Starting phenix.real_space_refine on Mon Sep 14 03:23:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oax_20004/09_2026/6oax_20004.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.62, per 1000 atoms: 0.24 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: 2.00 Conformation dependent library (CDL) restraints added in 918.3 milliseconds 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: 0.68 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: 4.47 Time building geometry restraints manager: 2.48 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: 16745 33.14 - 66.27: 540 66.27 - 99.41: 39 99.41 - 132.54: 5 132.54 - 165.68: 3 Dihedral angle restraints: 17332 sinusoidal: 7290 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 17329 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.530 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 16.145 165.676 10866 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 are 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/Z covalent geometry : bond 0.01171 / 0.50 (28296) covalent geometry : angle 1.18415 / 0.67 (38259) hydrogen bonds : bond 0.29761 / 19.51 ( 719) hydrogen bonds : angle 12.16750 / 8.28 ( 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 : 1.059 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: 0.7837 time to fit residues: 542.6557 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 : 0.983 ------------------------------------------------------------------------------- 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... C 225 ASN C 297 ASN C 748 ASN C 778 GLN F 404 GLN F 776 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 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 281 HIS A 297 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 794 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.211805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155824 restraints weight = 28428.575| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.99 r_work: 0.3552 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28296 Z= 0.153 Angle : 0.690 8.899 38259 Z= 0.354 Chirality : 0.046 0.198 4328 Planarity : 0.006 0.069 4991 Dihedral : 10.449 168.203 4002 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 3.33 % Allowed : 15.88 % 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 are not related in a simple way. whole: -4.05 (0.12), residues: 3448 helix: -3.14 (0.10), residues: 1578 sheet: -2.93 (0.30), residues: 242 loop : -2.03 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 550 TYR 0.015 0.001 TYR F 661 PHE 0.019 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/Z covalent geometry : bond 0.00340 / 0.15 (28296) covalent geometry : angle 0.69019 / 0.35 (38259) hydrogen bonds : bond 0.04522 / 3.02 ( 719) hydrogen bonds : angle 6.70232 / 4.58 ( 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 562 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 465 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8654 (mt0) cc_final: 0.8283 (mt0) REVERT: C 305 ARG cc_start: 0.6436 (mtt-85) cc_final: 0.5333 (mtm-85) REVERT: C 307 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8636 (mt-10) REVERT: C 561 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6527 (ptt-90) REVERT: C 710 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8153 (mtt-85) REVERT: C 798 GLU cc_start: 0.8280 (mp0) cc_final: 0.8017 (tp30) REVERT: F 251 TYR cc_start: 0.4862 (m-80) cc_final: 0.4385 (m-80) REVERT: F 252 ARG cc_start: 0.5753 (tpt170) cc_final: 0.2982 (pmt-80) REVERT: F 276 PHE cc_start: 0.6600 (m-10) cc_final: 0.6117 (m-80) REVERT: F 300 LYS cc_start: 0.3377 (OUTLIER) cc_final: 0.2796 (mmtt) REVERT: F 320 ARG cc_start: 0.5991 (mtm110) cc_final: 0.5660 (ttm110) REVERT: F 331 ARG cc_start: 0.6573 (tpp-160) cc_final: 0.4580 (ttm-80) REVERT: F 356 ARG cc_start: 0.3119 (tpt170) cc_final: 0.2357 (tmt-80) REVERT: F 585 ARG cc_start: 