Starting phenix.real_space_refine on Mon Aug 25 11:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.map" model { file = "/net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oax_20004/08_2025/6oax_20004.cif" } resolution = 2.9 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= 0.003 sd= 0.189 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 104 5.16 5 C 17381 2.51 5 N 5047 2.21 5 O 5306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s 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: 27871 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4518 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Chain: "E" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4555 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 23, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "P" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.42, per 1000 atoms: 0.27 Number of scatterers: 27871 At special positions: 0 Unit cell: (119.712, 143.448, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 33 15.00 O 5306 8.00 N 5047 7.00 C 17381 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 0 sheets defined 49.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.629A pdb=" N GLN C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.929A pdb=" N VAL C 246 " --> pdb=" O MET C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 280 through 284 removed outlier: 4.084A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 284' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.765A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 332 removed outlier: 3.882A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.565A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.909A pdb=" N LEU C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.615A pdb=" N ARG C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 567 removed outlier: 5.379A pdb=" N GLU C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 589 removed outlier: 4.085A pdb=" N ALA C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 639 through 648 removed outlier: 4.407A pdb=" N VAL C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER C 644 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG C 645 " --> pdb=" O HIS C 641 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU C 646 " --> pdb=" O SER C 642 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 647 " --> pdb=" O VAL C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 669 Processing helix chain 'C' and resid 678 through 682 removed outlier: 4.101A pdb=" N ALA C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 678 through 682' Processing helix chain 'C' and resid 685 through 693 removed outlier: 5.247A pdb=" N ILE C 689 " --> pdb=" O ASP C 685 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 728 removed outlier: 3.588A pdb=" N GLU C 727 " --> pdb=" O ASP C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 748 removed outlier: 3.789A pdb=" N GLU C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL C 741 " --> pdb=" O MET C 737 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N LEU C 742 " --> pdb=" O LYS C 738 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLY C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL C 744 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL C 745 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N SER C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N HIS C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 756 removed outlier: 4.694A pdb=" N ILE C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN C 755 " --> pdb=" O PRO C 751 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 756 " --> pdb=" O GLU C 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 750 through 756' Processing helix chain 'C' and resid 767 through 788 removed outlier: 3.851A pdb=" N SER C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 805 Processing helix chain 'C' and resid 814 through 835 removed outlier: 3.907A pdb=" N GLU C 826 " --> pdb=" O GLN C 822 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 827 " --> pdb=" O GLN C 823 " (cutoff:3.500A) Proline residue: C 828 - end of helix removed outlier: 3.522A pdb=" N GLN C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 213 through 221 removed outlier: 3.506A pdb=" N GLU F 217 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 5.237A pdb=" N VAL F 246 " --> pdb=" O MET F 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 246' Processing helix chain 'F' and resid 253 through 268 removed outlier: 4.394A pdb=" N ARG F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 264 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS F 268 " --> pdb=" O ASN F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 305 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.093A pdb=" N ILE F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 366 through 371 removed outlier: 3.723A pdb=" N VAL F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 removed outlier: 6.325A pdb=" N HIS F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 374 through 379' Processing helix chain 'F' and resid 387 through 405 removed outlier: 3.990A pdb=" N ASP F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 395 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 541 removed outlier: 3.745A pdb=" N VAL F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 551 removed outlier: 4.608A pdb=" N MET F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 547 through 551' Processing helix chain 'F' and resid 556 through 560 removed outlier: 4.665A pdb=" N LEU F 560 " --> pdb=" O ARG F 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 556 through 560' Processing helix chain 'F' and resid 565 through 569 removed outlier: 3.994A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 565 through 569' Processing helix chain 'F' and resid 574 through 589 removed outlier: 5.246A pdb=" N ASP F 578 " --> pdb=" O ASN F 574 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL F 580 " --> pdb=" O ALA F 576 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER F 581 " --> pdb=" O VAL F 577 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 583 " --> pdb=" O ALA F 579 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG F 586 " --> pdb=" O ASN F 582 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 623 removed outlier: 3.545A pdb=" N LEU F 614 " --> pdb=" O GLY F 610 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 619 " --> pdb=" O CYS F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 646 removed outlier: 5.637A pdb=" N SER F 644 " --> pdb=" O LYS F 640 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG F 645 " --> pdb=" O HIS F 641 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 640 through 646' Processing helix chain 'F' and resid 660 through 664 removed outlier: 4.174A pdb=" N GLU F 664 " --> pdb=" O GLY F 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 660 through 664' Processing helix chain 'F' and resid 684 through 694 removed outlier: 5.350A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU F 690 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 691 " --> pdb=" O PHE F 687 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLN F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL F 693 " --> pdb=" O ILE F 689 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU F 694 " --> pdb=" O LEU F 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 684 through 694' Processing helix chain 'F' and resid 722 through 728 removed outlier: 4.466A pdb=" N GLN F 726 " --> pdb=" O SER F 722 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU F 727 " --> pdb=" O ASP F 723 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG F 728 " --> pdb=" O LEU F 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 722 through 728' Processing helix chain 'F' and resid 734 through 748 removed outlier: 5.487A pdb=" N LYS F 738 " --> pdb=" O TYR F 734 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU F 739 " --> pdb=" O ALA F 735 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU F 740 " --> pdb=" O HIS F 736 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL F 741 " --> pdb=" O MET F 737 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 742 " --> pdb=" O LYS F 738 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 743 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL F 744 " --> pdb=" O LEU F 740 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL F 745 " --> pdb=" O VAL F 741 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER F 746 " --> pdb=" O LEU F 742 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N HIS F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN F 748 " --> pdb=" O VAL F 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 734 through 748' Processing helix chain 'F' and resid 750 through 756 removed outlier: 5.454A pdb=" N ILE F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN F 755 " --> pdb=" O PRO F 751 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 750 through 756' Processing helix chain 'F' and resid 768 through 784 removed outlier: 3.730A pdb=" N ILE F 774 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 779 " --> pdb=" O ALA F 775 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 786 through 790 Processing helix chain 'F' and resid 796 through 806 removed outlier: 3.818A pdb=" N LYS F 801 " --> pdb=" O ASP F 797 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU F 803 " --> pdb=" O ALA F 799 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER F 804 " --> pdb=" O LEU F 800 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU F 805 " --> pdb=" O LYS F 801 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 834 removed outlier: 5.251A pdb=" N ASN F 827 " --> pdb=" O GLN F 823 " (cutoff:3.500A) Proline residue: F 828 - end of helix Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.717A pdb=" N ARG E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 212 through 225 removed outlier: 3.553A pdb=" N VAL E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 4.652A pdb=" N LEU E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 262 " --> pdb=" O ARG E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.943A pdb=" N MET E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 303 removed outlier: 3.740A pdb=" N LEU E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 299 through 303' Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 343 through 351 removed outlier: 3.687A pdb=" N ALA E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 removed outlier: 3.549A pdb=" N TYR E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 380 removed outlier: 3.667A pdb=" N SER E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 407 Processing helix chain 'E' and resid 532 through 544 removed outlier: 3.656A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 567 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.873A pdb=" N ALA E 