31 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 371 TYR 0.010 0.001 TYR D 364 PHE 0.011 0.001 PHE E 504 TRP 0.006 0.001 TRP F 292 HIS 0.002 0.000 HIS E 347 Details of bonding type rmsd covalent geometry : bond 0.00251 (16551) covalent geometry : angle 0.68636 (22407) hydrogen bonds : bond 0.02996 ( 531) hydrogen bonds : angle 3.81595 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.14 seconds wall clock time: 39 minutes 20.86 seconds (2360.86 seconds total)