0.5034 (mtp85) cc_final: 0.4464 (tpm-80) REVERT: F 629 MET cc_start: 0.5181 (ttt) cc_final: 0.4641 (mmt) REVERT: F 638 MET cc_start: -0.1023 (mmp) cc_final: -0.1270 (mpt) REVERT: F 720 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4994 (tp) REVERT: F 752 GLU cc_start: 0.1758 (tm-30) cc_final: 0.1377 (pm20) REVERT: F 768 GLU cc_start: 0.4144 (OUTLIER) cc_final: 0.3398 (mp0) REVERT: E 164 TYR cc_start: 0.7657 (m-10) cc_final: 0.6999 (m-10) REVERT: E 217 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6241 (mp0) REVERT: E 252 ARG cc_start: 0.6301 (mpp-170) cc_final: 0.5141 (tpt170) REVERT: E 317 ASP cc_start: 0.7741 (m-30) cc_final: 0.7323 (m-30) REVERT: E 561 ARG cc_start: 0.6891 (mtm110) cc_final: 0.6119 (ptt90) REVERT: E 616 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7709 (mtpt) REVERT: E 629 MET cc_start: 0.8911 (ptt) cc_final: 0.8483 (ptp) REVERT: E 638 MET cc_start: 0.8372 (mtm) cc_final: 0.7883 (mtm) REVERT: E 656 TYR cc_start: 0.7733 (p90) cc_final: 0.7230 (p90) REVERT: E 696 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5428 (t0) REVERT: E 705 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5638 (mtt180) REVERT: E 737 MET cc_start: 0.7236 (tpp) cc_final: 0.6467 (tpt) REVERT: E 751 PRO cc_start: 0.8043 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: E 752 GLU cc_start: 0.7517 (pm20) cc_final: 0.6938 (pm20) REVERT: E 780 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7072 (mttp) REVERT: E 798 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: E 822 GLN cc_start: 0.7833 (mt0) cc_final: 0.6862 (tt0) REVERT: D 163 LYS cc_start: 0.9045 (mtmt) cc_final: 0.7997 (mptt) REVERT: D 184 ASP cc_start: 0.8163 (t0) cc_final: 0.7919 (m-30) REVERT: D 185 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7739 (tp30) REVERT: D 260 LYS cc_start: 0.7271 (mttt) cc_final: 0.6839 (mttm) REVERT: D 552 MET cc_start: 0.4224 (mmt) cc_final: 0.3785 (mmm) REVERT: D 705 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7974 (mtm180) REVERT: D 750 ARG cc_start: 0.7675 (mtp85) cc_final: 0.6865 (mmp80) REVERT: D 769 GLN cc_start: 0.8379 (pm20) cc_final: 0.7933 (pm20) REVERT: D 831 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7296 (tm130) REVERT: B 162 LYS cc_start: 0.8500 (tttm) cc_final: 0.8062 (mtpp) REVERT: B 268 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7584 (mttp) REVERT: B 555 GLU cc_start: 0.7497 (tt0) cc_final: 0.6963 (tm-30) REVERT: B 558 LYS cc_start: 0.7826 (tttm) cc_final: 0.7328 (ttpt) REVERT: B 561 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6429 (ptp90) REVERT: B 565 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 831 GLN cc_start: 0.7129 (pp30) cc_final: 0.6779 (pp30) REVERT: B 832 GLN cc_start: 0.7457 (tt0) cc_final: 0.6942 (tm-30) REVERT: A 256 GLU cc_start: 0.8093 (mp0) cc_final: 0.7885 (mp0) REVERT: A 293 MET cc_start: 0.3603 (ttp) cc_final: 0.3222 (ttp) REVERT: A 396 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6362 (mt-10) REVERT: A 551 MET cc_start: 0.1016 (mpp) cc_final: 0.0777 (mmm) REVERT: A 564 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: A 616 LYS cc_start: 0.7986 (mttt) cc_final: 0.7595 (mttm) REVERT: A 716 MET cc_start: 0.7782 (mtp) cc_final: 0.7517 (mtp) outliers start: 97 outliers final: 24 residues processed: 526 average time/residue: 0.6995 time to fit residues: 423.4946 Evaluate side-chains 412 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 F residue 768 GLU 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: 0.1980 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 328 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 281 HIS ** 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 360 HIS D 822 GLN B 195 GLN B 755 ASN B 770 HIS B 823 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.213779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.157300 restraints weight = 