579 " --> pdb=" O GLU E 575 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 582 " --> pdb=" O ASP E 578 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 583 " --> pdb=" O ALA E 579 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 587 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 623 removed outlier: 3.739A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 637 No H-bonds generated for 'chain 'E' and resid 635 through 637' Processing helix chain 'E' and resid 639 through 646 removed outlier: 4.428A pdb=" N VAL E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER E 644 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG E 645 " --> pdb=" O HIS E 641 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU E 646 " --> pdb=" O SER E 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 639 through 646' Processing helix chain 'E' and resid 655 through 659 removed outlier: 4.181A pdb=" N GLY E 659 " --> pdb=" O GLY E 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 655 through 659' Processing helix chain 'E' and resid 662 through 668 Processing helix chain 'E' and resid 679 through 682 No H-bonds generated for 'chain 'E' and resid 679 through 682' Processing helix chain 'E' and resid 686 through 696 removed outlier: 3.705A pdb=" N GLN E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL E 693 " --> pdb=" O ILE E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 728 removed outlier: 3.873A pdb=" N GLN E 726 " --> pdb=" O SER E 722 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU E 727 " --> pdb=" O ASP E 723 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG E 728 " --> pdb=" O LEU E 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 722 through 728' Processing helix chain 'E' and resid 734 through 748 removed outlier: 3.523A pdb=" N LYS E 738 " --> pdb=" O TYR E 734 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 739 " --> pdb=" O ALA E 735 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 746 " --> pdb=" O LEU E 742 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS E 747 " --> pdb=" O GLY E 743 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN E 748 " --> pdb=" O VAL E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 756 removed outlier: 3.502A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 784 removed outlier: 3.594A pdb=" N SER E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN E 776 " --> pdb=" O ALA E 772 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 807 removed outlier: 3.745A pdb=" N LEU E 802 " --> pdb=" O GLU E 798 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 834 removed outlier: 4.845A pdb=" N GLU E 826 " --> pdb=" O GLN E 822 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN E 827 " --> pdb=" O GLN E 823 " (cutoff:3.500A) Proline residue: E 828 - end of helix removed outlier: 3.543A pdb=" N GLN E 831 " --> pdb=" O ASN E 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.524A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 215 through 226 removed outlier: 3.911A pdb=" N GLN D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 279 through 284 removed outlier: 4.216A pdb=" N MET D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 284' Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.646A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.501A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 4.183A pdb=" N PHE D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 342 through 362 removed outlier: 4.941A pdb=" N GLU D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.695A pdb=" N LEU D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 404 removed outlier: 3.541A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.635A pdb=" N ALA D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 567 removed outlier: 3.606A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU D 563 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.546A pdb=" N ALA D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 582 " --> pdb=" O ASP D 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 624 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.763A pdb=" N VAL D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER D 644 " --> pdb=" O LYS D 640 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG D 645 " --> pdb=" O HIS D 641 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 646 " --> pdb=" O SER D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.599A pdb=" N ARG D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.990A pdb=" N ALA D 682 " --> pdb=" O GLU D 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 685 through 695 removed outlier: 4.213A pdb=" N ILE D 689 " --> pdb=" O ASP D 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 693 " --> pdb=" O ILE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.665A pdb=" N GLN D 726 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 727 " --> pdb=" O ASP D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 748 removed outlier: 3.640A pdb=" N GLY D 743 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 748 " --> pdb=" O VAL D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 756 Processing helix chain 'D' and resid 767 through 785 removed outlier: 3.797A pdb=" N SER D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 803 Processing helix chain 'D' and resid 814 through 835 removed outlier: 4.302A pdb=" N GLU D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN D 827 " --> pdb=" O GLN D 823 " (cutoff:3.500A) Proline residue: D 828 - end of helix removed outlier: 3.625A pdb=" N GLN D 831 " --> pdb=" O ASN D 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.832A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.765A pdb=" N LEU B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.505A pdb=" N LYS B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.331A pdb=" N MET B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 284' Processing helix chain 'B' and resid 294 through 305 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 315 through 321 removed outlier: 3.610A pdb=" N GLN B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 362 removed outlier: 4.695A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.589A pdb=" N SER B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 407 removed outlier: 4.138A pdb=" N ILE B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 573 through 589 Processing helix chain 'B' and resid 610 through 624 Processing helix chain 'B' and resid 639 through 648 removed outlier: 4.652A pdb=" N VAL B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ARG B 645 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.676A pdb=" N ARG B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 removed outlier: 4.341A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 728 removed outlier: 5.399A pdb=" N GLN B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B 727 " --> pdb=" O ASP B 723 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 728 " --> pdb=" O LEU B 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 722 through 728' Processing helix chain 'B' and resid 734 through 748 removed outlier: 3.602A pdb=" N GLU B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 743 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.677A pdb=" N ARG B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 785 removed outlier: 3.578A pdb=" N SER B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 807 removed outlier: 4.120A pdb=" N LYS B 801 " --> pdb=" O ASP B 797 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU B 802 " --> pdb=" O GLU B 798 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 803 " --> pdb=" O ALA B 799 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 removed outlier: 3.774A pdb=" N GLN B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU B 826 " --> pdb=" O GLN B 822 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) Proline residue: B 828 - end of helix removed outlier: 3.951A pdb=" N GLN B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.684A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.627A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.805A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.618A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.605A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 407 removed outlier: 3.681A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.280A pdb=" N ARG A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 573 through 589 removed outlier: 4.184A pdb=" N ASN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.815A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 5.358A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG A 645 " --> pdb=" O HIS A 641 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 646' Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.922A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 4.582A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.863A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 748 removed outlier: 6.009A pdb=" N LYS A 738 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 740 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N HIS A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 748' Processing helix chain 'A' and resid 750 through 756 removed outlier: 4.517A pdb=" N ILE A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 756' Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.584A pdb=" N ILE A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLN A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 785 removed outlier: 5.213A pdb=" N ARG A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 785' Processing helix chain 'A' and resid 799 through 807 removed outlier: 4.024A pdb=" N LEU A 803 " --> pdb=" O ALA A 799 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.508A pdb=" N LYS A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2157 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: 4.54 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 9899 1.36 - 1.51: 8397 1.51 - 1.66: 9813 1.66 - 1.81: 173 1.81 - 1.96: 14 Bond restraints: 28296 Sorted by residual: bond pdb=" C ARG A 815 " pdb=" N PRO A 816 " ideal model delta sigma weight residual 1.337 1.397 -0.060 9.80e-03 1.04e+04 3.78e+01 bond pdb=" C GLY C 648 " pdb=" N ALA C 649 " ideal model delta sigma weight residual 1.329 1.246 0.083 1.86e-02 2.89e+03 1.97e+01 bond pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 1.527 1.451 0.076 1.75e-02 3.27e+03 1.89e+01 bond pdb=" CA LEU B 676 " pdb=" CB LEU B 676 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.76e-02 3.23e+03 1.75e+01 bond pdb=" CB THR B 314 " pdb=" CG2 THR B 314 " ideal model delta sigma weight residual 1.521 1.414 0.107 3.30e-02 9.18e+02 1.04e+01 ... (remaining 28291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 36792 2.72 - 5.44: 1286 5.44 - 8.17: 154 8.17 - 10.89: 25 10.89 - 13.61: 2 Bond angle restraints: 38259 