28258.864| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.03 r_work: 0.3570 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 28296 Z= 0.125 Angle : 0.609 7.522 38259 Z= 0.308 Chirality : 0.045 0.227 4328 Planarity : 0.005 0.059 4991 Dihedral : 9.761 168.512 3985 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.40 % Allowed : 18.76 % Favored : 77.85 % 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 are not related in a simple way. whole: -3.11 (0.13), residues: 3448 helix: -2.15 (0.12), residues: 1576 sheet: -2.91 (0.31), residues: 228 loop : -1.71 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 728 TYR 0.025 0.001 TYR B 783 PHE 0.017 0.001 PHE D 729 TRP 0.014 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (28296) covalent geometry : angle 0.60871 / 0.31 (38259) hydrogen bonds : bond 0.03952 / 2.63 ( 719) hydrogen bonds : angle 5.95448 / 4.07 ( 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 517 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 418 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8732 (mt0) cc_final: 0.8466 (mt0) REVERT: C 305 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5299 (mtm-85) REVERT: C 307 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8629 (mt-10) REVERT: C 710 ARG cc_start: 0.8339 (mtt90) cc_final: 0.8018 (mtt-85) REVERT: C 784 LYS cc_start: 0.7768 (mptt) cc_final: 0.7416 (mppt) REVERT: C 798 GLU cc_start: 0.8424 (mp0) cc_final: 0.8197 (tp30) REVERT: C 817 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8400 (tm) REVERT: F 251 TYR cc_start: 0.4803 (m-80) cc_final: 0.4284 (m-80) REVERT: F 275 LEU cc_start: 0.6598 (tp) cc_final: 0.6108 (tm) REVERT: F 300 LYS cc_start: 0.3597 (OUTLIER) cc_final: 0.2717 (mmtt) REVERT: F 320 ARG cc_start: 0.6084 (mtm110) cc_final: 0.5809 (ttm-80) REVERT: F 331 ARG cc_start: 0.6399 (tpp-160) cc_final: 0.4446 (ttm-80) REVERT: F 569 ARG cc_start: 0.4659 (OUTLIER) cc_final: 0.4409 (ptm-80) REVERT: F 585 ARG cc_start: 0.5017 (mtp85) cc_final: 0.4459 (tpm-80) REVERT: F 629 MET cc_start: 0.5238 (ttt) cc_final: 0.4651 (mmt) REVERT: F 638 MET cc_start: -0.1428 (mmp) cc_final: -0.1749 (mpt) REVERT: F 800 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5887 (pp) REVERT: E 164 TYR cc_start: 0.7642 (m-10) cc_final: 0.6942 (m-10) REVERT: E 217 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6249 (mp0) REVERT: E 252 ARG cc_start: 0.6252 (mpp-170) cc_final: 0.5167 (tpt170) REVERT: E 317 ASP cc_start: 0.7763 (m-30) cc_final: 0.7375 (m-30) REVERT: E 353 LEU cc_start: 0.8052 (tp) cc_final: 0.7670 (mt) REVERT: E 561 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6228 (ptt90) REVERT: E 616 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7731 (mtpt) REVERT: E 629 MET cc_start: 0.8905 (ptt) cc_final: 0.8380 (ptp) REVERT: E 638 MET cc_start: 0.8275 (mtm) cc_final: 0.7725 (mtm) REVERT: E 656 TYR cc_start: 0.7744 (p90) cc_final: 0.7210 (p90) REVERT: E 696 ASP cc_start: 0.6010 (OUTLIER) cc_final: 0.5423 (t0) REVERT: E 705 ARG cc_start: 0.6546 (mtt180) cc_final: 0.5735 (mtt180) REVERT: E 737 MET cc_start: 0.7100 (tpp) cc_final: 0.6463 (tpt) REVERT: E 752 GLU cc_start: 0.7469 (pm20) cc_final: 0.6986 (pm20) REVERT: E 822 GLN cc_start: 0.7644 (mt0) cc_final: 0.6836 (tt0) REVERT: D 162 LYS cc_start: 0.8488 (mttt) cc_final: 0.8183 (ttmm) REVERT: D 163 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8011 (mptt) REVERT: D 184 ASP cc_start: 0.8128 (t0) cc_final: 0.7866 (m-30) REVERT: D 260 LYS cc_start: 0.7444 (mttt) cc_final: 0.7054 (mttm) REVERT: D 324 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8486 (mt-10) REVERT: D 535 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7196 (pp20) REVERT: D 552 MET cc_start: 0.4557 (mmt) cc_final: 0.4025 (mmm) REVERT: D 563 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: D 750 ARG cc_start: 0.7680 (mtp85) cc_final: 0.6966 (mmp80) REVERT: D 769 GLN cc_start: 0.8338 (pm20) cc_final: 0.7890 (pm20) REVERT: D 831 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7186 (tm130) REVERT: B 162 LYS cc_start: 0.8475 (tttm) cc_final: 0.8036 (mtpp) REVERT: B 268 LYS cc_start: 0.8229 (mmpt) cc_final: 0.7605 (mttp) REVERT: B 283 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8086 (ttm) REVERT: B 551 MET cc_start: 0.7753 (ttp) cc_final: 0.7291 (ttp) REVERT: B 555 GLU cc_start: 0.7448 (tt0) cc_final: 0.6952 (tm-30) REVERT: B 558 LYS cc_start: 0.7858 (tttm) cc_final: 0.7194 (tttt) REVERT: B 561 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6643 (ptp90) REVERT: B 831 GLN cc_start: 0.7193 (pp30) cc_final: 0.6885 (pp30) REVERT: B 832 GLN cc_start: 0.7482 (tt0) cc_final: 0.7069 (tm-30) REVERT: A 256 GLU cc_start: 0.8071 (mp0) cc_final: 0.7788 (mp0) REVERT: A 396 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6395 (mt-10) REVERT: A 551 MET cc_start: 0.1112 (mpp) cc_final: 0.0879 (mmm) REVERT: A 681 LYS cc_start: 0.7027 (mttt) cc_final: 0.6717 (mtpt) REVERT: A 752 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6646 (mt-10) outliers start: 99 outliers final: 36 residues processed: 485 average time/residue: 0.6899 time to fit residues: 386.0569 Evaluate side-chains 417 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 372 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 741 VAL Chi-restraints excluded: chain C residue 817 LEU 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 246 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 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 843 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 359 LEU 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 283 MET 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 780 LYS Chi-restraints excluded: chain A residue 232 LEU 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 532 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 752 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 302 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 329 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 248 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 323 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 824 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 GLN 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 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 = 0.4361 r_free = 0.4361 target = 0.211750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157074 restraints weight = 28042.627| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.14 r_work: 0.3553 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2694 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= 0.131 Angle : 0.594 9.065 38259 Z= 0.297 Chirality : 0.045 0.233 4328 Planarity : 0.004 0.058 4991 Dihedral : 9.506 169.096 3984 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.33 % Allowed : 20.34 % Favored : 76.34 % 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 are not related in a simple way. whole: -2.55 (0.14), residues: 3448 helix: -1.57 (0.12), residues: 1571 sheet: -2.78 (0.29), residues: 266 loop : -1.47 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 631 TYR 0.025 0.001 TYR D 734 PHE 0.019 0.001 PHE F 276 TRP 0.013 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (28296) covalent geometry : angle 0.59371 / 0.30 (38259) hydrogen bonds : bond 0.03650 / 2.44 ( 719) hydrogen bonds : angle 5.58032 / 3.81 ( 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 505 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 408 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8682 (mt0) cc_final: 0.8403 (mt0) REVERT: C 305 ARG cc_start: 0.6576 (mtt-85) cc_final: 0.5382 (mtm-85) REVERT: C 307 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 555 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 710 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7957 (mtt-85) REVERT: C 784 LYS cc_start: 0.7634 (mptt) cc_final: 0.7290 (mppt) REVERT: C 798 GLU cc_start: 0.8455 (mp0) cc_final: 0.8152 (tp30) REVERT: C 817 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8381 (tm) REVERT: F 251 TYR cc_start: 0.4858 (m-80) cc_final: 0.4321 (m-80) REVERT: F 275 LEU cc_start: 0.6322 (tp) cc_final: 0.5784 (tm) REVERT: F 276 PHE cc_start: 0.6991 (m-10) cc_final: 0.5962 (m-80) REVERT: F 300 LYS cc_start: 0.3548 (OUTLIER) cc_final: 0.2696 (mmtt) REVERT: F 320 ARG cc_start: 0.6069 (mtm110) cc_final: 0.5823 (ttm-80) REVERT: F 331 ARG cc_start: 0.6568 (tpp-160) cc_final: 0.4524 (ttm-80) REVERT: F 356 ARG cc_start: 0.2765 (tpt170) cc_final: 0.2195 (tmt-80) REVERT: F 585 ARG cc_start: 0.5097 (mtp85) cc_final: 0.4498 (tpm-80) REVERT: F 629 MET cc_start: 0.5321 (ttt) cc_final: 0.4620 (mmt) REVERT: F 638 MET cc_start: -0.1491 (mmp) cc_final: -0.1855 (mpt) REVERT: F 752 GLU cc_start: 0.1532 (tm-30) cc_final: 0.1163 (pm20) REVERT: F 800 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5816 (pp) REVERT: E 164 TYR cc_start: 0.7647 (m-10) cc_final: 0.6934 (m-10) REVERT: E 217 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6277 (mp0) REVERT: E 252 ARG cc_start: 0.6242 (mpp-170) cc_final: 0.4846 (tpt90) REVERT: E 317 ASP cc_start: 0.7771 (m-30) cc_final: 0.7391 (m-30) REVERT: E 353 LEU cc_start: 0.8006 (tp) cc_final: 0.7643 (mt) REVERT: E 561 ARG cc_start: 0.6867 (mtm110) cc_final: 0.6208 (ptt90) REVERT: E 629 MET cc_start: 0.8871 (ptt) cc_final: 0.8306 (ptp) REVERT: E 638 MET cc_start: 0.8280 (mtm) cc_final: 0.7689 (mtm) REVERT: E 656 TYR cc_start: 0.7648 (p90) cc_final: 0.6972 (p90) REVERT: E 696 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5337 (t0) REVERT: E 705 ARG cc_start: 0.6442 (mtt180) cc_final: 0.5781 (mtt180) REVERT: E 752 GLU cc_start: 0.7353 (pm20) cc_final: 0.6885 (pm20) REVERT: E 822 GLN cc_start: 0.7559 (mt0) cc_final: 0.6884 (tt0) REVERT: D 163 LYS cc_start: 0.9034 (mtmt) cc_final: 0.7891 (mptt) REVERT: D 260 LYS cc_start: 0.7432 (mttt) cc_final: 0.6988 (mttm) REVERT: D 324 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8527 (mt-10) REVERT: D 527 LEU cc_start: 0.4382 (OUTLIER) cc_final: 0.4135 (pp) REVERT: D 535 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: D 552 MET cc_start: 0.4564 (mmt) cc_final: 0.4035 (mmm) REVERT: D 563 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: D 823 GLN cc_start: 0.7928 (mt0) cc_final: 0.7535 (mp10) REVERT: D 831 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7063 (tm130) REVERT: B 162 LYS cc_start: 0.8390 (tttm) cc_final: 0.7952 (mtpp) REVERT: B 188 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7055 (ttp-110) REVERT: B 268 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7623 (mttt) REVERT: B 283 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8063 (ttm) REVERT: B 555 GLU cc_start: 0.7491 (tt0) cc_final: 0.7051 (tm-30) REVERT: B 558 LYS cc_start: 0.7737 (tttm) cc_final: 0.7121 (tttt) REVERT: B 560 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 657 GLU cc_start: 0.8080 (mp0) cc_final: 0.7783 (mp0) REVERT: B 831 GLN cc_start: 0.7137 (pp30) cc_final: 0.6902 (pp30) REVERT: B 832 GLN cc_start: 0.7601 (tt0) cc_final: 0.7028 (tm-30) REVERT: A 256 GLU cc_start: 0.7902 (mp0) cc_final: 0.7558 (mp0) REVERT: A 396 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6424 (mt-10) REVERT: A 551 MET cc_start: 0.1211 (mpp) cc_final: 0.0988 (mmm) REVERT: A 681 LYS cc_start: 0.7144 (mttt) cc_final: 0.6860 (mtpt) REVERT: A 716 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7199 (mtm) REVERT: A 752 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6622 (mt-10) outliers start: 97 outliers final: 32 residues processed: 475 average time/residue: 0.6784 time to fit residues: 374.0356 Evaluate side-chains 415 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 817 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 632 ILE 