Sorted by residual: angle pdb=" N PHE E 337 " pdb=" CA PHE E 337 " pdb=" C PHE E 337 " ideal model delta sigma weight residual 110.23 121.97 -11.74 1.45e+00 4.76e-01 6.55e+01 angle pdb=" N GLU C 850 " pdb=" CA GLU C 850 " pdb=" C GLU C 850 " ideal model delta sigma weight residual 109.95 100.71 9.24 1.44e+00 4.82e-01 4.12e+01 angle pdb=" N VAL F 343 " pdb=" CA VAL F 343 " pdb=" C VAL F 343 " ideal model delta sigma weight residual 113.22 105.80 7.42 1.23e+00 6.61e-01 3.64e+01 angle pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" C ILE A 215 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N VAL B 548 " pdb=" CA VAL B 548 " pdb=" C VAL B 548 " ideal model delta sigma weight residual 112.29 106.81 5.48 9.40e-01 1.13e+00 3.40e+01 ... (remaining 38254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 16774 33.14 - 66.27: 610 66.27 - 99.41: 39 99.41 - 132.54: 5 132.54 - 165.68: 3 Dihedral angle restraints: 17431 sinusoidal: 7389 harmonic: 10042 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.90 -115.91 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 53.29 -113.30 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N LEU A 386 " pdb=" CA LEU A 386 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 17428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3301 0.073 - 0.145: 908 0.145 - 0.218: 96 0.218 - 0.290: 19 0.290 - 0.363: 4 Chirality restraints: 4328 Sorted by residual: chirality pdb=" CB VAL C 228 " pdb=" CA VAL C 228 " pdb=" CG1 VAL C 228 " pdb=" CG2 VAL C 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB VAL D 609 " pdb=" CA VAL D 609 " pdb=" CG1 VAL D 609 " pdb=" CG2 VAL D 609 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE F 571 " pdb=" CA ILE F 571 " pdb=" CG1 ILE F 571 " pdb=" CG2 ILE F 571 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 4325 not shown) Planarity restraints: 4991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 300 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO E 301 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 367 " 0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 368 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 367 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO E 368 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " 0.042 5.00e-02 4.00e+02 ... (remaining 4988 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 123 2.43 - 3.04: 15019 3.04 - 3.66: 43697 3.66 - 4.28: 68102 4.28 - 4.90: 110750 Nonbonded interactions: 237691 Sorted by model distance: nonbonded pdb=" O ALA E 339 " pdb=" O GLU E 340 " model vdw 1.807 3.040 nonbonded pdb=" O MET E 298 " pdb=" CG PRO E 301 " model vdw 2.214 3.440 nonbonded pdb=" CD2 LEU D 204 " pdb=" O LYS D 212 " model vdw 2.217 3.460 nonbonded pdb=" O2A AGS D 901 " pdb=" O2B AGS D 901 " model vdw 2.223 3.040 nonbonded pdb=" O PRO C 651 " pdb=" OG SER D 644 " model vdw 2.227 3.040 ... (remaining 237686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'B' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'C' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'D' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'E' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'F' and (resid 161 through 408 or resid 529 through 857)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.760 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.012 0.124 28296 Z= 0.495 Angle : 1.184 13.611 38259 Z= 0.667 Chirality : 0.066 0.363 4328 Planarity : 0.008 0.085 4991 Dihedral : 16.589 165.676 10965 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 0.93 % Allowed : 9.09 % Favored : 89.99 % 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: -5.39 (0.10), residues: 3448 helix: -4.58 (0.06), residues: 1524 sheet: -3.40 (0.25), residues: 260 loop : -2.45 (0.13), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 585 TYR 0.020 0.003 TYR B 653 PHE 0.024 0.004 PHE E 276 TRP 0.011 0.002 TRP E 543 HIS 0.016 0.002 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.01171 (28296) covalent geometry : angle 1.18415 (38259) hydrogen bonds : bond 0.29761 ( 719) hydrogen bonds : angle 12.16750 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 593 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8654 (mt0) cc_final: 0.8410 (mt0) REVERT: F 251 TYR cc_start: 0.5641 (m-80) cc_final: 0.5347 (m-80) REVERT: F 275 LEU cc_start: 0.6701 (tp) cc_final: 0.6148 (tm) REVERT: F 276 PHE cc_start: 0.6791 (m-10) cc_final: 0.6191 (m-80) REVERT: F 314 THR cc_start: 0.7200 (p) cc_final: 0.6988 (p) REVERT: F 331 ARG cc_start: 0.6814 (tpp-160) cc_final: 0.5226 (ttm-80) REVERT: F 333 PHE cc_start: 0.6663 (m-80) cc_final: 0.6322 (m-80) REVERT: F 356 ARG cc_start: 0.3801 (tpt170) cc_final: 0.2794 (tmt-80) REVERT: F 569 ARG cc_start: 0.5713 (ttp80) cc_final: 0.5236 (ptp-170) REVERT: F 585 ARG cc_start: 0.4975 (mtp85) cc_final: 0.4447 (tpm-80) REVERT: F 629 MET cc_start: 0.5200 (ttt) cc_final: 0.4928 (mmt) REVERT: F 634 MET cc_start: 0.4233 (mmp) cc_final: 0.4013 (mmt) REVERT: F 638 MET cc_start: 0.0537 (mmp) cc_final: 0.0144 (mpt) REVERT: E 217 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6643 (mp0) REVERT: E 252 ARG cc_start: 0.6710 (mpp-170) cc_final: 0.5693 (tpt170) REVERT: E 298 MET cc_start: 0.6019 (mtp) cc_final: 0.5534 (mtt) REVERT: E 317 ASP cc_start: 0.7654 (m-30) cc_final: 0.7136 (m-30) REVERT: E 322 TYR cc_start: 0.7720 (m-80) cc_final: 0.7449 (m-80) REVERT: E 638 MET cc_start: 0.8553 (mtm) cc_final: 0.8129 (mtm) REVERT: E 705 ARG cc_start: 0.6639 (mtt180) cc_final: 0.6260 (mtt180) REVERT: E 734 TYR cc_start: 0.7764 (t80) cc_final: 0.7556 (t80) REVERT: E 751 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8368 (Cg_endo) REVERT: E 752 GLU cc_start: 0.7273 (pm20) cc_final: 0.7069 (pm20) REVERT: E 822 GLN cc_start: 0.7999 (mt0) cc_final: 0.7400 (tt0) REVERT: D 163 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8051 (mptt) REVERT: D 260 LYS cc_start: 0.7629 (mttt) cc_final: 0.7277 (mttm) REVERT: D 300 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8590 (mtmm) REVERT: D 695 ASP cc_start: 0.7698 (t0) cc_final: 0.7228 (t70) REVERT: D 769 GLN cc_start: 0.8040 (pm20) cc_final: 0.7665 (pm20) REVERT: D 847 GLU cc_start: 0.7446 (mp0) cc_final: 0.7175 (mm-30) REVERT: D 857 GLN cc_start: 0.6715 (mm-40) cc_final: 0.6513 (tp40) REVERT: B 251 TYR cc_start: 0.8344 (m-80) cc_final: 0.7879 (m-10) REVERT: B 264 ASN cc_start: 0.7936 (m-40) cc_final: 0.7696 (m-40) REVERT: B 376 LEU cc_start: 0.8412 (mt) cc_final: 0.8200 (mp) REVERT: B 558 LYS cc_start: 0.8133 (tttm) cc_final: 0.7925 (ttpt) REVERT: B 831 GLN cc_start: 0.7274 (pp30) cc_final: 0.7016 (pp30) REVERT: B 832 GLN cc_start: 0.7760 (tt0) cc_final: 0.7556 (tm-30) REVERT: A 288 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6476 (tttt) REVERT: A 551 MET cc_start: 0.1061 (mpp) cc_final: 0.0821 (mmm) REVERT: A 616 LYS cc_start: 0.8420 (mttt) cc_final: 0.8160 (mttm) outliers start: 27 outliers final: 8 residues processed: 610 average time/residue: 0.8516 time to fit residues: 586.6631 Evaluate side-chains 416 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 407 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 626 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN C 297 ASN C 748 ASN F 404 GLN F 776 GLN E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS E 564 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN E 823 GLN E 824 GLN D 272 ASN D 297 ASN D 309 HIS D 334 GLN D 385 GLN D 688 ASN D 806 ASN D 824 GLN B 364 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B 832 GLN A 272 ASN A 297 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 794 HIS A 831 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.211664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155121 restraints weight = 28430.800| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.03 r_work: 0.3542 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28296 Z= 0.152 Angle : 0.696 8.744 38259 Z= 0.354 Chirality : 0.046 0.204 4328 Planarity : 0.006 0.070 4991 Dihedral : 12.261 171.771 4101 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 3.26 % Allowed : 15.95 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.07 (0.12), residues: 3448 helix: -3.16 (0.10), residues: 1570 sheet: -2.92 (0.30), residues: 242 loop : -2.04 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 561 TYR 0.015 0.001 TYR F 661 PHE 0.018 0.001 PHE D 729 TRP 0.017 0.002 TRP D 543 HIS 0.005 0.001 HIS C 361 Details of bonding type rmsd covalent geometry : bond 0.00339 (28296) covalent geometry : angle 0.69579 (38259) hydrogen bonds : bond 0.04786 ( 719) hydrogen bonds : angle 6.75384 ( 2157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 458 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8659 (mt0) cc_final: 0.8283 (mt0) REVERT: C 305 ARG cc_start: 0.6446 (mtt-85) cc_final: 0.5354 (mtm-85) REVERT: C 307 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 561 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6607 (ptt-90) REVERT: C 710 ARG cc_start: 0.8394 (mtt90) cc_final: 0.8118 (mtt-85) REVERT: C 798 GLU cc_start: 0.8270 (mp0) cc_final: 0.8042 (tp30) REVERT: F 251 TYR cc_start: 0.4877 (m-80) cc_final: 0.4392 (m-80) REVERT: F 276 PHE cc_start: 0.6644 (m-10) cc_final: 0.6176 (m-80) REVERT: F 300 LYS cc_start: 0.3397 (OUTLIER) cc_final: 0.2805 (mmtt) REVERT: F 320 ARG cc_start: 0.6026 (mtm110) cc_final: 0.5658 (ttm110) REVERT: F 331 ARG cc_start: 0.6589 (tpp-160) cc_final: 0.4586 (ttm-80) REVERT: F 356 ARG cc_start: 0.3124 (tpt170) cc_final: 0.2358 (tmt-80) REVERT: F 585 ARG cc_start: 0.5038 (mtp85) cc_final: 0.4468 (tpm-80) REVERT: F 629 MET cc_start: 0.5290 (ttt) cc_final: 0.4678 (mmt) REVERT: F 638 MET cc_start: -0.1018 (mmp) cc_final: -0.1258 (mpt) REVERT: F 720 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4975 (tp) REVERT: F 752 GLU cc_start: 0.1806 (tm-30) cc_final: 0.1342 (pm20) REVERT: E 164 TYR cc_start: 0.7708 (m-10) cc_final: 0.7113 (m-10) REVERT: E 217 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6215 (mp0) REVERT: E 252 ARG cc_start: 0.6310 (mpp-170) cc_final: 0.5134 (tpt170) REVERT: E 317 ASP cc_start: 0.7723 (m-30) cc_final: 0.7273 (m-30) REVERT: E 561 ARG cc_start: 0.6914 (mtm110) cc_final: 0.6133 (ptt90) REVERT: E 616 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7699 (mtpt) REVERT: E 629 MET cc_start: 0.8904 (ptt) cc_final: 0.8498 (ptp) REVERT: E 638 MET cc_start: 0.8381 (mtm) cc_final: 0.7891 (mtm) REVERT: E 656 TYR cc_start: 0.7732 (p90) cc_final: 0.7174 (p90) REVERT: E 696 ASP cc_start: 0.6206 (OUTLIER) cc_final: 0.5423 (t0) REVERT: E 705 ARG cc_start: 0.6333 (mtt180) cc_final: 0.5664 (mtt180) REVERT: E 734 TYR cc_start: 0.7928 (t80) cc_final: 0.7680 (t80) REVERT: E 737 MET cc_start: 0.7249 (tpp) cc_final: 0.6507 (tpt) REVERT: E 751 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7951 (Cg_endo) REVERT: E 752 GLU cc_start: 0.7512 (pm20) cc_final: 0.6934 (pm20) REVERT: E 780 LYS cc_start: 0.7629 (mtmt) cc_final: 0.7092 (mttp) REVERT: E 798 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: E 822 GLN cc_start: 0.7850 (mt0) cc_final: 0.6870 (tt0) REVERT: D 163 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8021 (mptt) REVERT: D 173 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 184 ASP cc_start: 0.8171 (t0) cc_final: 0.7940 (m-30) REVERT: D 185 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7734 (tp30) REVERT: D 260 LYS cc_start: 0.7284 (mttt) cc_final: 0.6847 (mttm) REVERT: D 552 MET cc_start: 0.4109 (mmt) cc_final: 0.3767 (mmm) REVERT: D 705 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7930 (mtm180) REVERT: D 750 ARG cc_start: 0.7670 (mtp85) cc_final: 0.6867 (mmp80) REVERT: D 769 GLN cc_start: 0.8404 (pm20) cc_final: 0.7973 (pm20) REVERT: D 831 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7274 (tm130) REVERT: B 162 LYS cc_start: 0.8504 (tttm) cc_final: 0.8060 (mtpp) REVERT: B 268 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7577 (mttp) REVERT: B 555 GLU cc_start: 0.7558 (tt0) cc_final: 0.6969 (tm-30) REVERT: B 558 LYS cc_start: 0.7837 (tttm) cc_final: 0.7335 (ttpt) REVERT: B 561 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6471 (ptp90) REVERT: B 831 GLN cc_start: 0.7187 (pp30) cc_final: 0.6827 (pp30) REVERT: B 832 GLN cc_start: 0.7490 (tt0) cc_final: 0.6954 (tm-30) REVERT: A 256 GLU cc_start: 0.8102 (mp0) cc_final: 0.7895 (mp0) REVERT: A 293 MET cc_start: 0.3576 (ttp) cc_final: 0.3167 (ttp) REVERT: A 396 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6435 (mt-10) REVERT: A 551 MET cc_start: 0.1023 (mpp) cc_final: 0.0776 (mmm) REVERT: A 564 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: A 616 LYS cc_start: 0.8079 (mttt) cc_final: 0.7691 (mttm) REVERT: A 716 MET cc_start: 0.7822 (mtp) cc_final: 0.7500 (mtp) outliers start: 95 outliers final: 24 residues processed: 519 average time/residue: 0.7222 time to fit residues: 431.1652 Evaluate side-chains 415 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 386 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 798 GLU Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 675 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 345 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 160 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 281 HIS F 770 HIS E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 360 HIS D 776 GLN D 822 GLN B 195 GLN B 755 ASN B 770 HIS B 823 GLN A 281 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.210009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154749 restraints weight = 28303.442| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.28 r_work: 0.3487 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28296 Z= 0.189 Angle : 0.653 7.474 38259 Z= 0.329 Chirality : 0.047 0.241 4328 Planarity : 0.005 0.062 4991 Dihedral : 11.657 173.967 4084 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.81 % Allowed : 18.79 % Favored : 77.40 % 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: -3.22 (0.13), residues: 3448 helix: -2.25 (0.11), residues: 1573 sheet: -2.88 (0.30), residues: 247 loop : -1.75 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 332 TYR 0.025 0.001 TYR B 783 PHE 0.017 0.002 PHE E 276 TRP 0.019 0.002 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00456 (28296) covalent geometry : angle 0.65255 (38259) hydrogen bonds : bond 0.04226 ( 719) hydrogen bonds : angle 6.07275 ( 2157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 413 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8692 (mt0) cc_final: 0.8388 (mt0) REVERT: C 305 ARG cc_start: 0.6657 (mtt-85) cc_final: 0.5460 (mtm-85) REVERT: C 307 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8667 (mt-10) REVERT: C 344 GLU cc_start: 0.7769 (mp0) cc_final: 0.7419 (mp0) REVERT: C 561 ARG cc_start: 0.7369 (mtm110) cc_final: 0.6774 (ptt-90) REVERT: C 710 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8145 (mtt-85) REVERT: C 784 LYS cc_start: 0.7803 (mptt) cc_final: 0.7440 (mppt) REVERT: C 798 GLU cc_start: 0.8506 (mp0) cc_final: 0.8187 (tp30) REVERT: F 251 TYR cc_start: 0.4711 (m-80) cc_final: 0.4241 (m-80) REVERT: F 275 LEU cc_start: 0.6614 (tp) cc_final: 0.6117 (tm) REVERT: F 300 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.2588 (mmtt) REVERT: F 320 ARG cc_start: 0.6125 (mtm110) cc_final: 0.5820 (ttm-80) REVERT: F 331 ARG cc_start: 0.6505 (tpp-160) cc_final: 0.4502 (ttm-80) REVERT: F 569 ARG cc_start: 0.4708 (OUTLIER) cc_final: 0.4455 (ptm-80) REVERT: F 585 ARG cc_start: 0.5049 (mtp85) cc_final: 0.4334 (tpm-80) REVERT: F 629 MET cc_start: 0.5187 (ttt) cc_final: 0.4601 (mmt) REVERT: F 638 MET cc_start: -0.1570 (mmp) cc_final: -0.1851 (mpt) REVERT: F 800 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5904 (pp) REVERT: E 164 TYR cc_start: 0.7661 (m-10) cc_final: 0.7079 (m-10) REVERT: E 217 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6326 (mp0) REVERT: E 252 ARG cc_start: 0.6316 (mpp-170) cc_final: 0.5055 (tpt170) REVERT: E 264 ASN cc_start: 0.7338 (m-40) cc_final: 0.7066 (t0) REVERT: E 317 ASP cc_start: 0.7731 (m-30) cc_final: 0.7332 (m-30) REVERT: E 353 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7705 (mt) REVERT: E 561 ARG cc_start: 0.7018 (mtm110) cc_final: 0.6283 (ptt90) REVERT: E 616 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7616 (mtmm) REVERT: E 629 MET cc_start: 0.8965 (ptt) cc_final: 0.8454 (ptp) REVERT: E 638 MET cc_start: 0.8444 (mtm) cc_final: 0.7873 (mtm) REVERT: E 656 TYR cc_start: 0.7733 (p90) cc_final: 0.7163 (p90) REVERT: E 696 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5325 (t0) REVERT: E 705 ARG cc_start: 0.6609 (mtt180) cc_final: 0.5856 (mtt180) REVERT: E 737 MET cc_start: 0.7131 (tpp) cc_final: 0.6496 (tpt) REVERT: E 752 GLU cc_start: 0.7486 (pm20) cc_final: 0.7021 (pm20) REVERT: E 798 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: E 822 GLN cc_start: 0.7771 (mt0) cc_final: 0.6930 (tt0) REVERT: D 162 LYS cc_start: 0.8544 (mttt) cc_final: 0.8209 (ttmm) REVERT: D 163 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8054 (mptt) REVERT: D 184 ASP cc_start: 0.8209 (t0) cc_final: 0.7961 (m-30) REVERT: D 260 LYS cc_start: 0.7370 (mttt) cc_final: 0.6995 (mttm) REVERT: D 308 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7060 (mp) REVERT: D 324 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: D 552 MET cc_start: 0.4246 (mmt) cc_final: 0.3804 (mmm) REVERT: D 563 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: D 769 GLN cc_start: 0.8407 (pm20) cc_final: 0.7980 (pm20) REVERT: D 831 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7268 (tm130) REVERT: B 162 LYS cc_start: 0.8518 (tttm) cc_final: 0.8094 (mtpp) REVERT: B 268 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7728 (mttt) REVERT: B 283 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8197 (ttm) REVERT: B 555 GLU cc_start: 0.7605 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 558 LYS cc_start: 0.7809 (tttm) cc_final: 0.7311 (ttpt) REVERT: B 561 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6643 (ptp90) REVERT: B 657 GLU cc_start: 0.8085 (mp0) cc_final: 0.7856 (mp0) REVERT: B 831 GLN cc_start: 0.7173 (pp30) cc_final: 0.6844 (pp30) REVERT: B 832 GLN cc_start: 0.7384 (tt0) cc_final: 0.6923 (tm-30) REVERT: A 256 GLU cc_start: 0.8149 (mp0) cc_final: 0.7895 (mp0) REVERT: A 363 VAL cc_start: 0.7869 (t) cc_final: 0.7596 (m) REVERT: A 396 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6439 (mt-10) REVERT: A 551 MET cc_start: 0.1142 (mpp) cc_final: 0.0902 (mmm) REVERT: A 681 LYS cc_start: 0.7111 (mttt) cc_final: 0.6756 (mtpt) outliers start: 111 outliers final: 46 residues processed: 486 average time/residue: 0.7638 time to fit residues: 426.5303 Evaluate side-chains 428 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 569 ARG Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 718 SER Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 798 GLU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 302 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 329 optimal weight: 0.8980 chunk 233 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 195 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.211505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156310 restraints weight = 28063.908| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.16 r_work: 0.3544 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28296 Z= 0.128 Angle : 0.597 9.376 38259 Z= 0.300 Chirality : 0.045 0.237 4328 Planarity : 0.005 0.074 4991 Dihedral : 11.212 179.407 4084 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.64 % Allowed : 20.23 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.62 (0.13), residues: 3448 helix: -1.60 (0.12), residues: 1573 sheet: -2.78 (0.29), residues: 267 loop : -1.54 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 728 TYR 0.021 0.001 TYR B 783 PHE 0.019 0.001 PHE F 276 TRP 0.012 0.001 TRP D 543 HIS 0.007 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00301 (28296) covalent geometry : angle 0.59741 (38259) hydrogen bonds : bond 0.03666 ( 719) hydrogen bonds : angle 5.61860 ( 2157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 412 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8699 (mt0) cc_final: 0.8409 (mt0) REVERT: C 305 ARG cc_start: 0.6643 (mtt-85) cc_final: 0.5369 (mtm-85) REVERT: C 307 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8595 (mt-10) REVERT: C 555 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6905 (tm-30) REVERT: C 613 GLU cc_start: 0.8657 (tp30) cc_final: 0.8457 (tp30) REVERT: C 696 ASP cc_start: 0.7829 (m-30) cc_final: 0.7603 (t70) REVERT: C 710 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7972 (mtt-85) REVERT: C 784 LYS cc_start: 0.7602 (mptt) cc_final: 0.7241 (mppt) REVERT: C 798 GLU cc_start: 0.8479 (mp0) cc_final: 0.8162 (tp30) REVERT: C 831 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: F 251 TYR cc_start: 0.4917 (m-80) cc_final: 0.4372 (m-80) REVERT: F 264 ASN cc_start: 0.5930 (OUTLIER) cc_final: 0.5522 (t0) REVERT: F 275 LEU cc_start: 0.6322 (tp) cc_final: 0.5799 (tm) REVERT: F 276 PHE cc_start: 0.6876 (m-10) cc_final: 0.5918 (m-80) REVERT: F 300 LYS cc_start: 0.3663 (OUTLIER) cc_final: 0.2821 (mmtt) REVERT: F 320 ARG cc_start: 0.6069 (mtm110) cc_final: 0.5845 (ttm-80) REVERT: F 331 ARG cc_start: 0.6462 (tpp-160) cc_final: 0.4428 (ttm-80) REVERT: F 356 ARG cc_start: 0.2862 (tpt170) cc_final: 0.2266 (tmt-80) REVERT: F 585 ARG cc_start: 0.5135 (mtp85) cc_final: 0.4512 (tpm-80) REVERT: F 629 MET cc_start: 0.5331 (ttt) cc_final: 0.4617 (mmt) REVERT: F 638 MET cc_start: -0.1442 (mmp) cc_final: -0.1842 (mpt) REVERT: F 716 MET cc_start: 0.5301 (mtt) cc_final: 0.4781 (mmm) REVERT: F 752 GLU cc_start: 0.1456 (tm-30) cc_final: 0.1182 (pm20) REVERT: F 800 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5794 (pp) REVERT: E 164 TYR cc_start: 0.7635 (m-10) cc_final: 0.6983 (m-10) REVERT: E 217 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6248 (mp0) REVERT: E 252 ARG cc_start: 0.6288 (mpp-170) cc_final: 0.4858 (tpt90) REVERT: E 264 ASN cc_start: 0.7225 (m-40) cc_final: 0.7017 (t0) REVERT: E 317 ASP cc_start: 0.7777 (m-30) cc_final: 0.7408 (m-30) REVERT: E 353 LEU cc_start: 0.8053 (tp) cc_final: 0.7632 (mt) REVERT: E 561 ARG cc_start: 0.6941 (mtm110) cc_final: 0.6148 (ptt90) REVERT: E 629 MET cc_start: 0.8881 (ptt) cc_final: 0.8298 (ptp) REVERT: E 638 MET cc_start: 0.8326 (mtm) cc_final: 0.7778 (mtm) REVERT: E 656 TYR cc_start: 0.7652 (p90) cc_final: 0.7113 (p90) REVERT: E 696 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5210 (t0) REVERT: E 705 ARG cc_start: 0.6601 (mtt180) cc_final: 0.5884 (mtt180) REVERT: E 752 GLU cc_start: 0.7356 (pm20) cc_final: 0.6878 (pm20) REVERT: E 780 LYS cc_start: 0.7512 (mtmt) cc_final: 0.6925 (mptm) REVERT: E 822 GLN cc_start: 0.7541 (mt0) cc_final: 0.6841 (tt0) REVERT: D 162 LYS cc_start: 0.8474 (mttt) cc_final: 0.8128 (ttmm) REVERT: D 163 LYS cc_start: 0.9112 (mtmt) cc_final: 0.8009 (mptt) REVERT: D 174 GLN cc_start: 0.9110 (mt0) cc_final: 0.8841 (mt0) REVERT: D 184 ASP cc_start: 0.8061 (t0) cc_final: 0.7837 (m-30) REVERT: D 260 LYS cc_start: 0.7418 (mttt) cc_final: 0.7017 (mttm) REVERT: D 308 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6948 (mp) REVERT: D 324 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: D 527 LEU cc_start: 0.4348 (OUTLIER) cc_final: 0.4095 (pp) REVERT: D 552 MET cc_start: 0.4603 (mmt) cc_final: 0.4096 (mmm) REVERT: D 563 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: D 734 TYR cc_start: 0.8656 (t80) cc_final: 0.8433 (t80) REVERT: B 162 LYS cc_start: 0.8413 (tttm) cc_final: 0.8007 (mtpp) REVERT: B 188 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7083 (ttp-110) REVERT: B 268 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7637 (mttt) REVERT: B 283 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8055 (ttm) REVERT: B 293 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5700 (pmt) REVERT: B 551 MET cc_start: 0.7810 (ttp) cc_final: 0.7326 (ttp) REVERT: B 555 GLU cc_start: 0.7475 (tt0) cc_final: 0.7028 (tm-30) REVERT: B 558 LYS cc_start: 0.7784 (tttm) cc_final: 0.7197 (ttpt) REVERT: B 560 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8490 (mt) REVERT: B 776 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7517 (mt0) REVERT: B 831 GLN cc_start: 0.7059 (pp30) cc_final: 0.6851 (pp30) REVERT: B 832 GLN cc_start: 0.7553 (tt0) cc_final: 0.7019 (tm-30) REVERT: A 256 GLU cc_start: 0.7906 (mp0) cc_final: 0.7566 (mp0) REVERT: A 396 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6422 (mt-10) REVERT: A 551 MET cc_start: 0.1216 (mpp) cc_final: 0.0967 (mmm) REVERT: A 664 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 681 LYS cc_start: 0.7075 (mttt) cc_final: 0.6850 (mtpt) REVERT: A 716 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7240 (mtm) outliers start: 106 outliers final: 35 residues processed: 481 average time/residue: 0.7937 time to fit residues: 437.4249 Evaluate side-chains 418 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 116 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 824 GLN F 703 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 703 GLN D 794 HIS D 822 GLN B 195 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.209805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153998 restraints weight = 28187.006| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.24 r_work: 0.3507 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28296 Z= 0.159 Angle : 0.606 7.864 38259 Z= 0.302 Chirality : 0.046 0.249 4328 Planarity : 0.004 0.062 4991 Dihedral : 11.053 175.373 4084 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.98 % Allowed : 21.43 % Favored : 74.59 % 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: -2.28 (0.14), residues: 3448 helix: -1.30 (0.13), residues: 1569 sheet: -2.68 (0.29), residues: 283 loop : -1.35 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 631 TYR 0.028 0.001 TYR F 783 PHE 0.015 0.001 PHE E 276 TRP 0.011 0.001 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00388 (28296) covalent geometry : angle 0.60576 (38259) hydrogen bonds : bond 0.03700 ( 719) hydrogen bonds : angle 5.46862 ( 2157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 398 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8666 (mt0) cc_final: 0.8380 (mt0) REVERT: C 305 ARG cc_start: 0.6672 (mtt-85) cc_final: 0.5465 (mtm-85) REVERT: C 307 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8662 (mt-10) REVERT: C 555 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 613 GLU cc_start: 0.8674 (tp30) cc_final: 0.8456 (tp30) REVERT: C 696 ASP cc_start: 0.7912 (m-30) cc_final: 0.7666 (t70) REVERT: C 710 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7995 (mtt-85) REVERT: C 739 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.5406 (pp20) REVERT: C 784 LYS cc_start: 0.7592 (mptt) cc_final: 0.7248 (mppt) REVERT: C 798 GLU cc_start: 0.8470 (mp0) cc_final: 0.8146 (tp30) REVERT: C 805 GLU cc_start: 0.7514 (tt0) cc_final: 0.7300 (tm-30) REVERT: F 251 TYR cc_start: 0.4851 (m-80) cc_final: 0.4352 (m-80) REVERT: F 264 ASN cc_start: 0.5945 (OUTLIER) cc_final: 0.5556 (t0) REVERT: F 275 LEU cc_start: 0.6252 (tp) cc_final: 0.5701 (tm) REVERT: F 276 PHE cc_start: 0.6873 (m-10) cc_final: 0.5903 (m-80) REVERT: F 300 LYS cc_start: 0.3581 (OUTLIER) cc_final: 0.2724 (mmtt) REVERT: F 320 ARG cc_start: 0.6148 (mtm110) cc_final: 0.5615 (mmm-85) REVERT: F 331 ARG cc_start: 0.6859 (tpp-160) cc_final: 0.4856 (ttm-80) REVERT: F 356 ARG cc_start: 0.2857 (tpt170) cc_final: 0.2263 (tmt-80) REVERT: F 585 ARG cc_start: 0.5106 (mtp85) cc_final: 0.4459 (tpm-80) REVERT: F 629 MET cc_start: 0.5174 (ttt) cc_final: 0.4479 (mmt) REVERT: F 638 MET cc_start: -0.1638 (mmp) cc_final: -0.2102 (mpt) REVERT: F 716 MET cc_start: 0.5382 (mtt) cc_final: 0.3172 (tpp) REVERT: E 164 TYR cc_start: 0.7724 (m-10) cc_final: 0.7221 (m-10) REVERT: E 167 ASP cc_start: 0.8267 (t70) cc_final: 0.7796 (t70) REVERT: E 217 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6284 (mp0) REVERT: E 252 ARG cc_start: 0.6325 (mpp-170) cc_final: 0.4817 (tpt90) REVERT: E 317 ASP cc_start: 0.7743 (m-30) cc_final: 0.7373 (m-30) REVERT: E 561 ARG cc_start: 0.6971 (mtm110) cc_final: 0.6163 (ptt90) REVERT: E 629 MET cc_start: 0.8920 (ptt) cc_final: 0.8361 (ptp) REVERT: E 638 MET cc_start: 0.8381 (mtm) cc_final: 0.7718 (mtm) REVERT: E 656 TYR cc_start: 0.7660 (p90) cc_final: 0.6935 (p90) REVERT: E 696 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5223 (t0) REVERT: E 698 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7515 (mmm160) REVERT: E 705 ARG cc_start: 0.6628 (mtt180) cc_final: 0.6098 (mtm180) REVERT: E 737 MET cc_start: 0.7113 (tpp) cc_final: 0.6449 (tpt) REVERT: E 752 GLU cc_start: 0.7340 (pm20) cc_final: 0.6883 (pm20) REVERT: E 768 GLU cc_start: 0.7764 (tt0) cc_final: 0.7257 (tp30) REVERT: E 822 GLN cc_start: 0.7514 (mt0) cc_final: 0.6811 (tt0) REVERT: D 163 LYS cc_start: 0.9056 (mtmt) cc_final: 0.7967 (mptt) REVERT: D 174 GLN cc_start: 0.9159 (mt0) cc_final: 0.8859 (mt0) REVERT: D 184 ASP cc_start: 0.8136 (t0) cc_final: 0.7910 (m-30) REVERT: D 230 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8386 (tp30) REVERT: D 260 LYS cc_start: 0.7482 (mttt) cc_final: 0.7079 (mttm) REVERT: D 324 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: D 552 MET cc_start: 0.4615 (mmt) cc_final: 0.4134 (mmm) REVERT: D 563 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: D 734 TYR cc_start: 0.8667 (t80) cc_final: 0.8391 (t80) REVERT: D 801 LYS cc_start: 0.7644 (ptmt) cc_final: 0.7244 (ttmt) REVERT: D 823 GLN cc_start: 0.8002 (mt0) cc_final: 0.7614 (mp10) REVERT: B 268 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7705 (mttt) REVERT: B 283 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8247 (ttm) REVERT: B 555 GLU cc_start: 0.7582 (tt0) cc_final: 0.7104 (tm-30) REVERT: B 558 LYS cc_start: 0.7764 (tttm) cc_final: 0.7180 (ttpp) REVERT: B 560 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 561 ARG cc_start: 0.7094 (mtm110) cc_final: 0.6677 (ptp90) REVERT: B 657 GLU cc_start: 0.8101 (mp0) cc_final: 0.7816 (mp0) REVERT: B 776 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7581 (mt0) REVERT: B 831 GLN cc_start: 0.7082 (pp30) cc_final: 0.6868 (pp30) REVERT: B 832 GLN cc_start: 0.7532 (tt0) cc_final: 0.6933 (tm-30) REVERT: A 242 MET cc_start: 0.8284 (mmt) cc_final: 0.7912 (mmt) REVERT: A 256 GLU cc_start: 0.7942 (mp0) cc_final: 0.7591 (mp0) REVERT: A 396 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6211 (mt-10) REVERT: A 551 MET cc_start: 0.1286 (mpp) cc_final: 0.1008 (mmm) REVERT: A 752 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: A 834 LEU cc_start: 0.0822 (OUTLIER) cc_final: 0.0328 (tm) outliers start: 116 outliers final: 51 residues processed: 475 average time/residue: 0.7975 time to fit residues: 435.8569 Evaluate side-chains 438 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 376 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 195 GLN B 770 HIS B 823 GLN A 297 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.210831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153556 restraints weight = 28102.101| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.92 r_work: 0.3558 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28296 Z= 0.130 Angle : 0.589 9.739 38259 Z= 0.291 Chirality : 0.045 0.205 4328 Planarity : 0.004 0.056 4991 Dihedral : 10.758 167.088 4084 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.67 % Allowed : 22.22 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.14), residues: 3448 helix: -1.00 (0.13), residues: 1570 sheet: -2.62 (0.29), residues: 276 loop : -1.26 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 852 TYR 0.031 0.001 TYR F 783 PHE 0.012 0.001 PHE E 276 TRP 0.009 0.001 TRP D 543 HIS 0.010 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00310 (28296) covalent geometry : angle 0.58905 (38259) hydrogen bonds : bond 0.03493 ( 719) hydrogen bonds : angle 5.29216 ( 2157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 402 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.5466 (mtm-85) REVERT: C 307 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 317 ASP cc_start: 0.8113 (p0) cc_final: 0.7640 (m-30) REVERT: C 555 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6813 (tm-30) REVERT: C 696 ASP cc_start: 0.7805 (m-30) cc_final: 0.7584 (t70) REVERT: C 710 ARG cc_start: 0.8352 (mtt90) cc_final: 0.8001 (mtt-85) REVERT: C 739 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.5280 (pp20) REVERT: C 784 LYS cc_start: 0.7582 (mptt) cc_final: 0.7266 (mppt) REVERT: C 798 GLU cc_start: 0.8462 (mp0) cc_final: 0.8190 (tp30) REVERT: C 801 LYS cc_start: 0.6916 (ttpp) cc_final: 0.6183 (tptp) REVERT: F 251 TYR cc_start: 0.4833 (m-80) cc_final: 0.4376 (m-80) REVERT: F 252 ARG cc_start: 0.5896 (tpt170) cc_final: 0.3104 (pmt-80) REVERT: F 264 ASN cc_start: 0.5952 (OUTLIER) cc_final: 0.5553 (t0) REVERT: F 275 LEU cc_start: 0.6221 (tp) cc_final: 0.5642 (tm) REVERT: F 276 PHE cc_start: 0.6904 (m-10) cc_final: 0.5988 (m-80) REVERT: F 300 LYS cc_start: 0.3645 (tptp) cc_final: 0.2805 (mmtt) REVERT: F 320 ARG cc_start: 0.6237 (mtm110) cc_final: 0.5808 (mtt-85) REVERT: F 322 TYR cc_start: 0.5615 (m-10) cc_final: 0.5359 (m-10) REVERT: F 331 ARG cc_start: 0.6872 (tpp-160) cc_final: 0.4867 (ttm-80) REVERT: F 356 ARG cc_start: 0.2820 (tpt170) cc_final: 0.2221 (tmt-80) REVERT: F 574 ASN cc_start: 0.5541 (p0) cc_final: 0.5329 (p0) REVERT: F 585 ARG cc_start: 0.5034 (mtp85) cc_final: 0.4512 (tpm170) REVERT: F 629 MET cc_start: 0.5127 (ttt) cc_final: 0.4356 (mmt) REVERT: F 638 MET cc_start: -0.1651 (mmp) cc_final: -0.2185 (mpt) REVERT: F 716 MET cc_start: 0.5327 (mtt) cc_final: 0.3188 (tpp) REVERT: F 800 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5716 (pp) REVERT: E 164 TYR cc_start: 0.7686 (m-10) cc_final: 0.7102 (m-10) REVERT: E 167 ASP cc_start: 0.8206 (t70) cc_final: 0.7606 (t0) REVERT: E 217 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6103 (mp0) REVERT: E 252 ARG cc_start: 0.6305 (mpp-170) cc_final: 0.4528 (tpm170) REVERT: E 317 ASP cc_start: 0.7729 (m-30) cc_final: 0.7351 (m-30) REVERT: E 532 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7035 (p) REVERT: E 561 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6195 (ptt90) REVERT: E 629 MET cc_start: 0.8846 (ptt) cc_final: 0.8324 (ptp) REVERT: E 638 MET cc_start: 0.8353 (mtm) cc_final: 0.7701 (mtm) REVERT: E 643 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (p) REVERT: E 656 TYR cc_start: 0.7673 (p90) cc_final: 0.6989 (p90) REVERT: E 696 ASP cc_start: 0.5816 (OUTLIER) cc_final: 0.5185 (t0) REVERT: E 698 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7452 (mmm160) REVERT: E 705 ARG cc_start: 0.6671 (mtt180) cc_final: 0.6052 (mtm180) REVERT: E 737 MET cc_start: 0.7077 (tpp) cc_final: 0.6845 (tpp) REVERT: E 752 GLU cc_start: 0.7344 (pm20) cc_final: 0.6895 (pm20) REVERT: E 768 GLU cc_start: 0.7716 (tt0) cc_final: 0.7226 (tp30) REVERT: E 822 GLN cc_start: 0.7463 (mt0) cc_final: 0.6801 (tt0) REVERT: D 163 LYS cc_start: 0.8963 (mtmt) cc_final: 0.7864 (mptt) REVERT: D 174 GLN cc_start: 0.9117 (mt0) cc_final: 0.8848 (mt0) REVERT: D 184 ASP cc_start: 0.8097 (t0) cc_final: 0.7877 (m-30) REVERT: D 230 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8379 (tp30) REVERT: D 260 LYS cc_start: 0.7516 (mttt) cc_final: 0.7095 (mttm) REVERT: D 535 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: D 552 MET cc_start: 0.4764 (mmt) cc_final: 0.4157 (mmm) REVERT: D 563 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: D 734 TYR cc_start: 0.8650 (t80) cc_final: 0.8414 (t80) REVERT: D 801 LYS cc_start: 0.7607 (ptmt) cc_final: 0.7323 (ttmt) REVERT: B 268 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7664 (mttt) REVERT: B 283 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8215 (ttm) REVERT: B 308 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7246 (tp) REVERT: B 403 MET cc_start: 0.8149 (mtp) cc_final: 0.7926 (mtm) REVERT: B 555 GLU cc_start: 0.7422 (tt0) cc_final: 0.7034 (tm-30) REVERT: B 558 LYS cc_start: 0.7802 (tttm) cc_final: 0.7214 (ttpp) REVERT: B 560 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 561 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6801 (ptp90) REVERT: B 657 GLU cc_start: 0.8028 (mp0) cc_final: 0.7755 (mp0) REVERT: B 776 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7558 (mt0) REVERT: B 832 GLN cc_start: 0.7550 (tt0) cc_final: 0.6932 (tm-30) REVERT: A 242 MET cc_start: 0.8187 (mmt) cc_final: 0.7906 (mmt) REVERT: A 256 GLU cc_start: 0.7839 (mp0) cc_final: 0.7447 (mp0) REVERT: A 396 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6212 (mt-10) REVERT: A 551 MET cc_start: 0.1212 (mpp) cc_final: 0.0978 (mmm) REVERT: A 675 LEU cc_start: 0.7125 (mt) cc_final: 0.6830 (mm) REVERT: A 737 MET cc_start: 0.5818 (mpp) cc_final: 0.5568 (mpp) REVERT: A 752 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: A 834 LEU cc_start: 0.0776 (OUTLIER) cc_final: 0.0299 (tm) outliers start: 107 outliers final: 47 residues processed: 475 average time/residue: 0.8009 time to fit residues: 437.9469 Evaluate side-chains 437 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 376 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 2 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 220 optimal weight: 0.0870 chunk 176 optimal weight: 0.8980 chunk 341 optimal weight: 0.2980 chunk 100 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 195 GLN B 770 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150209 restraints weight = 27967.131| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.85 r_work: 0.3514 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28296 Z= 0.190 Angle : 0.625 9.441 38259 Z= 0.308 Chirality : 0.047 0.189 4328 Planarity : 0.004 0.062 4991 Dihedral : 10.789 165.430 4083 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.84 % Allowed : 22.67 % Favored : 73.49 % 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: -1.94 (0.14), residues: 3448 helix: -0.95 (0.13), residues: 1569 sheet: -2.69 (0.28), residues: 291 loop : -1.21 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 852 TYR 0.011 0.001 TYR C 357 PHE 0.017 0.001 PHE E 276 TRP 0.009 0.001 TRP D 543 HIS 0.011 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00465 (28296) covalent geometry : angle 0.62463 (38259) hydrogen bonds : bond 0.03676 ( 719) hydrogen bonds : angle 5.29824 ( 2157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 388 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8673 (mt0) cc_final: 0.8407 (mt0) REVERT: C 265 ASP cc_start: 0.8233 (m-30) cc_final: 0.7606 (m-30) REVERT: C 305 ARG cc_start: 0.6620 (mtt-85) cc_final: 0.5461 (mtm-85) REVERT: C 307 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 317 ASP cc_start: 0.8145 (p0) cc_final: 0.7707 (m-30) REVERT: C 551 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5686 (mmp) REVERT: C 555 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6831 (tm-30) REVERT: C 561 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6922 (ptt90) REVERT: C 696 ASP cc_start: 0.7878 (m-30) cc_final: 0.7627 (t70) REVERT: C 710 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8016 (mtt-85) REVERT: C 739 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.5145 (pp20) REVERT: C 784 LYS cc_start: 0.7605 (mptt) cc_final: 0.7275 (mppt) REVERT: C 798 GLU cc_start: 0.8499 (mp0) cc_final: 0.8117 (tp30) REVERT: F 251 TYR cc_start: 0.4830 (m-80) cc_final: 0.4380 (m-80) REVERT: F 252 ARG cc_start: 0.5889 (tpt170) cc_final: 0.3119 (pmt-80) REVERT: F 264 ASN cc_start: 0.6021 (OUTLIER) cc_final: 0.5648 (t0) REVERT: F 275 LEU cc_start: 0.6194 (tp) cc_final: 0.5768 (tm) REVERT: F 276 PHE cc_start: 0.6899 (m-10) cc_final: 0.6634 (m-10) REVERT: F 300 LYS cc_start: 0.3604 (OUTLIER) cc_final: 0.2736 (mmtt) REVERT: F 320 ARG cc_start: 0.6256 (mtm110) cc_final: 0.5800 (mtt-85) REVERT: F 322 TYR cc_start: 0.5652 (m-10) cc_final: 0.5384 (m-10) REVERT: F 331 ARG cc_start: 0.6914 (tpp-160) cc_final: 0.4796 (ttm-80) REVERT: F 356 ARG cc_start: 0.2951 (tpt170) cc_final: 0.2308 (tmt-80) REVERT: F 629 MET cc_start: 0.5158 (ttt) cc_final: 0.4392 (mmt) REVERT: F 638 MET cc_start: -0.1876 (mmp) cc_final: -0.2260 (mpt) REVERT: F 716 MET cc_start: 0.5371 (mtt) cc_final: 0.3242 (tpp) REVERT: F 763 PHE cc_start: 0.2319 (OUTLIER) cc_final: 0.1426 (t80) REVERT: F 800 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5683 (pp) REVERT: E 164 TYR cc_start: 0.7691 (m-10) cc_final: 0.7091 (m-10) REVERT: E 167 ASP cc_start: 0.8196 (t70) cc_final: 0.7577 (t0) REVERT: E 252 ARG cc_start: 0.6334 (mpp-170) cc_final: 0.4527 (tpm170) REVERT: E 317 ASP cc_start: 0.7632 (m-30) cc_final: 0.7263 (m-30) REVERT: E 405 ILE cc_start: 0.8244 (mt) cc_final: 0.8034 (mp) REVERT: E 532 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7103 (p) REVERT: E 629 MET cc_start: 0.8919 (ptt) cc_final: 0.8342 (ptp) REVERT: E 638 MET cc_start: 0.8368 (mtm) cc_final: 0.7785 (mtm) REVERT: E 643 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 656 TYR cc_start: 0.7673 (p90) cc_final: 0.6991 (p90) REVERT: E 696 ASP cc_start: 0.5764 (OUTLIER) cc_final: 0.5155 (t0) REVERT: E 698 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7421 (mmm160) REVERT: E 705 ARG cc_start: 0.6573 (mtt180) cc_final: 0.6099 (mtm180) REVERT: E 737 MET cc_start: 0.7102 (tpp) cc_final: 0.6878 (tpp) REVERT: E 752 GLU cc_start: 0.7295 (pm20) cc_final: 0.6810 (pm20) REVERT: E 768 GLU cc_start: 0.7738 (tt0) cc_final: 0.7248 (tp30) REVERT: E 822 GLN cc_start: 0.7480 (mt0) cc_final: 0.6834 (tt0) REVERT: D 163 LYS cc_start: 0.9024 (mtmt) cc_final: 0.7932 (mptt) REVERT: D 184 ASP cc_start: 0.8115 (t0) cc_final: 0.7890 (m-30) REVERT: D 230 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8402 (tp30) REVERT: D 260 LYS cc_start: 0.7528 (mttt) cc_final: 0.7118 (mttm) REVERT: D 535 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: D 552 MET cc_start: 0.4822 (mmt) cc_final: 0.4299 (mmm) REVERT: D 563 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: D 769 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: D 801 LYS cc_start: 0.7662 (ptmt) cc_final: 0.7422 (ttmt) REVERT: D 831 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7066 (tm130) REVERT: B 188 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7077 (ttp-110) REVERT: B 268 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7742 (mttt) REVERT: B 283 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: B 403 MET cc_start: 0.8171 (mtp) cc_final: 0.7931 (mtm) REVERT: B 552 MET cc_start: 0.5104 (OUTLIER) cc_final: 0.4785 (mpp) REVERT: B 555 GLU cc_start: 0.7509 (tt0) cc_final: 0.6974 (tt0) REVERT: B 558 LYS cc_start: 0.7753 (tttm) cc_final: 0.7245 (ttpt) REVERT: B 561 ARG cc_start: 0.7085 (mtm110) cc_final: 0.6713 (ptp90) REVERT: B 657 GLU cc_start: 0.7904 (mp0) cc_final: 0.7656 (mp0) REVERT: B 776 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7610 (mt0) REVERT: B 832 GLN cc_start: 0.7464 (tt0) cc_final: 0.6864 (tm-30) REVERT: A 242 MET cc_start: 0.8189 (mmt) cc_final: 0.7777 (mmt) REVERT: A 256 GLU cc_start: 0.7892 (mp0) cc_final: 0.7492 (mp0) REVERT: A 355 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: A 396 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6295 (mt-10) REVERT: A 551 MET cc_start: 0.1122 (mpp) cc_final: 0.0922 (mmm) REVERT: A 664 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7290 (mm-30) REVERT: A 668 ARG cc_start: 0.7564 (mmt-90) cc_final: 0.6782 (mtm110) REVERT: A 675 LEU cc_start: 0.7243 (mt) cc_final: 0.6835 (mm) REVERT: A 752 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: A 834 LEU cc_start: 0.0809 (OUTLIER) cc_final: 0.0334 (tm) outliers start: 112 outliers final: 57 residues processed: 465 average time/residue: 0.7565 time to fit residues: 404.8401 Evaluate side-chains 444 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 369 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 769 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 138 