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 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP 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 359 LEU Chi-restraints excluded: chain D residue 527 LEU 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 283 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 607 THR 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 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 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU 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: 10.0000 chunk 241 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 334 GLN D 703 GLN D 776 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.210492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154892 restraints weight = 28196.821| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.20 r_work: 0.3520 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28296 Z= 0.156 Angle : 0.600 7.966 38259 Z= 0.299 Chirality : 0.046 0.186 4328 Planarity : 0.004 0.053 4991 Dihedral : 9.390 170.034 3984 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.98 % Allowed : 21.16 % Favored : 74.86 % 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 are not related in a simple way. whole: -2.26 (0.14), residues: 3448 helix: -1.30 (0.13), residues: 1578 sheet: -2.68 (0.29), residues: 284 loop : -1.32 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 852 TYR 0.028 0.001 TYR F 783 PHE 0.015 0.001 PHE E 276 TRP 0.012 0.001 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (28296) covalent geometry : angle 0.59983 / 0.30 (38259) hydrogen bonds : bond 0.03646 / 2.43 ( 719) hydrogen bonds : angle 5.42368 / 3.71 ( 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 516 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 400 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8686 (mt0) cc_final: 0.8408 (mt0) REVERT: C 305 ARG cc_start: 0.6603 (mtt-85) cc_final: 0.5363 (mtm-85) REVERT: C 307 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8640 (mt-10) REVERT: C 555 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6924 (tm-30) REVERT: C 710 ARG cc_start: 0.8374 (mtt90) cc_final: 0.8001 (mtt-85) REVERT: C 784 LYS cc_start: 0.7604 (mptt) cc_final: 0.7257 (mppt) REVERT: C 798 GLU cc_start: 0.8469 (mp0) cc_final: 0.8128 (tp30) REVERT: C 817 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8327 (tm) REVERT: F 251 TYR cc_start: 0.4771 (m-80) cc_final: 0.4270 (m-80) REVERT: F 275 LEU cc_start: 0.6242 (tp) cc_final: 0.5663 (tm) REVERT: F 276 PHE cc_start: 0.6927 (m-10) cc_final: 0.5907 (m-80) REVERT: F 300 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.2682 (mmtt) REVERT: F 320 ARG cc_start: 0.6152 (mtm110) cc_final: 0.5738 (mtt-85) REVERT: F 331 ARG cc_start: 0.6721 (tpp-160) cc_final: 0.4809 (ttm-80) REVERT: F 356 ARG cc_start: 0.2844 (tpt170) cc_final: 0.2204 (tmt-80) REVERT: F 585 ARG cc_start: 0.5024 (mtp85) cc_final: 0.4399 (tpm-80) REVERT: F 629 MET cc_start: 0.5260 (ttt) cc_final: 0.4529 (mmt) REVERT: F 638 MET cc_start: -0.1587 (mmp) cc_final: -0.2036 (mpt) REVERT: F 716 MET cc_start: 0.5357 (mtt) cc_final: 0.3177 (tpp) REVERT: E 164 TYR cc_start: 0.7706 (m-10) cc_final: 0.6989 (m-10) REVERT: E 167 ASP cc_start: 0.8270 (t70) cc_final: 0.7708 (t0) REVERT: E 217 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6257 (mp0) REVERT: E 252 ARG cc_start: 0.6264 (mpp-170) cc_final: 0.4794 (tpt90) REVERT: E 317 ASP cc_start: 0.7745 (m-30) cc_final: 0.7386 (m-30) REVERT: E 353 LEU cc_start: 0.8020 (tp) cc_final: 0.7614 (mt) REVERT: E 561 ARG cc_start: 0.6855 (mtm110) cc_final: 0.6202 (ptt90) REVERT: E 629 MET cc_start: 0.8913 (ptt) cc_final: 0.8343 (ptp) REVERT: E 638 MET cc_start: 0.8292 (mtm) cc_final: 0.7682 (mtm) REVERT: E 656 TYR cc_start: 0.7647 (p90) cc_final: 0.6962 (p90) REVERT: E 696 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5236 (t0) REVERT: E 705 ARG cc_start: 