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 126 optimal weight: 0.3980 chunk 339 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 703 GLN D 794 HIS D 822 GLN B 195 GLN B 361 HIS B 770 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149918 restraints weight = 28184.935| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.87 r_work: 0.3508 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28296 Z= 0.189 Angle : 0.631 8.904 38259 Z= 0.310 Chirality : 0.047 0.179 4328 Planarity : 0.005 0.058 4991 Dihedral : 10.725 160.972 4083 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.64 % Allowed : 23.39 % Favored : 72.98 % 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: -1.91 (0.14), residues: 3448 helix: -0.92 (0.13), residues: 1582 sheet: -2.64 (0.28), residues: 298 loop : -1.20 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 561 TYR 0.012 0.001 TYR C 357 PHE 0.018 0.001 PHE E 276 TRP 0.008 0.001 TRP D 543 HIS 0.011 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00464 (28296) covalent geometry : angle 0.63061 (38259) hydrogen bonds : bond 0.03700 ( 719) hydrogen bonds : angle 5.28784 ( 2157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 384 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8609 (mt0) cc_final: 0.8333 (mt0) REVERT: C 265 ASP cc_start: 0.8226 (m-30) cc_final: 0.7602 (m-30) REVERT: C 305 ARG cc_start: 0.6583 (mtt-85) cc_final: 0.5435 (mtm-85) REVERT: C 307 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8677 (mt-10) REVERT: C 317 ASP cc_start: 0.8144 (p0) cc_final: 0.7751 (m-30) REVERT: C 555 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6841 (tm-30) REVERT: C 561 ARG cc_start: 0.7255 (mtm110) cc_final: 0.6942 (ptt90) REVERT: C 696 ASP cc_start: 0.7765 (m-30) cc_final: 0.7552 (t70) REVERT: C 710 ARG cc_start: 0.8343 (mtt90) cc_final: 0.8008 (mtt-85) REVERT: C 739 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.5198 (pp20) REVERT: C 784 LYS cc_start: 0.7603 (mptt) cc_final: 0.7275 (mppt) REVERT: C 798 GLU cc_start: 0.8468 (mp0) cc_final: 0.8193 (tp30) REVERT: C 801 LYS cc_start: 0.6876 (ttpp) cc_final: 0.6320 (tptp) REVERT: C 831 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: F 251 TYR cc_start: 0.4834 (m-80) cc_final: 0.4395 (m-80) REVERT: F 252 ARG cc_start: 0.5882 (tpt170) cc_final: 0.3111 (pmt-80) REVERT: F 264 ASN cc_start: 0.6081 (OUTLIER) cc_final: 0.5726 (t0) REVERT: F 275 LEU cc_start: 0.6117 (tp) cc_final: 0.5680 (tm) REVERT: F 276 PHE cc_start: 0.6893 (m-10) cc_final: 0.6637 (m-10) REVERT: F 300 LYS cc_start: 0.3414 (OUTLIER) cc_final: 0.2594 (mmtt) REVERT: F 320 ARG cc_start: 0.6176 (mtm110) cc_final: 0.5628 (mmm-85) REVERT: F 331 ARG cc_start: 0.6908 (tpp-160) cc_final: 0.4816 (ttm-80) REVERT: F 356 ARG cc_start: 0.2988 (tpt170) cc_final: 0.2315 (tmt-80) REVERT: F 585 ARG cc_start: 0.5033 (mtp85) cc_final: 0.4191 (tpm-80) REVERT: F 629 MET cc_start: 0.5393 (ttt) cc_final: 0.4681 (mmt) REVERT: F 638 MET cc_start: -0.1885 (mmp) cc_final: -0.2455 (mpt) REVERT: F 716 MET cc_start: 0.5272 (mtt) cc_final: 0.3270 (tpp) REVERT: F 763 PHE cc_start: 0.2436 (OUTLIER) cc_final: 0.1493 (t80) REVERT: F 800 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5661 (pp) REVERT: E 164 TYR cc_start: 0.7748 (m-10) cc_final: 0.7113 (m-10) REVERT: E 167 ASP cc_start: 0.8172 (t70) cc_final: 0.7499 (t0) REVERT: E 252 ARG cc_start: 0.6337 (mpp-170) cc_final: 0.4516 (tpm170) REVERT: E 317 ASP cc_start: 0.7552 (m-30) cc_final: 0.7207 (m-30) REVERT: E 405 ILE cc_start: 0.8251 (mt) cc_final: 0.8031 (mp) REVERT: E 532 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7112 (p) REVERT: E 561 ARG cc_start: 0.6856 (mtm110) cc_final: 0.6080 (ptt90) REVERT: E 629 MET cc_start: 0.8929 (ptt) cc_final: 0.8342 (ptp) REVERT: E 638 MET cc_start: 0.8358 (mtm) cc_final: 0.7720 (mtm) REVERT: E 640 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8118 (ttmt) REVERT: E 643 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7925 (p) REVERT: E 656 TYR cc_start: 0.7665 (p90) cc_final: 0.6972 (p90) REVERT: E 696 ASP cc_start: 0.5727 (OUTLIER) cc_final: 0.5083 (t0) REVERT: E 698 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: E 705 ARG cc_start: 0.6613 (mtt180) cc_final: 0.6163 (mtm180) REVERT: E 737 MET cc_start: 0.7100 (tpp) cc_final: 0.6604 (tpt) REVERT: E 752 GLU cc_start: 0.7280 (pm20) cc_final: 0.6812 (pm20) REVERT: E 768 GLU cc_start: 0.7642 (tt0) cc_final: 0.7195 (tp30) REVERT: E 822 GLN cc_start: 0.7547 (mt0) cc_final: 0.6857 (tt0) REVERT: D 163 LYS cc_start: 0.9002 (mtmt) cc_final: 0.7905 (mptt) REVERT: D 184 ASP cc_start: 0.8124 (t0) cc_final: 0.7919 (m-30) REVERT: D 230 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8384 (tp30) REVERT: D 260 LYS cc_start: 0.7498 (mttt) cc_final: 0.7097 (mttm) REVERT: D 535 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: D 552 MET cc_start: 0.4814 (mmt) cc_final: 0.4258 (mmm) REVERT: D 695 ASP cc_start: 0.8168 (t0) cc_final: 0.7773 (t0) REVERT: D 780 LYS cc_start: 0.7743 (mttt) cc_final: 0.7530 (mppt) REVERT: D 801 LYS cc_start: 0.7695 (ptmt) cc_final: 0.7469 (ttmt) REVERT: D 831 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7002 (tm130) REVERT: D 857 GLN cc_start: 0.5898 (OUTLIER) cc_final: 0.5390 (mp10) REVERT: B 188 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7069 (ttp-110) REVERT: B 232 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8632 (mp) REVERT: B 268 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7742 (mttt) REVERT: B 283 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8218 (ttm) REVERT: B 403 MET cc_start: 0.8158 (mtp) cc_final: 0.7898 (mtm) REVERT: B 552 MET cc_start: 0.5155 (OUTLIER) cc_final: 0.4807 (mpp) REVERT: B 555 GLU cc_start: 0.7479 (tt0) cc_final: 0.6952 (tt0) REVERT: B 558 LYS cc_start: 0.7753 (tttm) cc_final: 0.7241 (ttpt) REVERT: B 561 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6707 (ptp90) REVERT: B 657 GLU cc_start: 0.7895 (mp0) cc_final: 0.7647 (mp0) REVERT: B 668 ARG cc_start: 0.8707 (mpt90) cc_final: 0.8464 (mmp80) REVERT: B 768 GLU cc_start: 0.8034 (mp0) cc_final: 0.7800 (mp0) REVERT: B 776 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7574 (mt0) REVERT: B 832 GLN cc_start: 0.7511 (tt0) cc_final: 0.6870 (tm-30) REVERT: A 242 MET cc_start: 0.8157 (mmt) cc_final: 0.7775 (mmt) REVERT: A 256 GLU cc_start: 0.7888 (mp0) cc_final: 0.7478 (mp0) REVERT: A 355 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: A 396 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6299 (mt-10) REVERT: A 664 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7199 (mm-30) REVERT: A 668 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.6743 (mtm110) REVERT: A 675 LEU cc_start: 0.7186 (mt) cc_final: 0.6776 (mm) REVERT: A 737 MET cc_start: 0.5733 (mpp) cc_final: 0.5526 (mpp) REVERT: A 752 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 834 LEU cc_start: 0.0875 (OUTLIER) cc_final: 0.0438 (tm) outliers start: 106 outliers final: 59 residues processed: 462 average time/residue: 0.7768 time to fit residues: 412.9102 Evaluate side-chains 448 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 371 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 739 GLU Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 718 SER Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 83 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 chunk 182 optimal weight: 0.0670 chunk 205 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 703 GLN D 770 HIS D 794 HIS D 822 GLN B 719 ASN B 770 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.212437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147186 restraints weight = 28043.018| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.95 r_work: 0.3568 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28296 Z= 0.118 Angle : 0.592 9.848 38259 Z= 0.290 Chirality : 0.044 0.272 4328 Planarity : 0.004 0.057 4991 Dihedral : 10.408 162.131 4083 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.98 % Allowed : 24.62 % Favored : 72.39 % 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: -1.62 (0.14), residues: 3448 helix: -0.64 (0.13), residues: 1581 sheet: -2.67 (0.28), residues: 288 loop : -1.07 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 852 TYR 0.017 0.001 TYR B 783 PHE 0.010 0.001 PHE E 276 TRP 0.007 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00279 (28296) covalent geometry : angle 0.59178 (38259) hydrogen bonds : bond 0.03370 ( 719) hydrogen bonds : angle 5.10531 ( 2157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 387 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 188 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7950 (ttm110) REVERT: C 265 ASP cc_start: 0.8243 (m-30) cc_final: 0.7755 (m-30) REVERT: C 305 ARG cc_start: 0.6738 (mtt-85) cc_final: 0.5502 (mtm-85) REVERT: C 307 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8662 (mt-10) REVERT: C 317 ASP cc_start: 0.8089 (p0) cc_final: 0.7700 (m-30) REVERT: C 325 LYS cc_start: 0.7829 (mttp) cc_final: 0.7406 (mmpt) REVERT: C 555 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 710 ARG cc_start: 0.8320 (mtt90) cc_final: 0.7969 (mtt-85) REVERT: C 784 LYS cc_start: 0.7597 (mptt) cc_final: 0.7247 (mppt) REVERT: C 798 GLU cc_start: 0.8465 (mp0) cc_final: 0.8177 (tp30) REVERT: C 801 LYS cc_start: 0.6723 (ttpp) cc_final: 0.6178 (tptp) REVERT: F 251 TYR cc_start: 0.4717 (m-80) cc_final: 0.4221 (m-80) REVERT: F 252 ARG cc_start: 0.5612 (tpt170) cc_final: 0.5355 (tpt170) REVERT: F 275 LEU cc_start: 0.6010 (tp) cc_final: 0.5575 (tm) REVERT: F 276 PHE cc_start: 0.6818 (m-10) cc_final: 0.6547 (m-10) REVERT: F 300 LYS cc_start: 0.3535 (tptp) cc_final: 0.2691 (mmtt) REVERT: F 320 ARG cc_start: 0.6185 (mtm110) cc_final: 0.5824 (mtt-85) REVERT: F 331 ARG cc_start: 0.6886 (tpp-160) cc_final: 0.4822 (ttm-80) REVERT: F 356 ARG cc_start: 0.2955 (tpt170) cc_final: 0.2310 (tmt-80) REVERT: F 538 GLU cc_start: 0.7056 (tp30) cc_final: 0.6309 (tp30) REVERT: F 551 MET cc_start: 0.1083 (OUTLIER) cc_final: 0.0701 (mmp) REVERT: F 585 ARG cc_start: 0.5069 (mtp85) cc_final: 0.4222 (tpm-80) REVERT: F 629 MET cc_start: 0.5474 (ttt) cc_final: 0.4785 (mmt) REVERT: F 638 MET cc_start: -0.1851 (mmp) cc_final: -0.2422 (mpt) REVERT: F 716 MET cc_start: 0.5302 (mtt) cc_final: 0.3297 (tpp) REVERT: F 763 PHE cc_start: 0.2364 (OUTLIER) cc_final: 0.1438 (t80) REVERT: E 164 TYR cc_start: 0.7686 (m-10) cc_final: 0.6841 (m-10) REVERT: E 167 ASP cc_start: 0.8251 (t70) cc_final: 0.7607 (t0) REVERT: E 252 ARG cc_start: 0.6323 (mpp-170) cc_final: 0.4543 (tpm170) REVERT: E 318 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6414 (tm-30) REVERT: E 405 ILE cc_start: 0.8286 (mt) cc_final: 0.8078 (mp) REVERT: E 532 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7209 (p) REVERT: E 561 ARG cc_start: 0.6605 (mtm110) cc_final: 0.5914 (ptt90) REVERT: E 629 MET cc_start: 0.8838 (ptt) cc_final: 0.8342 (ptp) REVERT: E 638 MET cc_start: 0.8333 (mtm) cc_final: 0.7724 (mtm) REVERT: E 643 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (p) REVERT: E 656 TYR cc_start: 0.7637 (p90) cc_final: 0.6950 (p90) REVERT: E 696 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.5002 (t0) REVERT: E 698 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7314 (mmm160) REVERT: E 705 ARG cc_start: 0.6621 (mtt180) cc_final: 0.6101 (mtm180) REVERT: E 737 MET cc_start: 0.7058 (tpp) cc_final: 0.6515 (tpt) REVERT: E 752 GLU cc_start: 0.7346 (pm20) cc_final: 0.6881 (pm20) REVERT: E 768 GLU cc_start: 0.7674 (tt0) cc_final: 0.7263 (tp30) REVERT: E 822 GLN cc_start: 0.7506 (mt0) cc_final: 0.6900 (tt0) REVERT: D 163 LYS cc_start: 0.8971 (mtmt) cc_final: 0.7871 (mptt) REVERT: D 174 GLN cc_start: 0.9107 (mt0) cc_final: 0.8874 (mt0) REVERT: D 260 LYS cc_start: 0.7622 (mttt) cc_final: 0.7288 (mttm) REVERT: D 535 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7063 (pp20) REVERT: D 552 MET cc_start: 0.4775 (mmt) cc_final: 0.4261 (mmm) REVERT: D 629 MET cc_start: 0.9155 (ptm) cc_final: 0.8937 (ptt) REVERT: D 734 TYR cc_start: 0.8652 (t80) cc_final: 0.8387 (t80) REVERT: D 780 LYS cc_start: 0.7785 (mttt) cc_final: 0.7565 (mppt) REVERT: D 801 LYS cc_start: 0.7634 (ptmt) cc_final: 0.7227 (ttmt) REVERT: D 857 GLN cc_start: 0.5814 (OUTLIER) cc_final: 0.5363 (mp10) REVERT: B 188 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7097 (ttp-110) REVERT: B 197 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.8208 (ttt-90) REVERT: B 232 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 268 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7674 (mttt) REVERT: B 283 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7971 (ttm) REVERT: B 317 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: B 558 LYS cc_start: 0.7797 (tttm) cc_final: 0.7255 (ttpp) REVERT: B 657 GLU cc_start: 0.7974 (mp0) cc_final: 0.7716 (mp0) REVERT: B 768 GLU cc_start: 0.7983 (mp0) cc_final: 0.7732 (mp0) REVERT: B 776 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7577 (mt0) REVERT: B 832 GLN cc_start: 0.7437 (tt0) cc_final: 0.6866 (tm-30) REVERT: A 242 MET cc_start: 0.8070 (mmt) cc_final: 0.7863 (mmt) REVERT: A 256 GLU cc_start: 0.7871 (mp0) cc_final: 0.7628 (mp0) REVERT: A 355 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 396 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6383 (mt-10) REVERT: A 551 MET cc_start: 0.0846 (mmm) cc_final: -0.0016 (mpp) REVERT: A 639 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6426 (pm20) REVERT: A 668 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.6947 (mtm110) REVERT: A 675 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6768 (mm) REVERT: A 737 MET cc_start: 0.5655 (mpp) cc_final: 0.5440 (mpp) REVERT: A 752 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: A 834 LEU cc_start: 0.1002 (OUTLIER) cc_final: 0.0545 (tm) outliers start: 87 outliers final: 40 residues processed: 446 average time/residue: 0.8057 time to fit residues: 413.1537 Evaluate side-chains 417 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 362 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 718 SER Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 719 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153492 restraints weight = 28039.086| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.25 r_work: 0.3497 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28296 Z= 0.183 Angle : 0.637 9.960 38259 Z= 0.312 Chirality : 0.047 0.236 4328 Planarity : 0.004 0.057 4991 Dihedral : 10.484 160.891 4083 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.54 % Allowed : 25.24 % Favored : 72.22 % 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 (0.14), residues: 3448 helix: -0.68 (0.13), residues: 1582 sheet: -2.67 (0.28), residues: 299 loop : -1.06 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 852 TYR 0.014 0.001 TYR B 783 PHE 0.018 0.001 PHE E 276 TRP 0.009 0.001 TRP D 543 HIS 0.010 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00450 (28296) covalent geometry : angle 0.63668 (38259) hydrogen bonds : bond 0.03610 ( 719) hydrogen bonds : angle 5.14951 ( 2157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 366 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8721 (mt0) cc_final: 0.8463 (mt0) REVERT: C 265 ASP cc_start: 0.8310 (m-30) cc_final: 0.7725 (m-30) REVERT: C 305 ARG cc_start: 0.6663 (mtt-85) cc_final: 0.5492 (mtm-85) REVERT: C 307 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 317 ASP cc_start: 0.8276 (p0) cc_final: 0.7878 (m-30) REVERT: C 325 LYS cc_start: 0.7761 (mttp) cc_final: 0.7496 (mmtp) REVERT: C 555 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6801 (tm-30) REVERT: C 710 ARG cc_start: 0.8452 (mtt90) cc_final: 0.8074 (mtt-85) REVERT: C 784 LYS cc_start: 0.7620 (mptt) cc_final: 0.7321 (mppt) REVERT: C 798 GLU cc_start: 0.8431 (mp0) cc_final: 0.8122 (tp30) REVERT: C 801 LYS cc_start: 0.6779 (ttpp) cc_final: 0.6219 (tptp) REVERT: F 251 TYR cc_start: 0.4764 (m-80) cc_final: 0.4297 (m-80) REVERT: F 252 ARG cc_start: 0.5630 (tpt170) cc_final: 0.5366 (tpt170) REVERT: F 275 LEU cc_start: 0.6098 (tp) cc_final: 0.5667 (tm) REVERT: F 276 PHE cc_start: 0.6932 (m-10) cc_final: 0.6672 (m-10) REVERT: F 300 LYS cc_start: 0.3507 (tptp) cc_final: 0.3170 (tptm) REVERT: F 320 ARG cc_start: 0.6188 (mtm110) cc_final: 0.5817 (mtt-85) REVERT: F 331 ARG cc_start: 0.6890 (tpp-160) cc_final: 0.4855 (ttm-80) REVERT: F 356 ARG cc_start: 0.2898 (tpt170) cc_final: 0.2275 (tmt-80) REVERT: F 538 GLU cc_start: 0.7000 (tp30) cc_final: 0.6249 (tp30) REVERT: F 551 MET cc_start: 0.1181 (OUTLIER) cc_final: 0.0795 (mmp) REVERT: F 585 ARG cc_start: 0.5066 (mtp85) cc_final: 0.4220 (tpm-80) REVERT: F 629 MET cc_start: 0.5456 (ttt) cc_final: 0.4802 (mmt) REVERT: F 638 MET cc_start: -0.1610 (mmp) cc_final: -0.2245 (mpt) REVERT: F 716 MET cc_start: 0.5397 (mtt) cc_final: 0.3395 (tpp) REVERT: F 763 PHE cc_start: 0.2429 (OUTLIER) cc_final: 0.1438 (t80) REVERT: E 164 TYR cc_start: 0.7733 (m-10) cc_final: 0.6977 (m-10) REVERT: E 167 ASP cc_start: 0.8237 (t70) cc_final: 0.7566 (t0) REVERT: E 252 ARG cc_start: 0.6324 (mpp-170) cc_final: 0.4484 (tpm170) REVERT: E 318 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6653 (tm-30) REVERT: E 405 ILE cc_start: 0.8340 (mt) cc_final: 0.8120 (mp) REVERT: E 532 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7249 (p) REVERT: E 561 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6203 (ptt90) REVERT: E 629 MET cc_start: 0.8915 (ptt) cc_final: 0.8405 (ptp) REVERT: E 638 MET cc_start: 0.8368 (mtm) cc_final: 0.7861 (mtm) REVERT: E 643 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7976 (p) REVERT: E 656 TYR cc_start: 0.7729 (p90) cc_final: 0.7041 (p90) REVERT: E 696 ASP cc_start: 0.5594 (OUTLIER) cc_final: 0.4999 (t0) REVERT: E 698 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7375 (mmm160) REVERT: E 705 ARG cc_start: 0.6675 (mtt180) cc_final: 0.6133 (mtm180) REVERT: E 737 MET cc_start: 0.7142 (tpp) cc_final: 0.6920 (tpp) REVERT: E 752 GLU cc_start: 0.7340 (pm20) cc_final: 0.6889 (pm20) REVERT: E 768 GLU cc_start: 0.7667 (tt0) cc_final: 0.7275 (tp30) REVERT: E 822 GLN cc_start: 0.7556 (mt0) cc_final: 0.6911 (tt0) REVERT: D 163 LYS cc_start: 0.9028 (mtmt) cc_final: 0.7968 (mptt) REVERT: D 260 LYS cc_start: 0.7645 (mttt) cc_final: 0.7250 (mttm) REVERT: D 535 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7371 (pp20) REVERT: D 552 MET cc_start: 0.4829 (mmt) cc_final: 0.4303 (mmm) REVERT: D 780 LYS cc_start: 0.7838 (mttt) cc_final: 0.7621 (mppt) REVERT: D 801 LYS cc_start: 0.7733 (ptmt) cc_final: 0.7513 (ttmt) REVERT: B 188 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7155 (ttp-110) REVERT: B 198 THR cc_start: 0.8671 (m) cc_final: 0.8463 (t) REVERT: B 232 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 268 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7730 (mttt) REVERT: B 283 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8219 (ttm) REVERT: B 317 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: B 403 MET cc_start: 0.8241 (mtp) cc_final: 0.7891 (mtm) REVERT: B 555 GLU cc_start: 0.7502 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 558 LYS cc_start: 0.7806 (tttm) cc_final: 0.7300 (ttpt) REVERT: B 561 ARG cc_start: 0.7293 (mtm110) cc_final: 0.6935 (ptp90) REVERT: B 657 GLU cc_start: 0.8030 (mp0) cc_final: 0.7799 (mp0) REVERT: B 768 GLU cc_start: 0.8020 (mp0) cc_final: 0.7763 (mp0) REVERT: B 776 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7506 (mt0) REVERT: B 832 GLN cc_start: 0.7502 (tt0) cc_final: 0.6915 (tm-30) REVERT: A 242 MET cc_start: 0.8153 (mmt) cc_final: 0.7924 (mmt) REVERT: A 256 GLU cc_start: 0.7980 (mp0) cc_final: 0.7754 (mp0) REVERT: A 355 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: A 396 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6365 (mt-10) REVERT: A 551 MET cc_start: 0.1222 (mmm) cc_final: 0.0279 (mpp) REVERT: A 664 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 668 ARG cc_start: 0.7578 (mmt-90) cc_final: 0.6910 (mtm110) REVERT: A 675 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6782 (mm) REVERT: A 752 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: A 834 LEU cc_start: 0.1014 (OUTLIER) cc_final: 0.0582 (tm) outliers start: 74 outliers final: 46 residues processed: 420 average time/residue: 0.7514 time to fit residues: 363.0496 Evaluate side-chains 420 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 360 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 718 SER Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 739 GLU Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 87 optimal weight: 40.0000 chunk 247 optimal weight: 0.0060 chunk 322 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 182 optimal weight: 0.0020 chunk 289 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 overall best weight: 0.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN E 824 GLN D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 719 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.212354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154328 restraints weight = 27967.438| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.00 r_work: 0.3577 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28296 Z= 0.118 Angle : 0.610 10.363 38259 Z= 0.297 Chirality : 0.044 0.225 4328 Planarity : 0.004 0.069 4991 Dihedral : 10.304 161.528 4083 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.16 % Allowed : 25.82 % Favored : 72.02 % 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: -1.44 (0.14), residues: 3448 helix: -0.46 (0.13), residues: 1578 sheet: -2.65 (0.28), residues: 288 loop : -0.99 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 852 TYR 0.024 0.001 TYR B 783 PHE 0.010 0.001 PHE D 729 TRP 0.008 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00279 (28296) covalent geometry : angle 0.61039 (38259) hydrogen bonds : bond 0.03372 ( 719) hydrogen bonds : angle 5.04835 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12740.80 seconds wall clock time: 217 minutes 0.40 seconds (13020.40 seconds total)