0.6363 (mtt180) cc_final: 0.5719 (mtt180) REVERT: E 737 MET cc_start: 0.7010 (tpp) cc_final: 0.6351 (tpt) REVERT: E 752 GLU cc_start: 0.7321 (pm20) cc_final: 0.6879 (pm20) REVERT: E 822 GLN cc_start: 0.7506 (mt0) cc_final: 0.6807 (tt0) REVERT: D 163 LYS cc_start: 0.9003 (mtmt) cc_final: 0.7889 (mptt) REVERT: D 230 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8365 (tp30) REVERT: D 260 LYS cc_start: 0.7409 (mttt) cc_final: 0.6986 (mttm) REVERT: D 324 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8530 (mt-10) REVERT: D 552 MET cc_start: 0.4662 (mmt) cc_final: 0.4227 (mmm) REVERT: D 563 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: D 747 HIS cc_start: 0.8571 (m90) cc_final: 0.8365 (m-70) REVERT: D 801 LYS cc_start: 0.7609 (ptmt) cc_final: 0.7292 (ttmt) REVERT: D 823 GLN cc_start: 0.7919 (mt0) cc_final: 0.7545 (mp10) REVERT: D 831 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7047 (tm130) REVERT: B 162 LYS cc_start: 0.8369 (tttm) cc_final: 0.7912 (mtpp) REVERT: B 188 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7037 (ttp-110) REVERT: B 268 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7619 (mttt) REVERT: B 283 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8218 (ttm) REVERT: B 403 MET cc_start: 0.8162 (mtp) cc_final: 0.7903 (mtm) REVERT: B 551 MET cc_start: 0.7796 (ttp) cc_final: 0.7103 (ttp) REVERT: B 555 GLU cc_start: 0.7519 (tt0) cc_final: 0.7043 (tm-30) REVERT: B 558 LYS cc_start: 0.7710 (tttm) cc_final: 0.7150 (ttpp) REVERT: B 560 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 561 ARG cc_start: 0.7129 (mtm110) cc_final: 0.6681 (ptp90) REVERT: B 657 GLU cc_start: 0.8128 (mp0) cc_final: 0.7828 (mp0) REVERT: B 776 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7544 (mt0) REVERT: B 832 GLN cc_start: 0.7523 (tt0) cc_final: 0.6956 (tm-30) REVERT: A 256 GLU cc_start: 0.7877 (mp0) cc_final: 0.7519 (mp0) REVERT: A 396 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6184 (mt-10) REVERT: A 551 MET cc_start: 0.1204 (mpp) cc_final: 0.0962 (mmm) REVERT: A 664 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 752 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: A 834 LEU cc_start: 0.0783 (OUTLIER) cc_final: 0.0284 (tm) outliers start: 116 outliers final: 44 residues processed: 475 average time/residue: 0.6877 time to fit residues: 377.8086 Evaluate side-chains 432 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 380 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 C residue 817 LEU Chi-restraints excluded: chain F residue 300 LYS 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 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 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 556 ARG Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 563 GLU Chi-restraints excluded: chain D residue 607 THR 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 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 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 232 LEU 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 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 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: 0.0980 chunk 102 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 188 optimal weight: 0.0970 chunk 198 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 770 HIS ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 ASN ** E 688 ASN ** 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.212892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157794 restraints weight = 28104.267| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.15 r_work: 0.3575 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3090 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= 0.114 Angle : 0.574 9.190 38259 Z= 0.284 Chirality : 0.044 0.258 4328 Planarity : 0.004 0.047 4991 Dihedral : 9.155 170.982 3984 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.29 % Allowed : 22.77 % Favored : 73.94 % 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 are not related in a simple way. whole: -1.90 (0.14), residues: 3448 helix: -0.94 (0.13), residues: 1571 sheet: -2.60 (0.29), residues: 269 loop : -1.20 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 852 TYR 0.032 0.001 TYR F 783 PHE 0.011 0.001 PHE D 729 TRP 0.009 0.001 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (28296) covalent geometry : angle 0.57363 / 0.28 (38259) hydrogen bonds : bond 0.03361 / 2.23 ( 719) hydrogen bonds : angle 5.21725 / 3.56 ( 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 508 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 412 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.5408 (mtm-85) REVERT: C 307 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8656 (mt-10) REVERT: C 317 ASP cc_start: 0.8092 (p0) cc_final: 0.7563 (m-30) REVERT: C 555 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 569 ARG cc_start: 0.8931 (ttt-90) cc_final: 0.8649 (mtp180) REVERT: C 710 ARG cc_start: 0.8354 (mtt90) cc_final: 0.8001 (mtt-85) REVERT: C 784 LYS cc_start: 0.7591 (mptt) cc_final: 0.7226 (mppt) REVERT: C 798 GLU cc_start: 0.8441 (mp0) cc_final: 0.8188 (tp30) REVERT: C 801 LYS cc_start: 0.6941 (ttpp) cc_final: 0.6205 (tptp) REVERT: F 251 TYR cc_start: 0.4765 (m-80) cc_final: 0.4284 (m-80) REVERT: F 275 LEU cc_start: 0.6072 (tp) cc_final: 0.5553 (tm) REVERT: F 276 PHE cc_start: 0.6833 (m-10) cc_final: 0.5975 (m-80) REVERT: F 300 LYS cc_start: 0.3559 (tptp) cc_final: 0.2757 (mmtt) REVERT: F 322 TYR cc_start: 0.5643 (m-10) cc_final: 0.5366 (m-10) REVERT: F 331 ARG cc_start: 0.6701 (tpp-160) cc_final: 0.4812 (ttm-80) REVERT: F 353 LEU cc_start: 0.1157 (OUTLIER) cc_final: 0.0918 (pp) REVERT: F 356 ARG cc_start: 0.2843 (tpt170) cc_final: 0.2242 (tmt-80) REVERT: F 585 ARG cc_start: 0.4986 (mtp85) cc_final: 0.4517 (tpm170) REVERT: F 629 MET cc_start: 0.5128 (ttt) cc_final: 0.4362 (mmt) REVERT: F 638 MET cc_start: -0.1494 (mmp) cc_final: -0.2007 (mpt) REVERT: F 716 MET cc_start: 0.5321 (mtt) cc_final: 0.3211 (tpp) REVERT: F 800 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5644 (pp) REVERT: E 164 TYR cc_start: 0.7699 (m-10) cc_final: 0.6885 (m-10) REVERT: E 167 ASP cc_start: 0.8294 (t70) cc_final: 0.7640 (t0) REVERT: E 217 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6208 (mp0) REVERT: E 252 ARG cc_start: 0.6265 (mpp-170) cc_final: 0.4488 (tpm170) REVERT: E 317 ASP cc_start: 0.7659 (m-30) cc_final: 0.7251 (m-30) REVERT: E 353 LEU cc_start: 0.8054 (tp) cc_final: 0.7629 (mt) REVERT: E 405 ILE cc_start: 0.8105 (mt) cc_final: 0.7896 (mp) REVERT: E 542 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: E 561 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6197 (ptt90) REVERT: E 629 MET cc_start: 0.8826 (ptt) cc_final: 0.8332 (ptp) REVERT: E 638 MET cc_start: 0.8191 (mtm) cc_final: 0.7608 (mtm) REVERT: E 656 TYR cc_start: 0.7632 (p90) cc_final: 0.6965 (p90) REVERT: E 696 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5069 (t0) REVERT: E 698 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7363 (mmm160) REVERT: E 705 ARG cc_start: 0.6377 (mtt180) cc_final: 0.5961 (mtm180) REVERT: E 737 MET cc_start: 0.7015 (tpp) cc_final: 0.6514 (tpt) REVERT: E 752 GLU cc_start: 0.7363 (pm20) cc_final: 0.6940 (pm20) REVERT: E 768 GLU cc_start: 0.7721 (tt0) cc_final: 0.7296 (tp30) REVERT: E 822 GLN cc_start: 0.7466 (mt0) cc_final: 0.6824 (tt0) REVERT: D 163 LYS cc_start: 0.8978 (mtmt) cc_final: 0.7838 (mptt) REVERT: D 174 GLN cc_start: 0.9101 (mt0) cc_final: 0.8880 (mt0) REVERT: D 230 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8428 (tp30) REVERT: D 260 LYS cc_start: 0.7528 (mttt) cc_final: 0.7115 (mttm) REVERT: D 324 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8519 (mt-10) REVERT: D 535 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7078 (pp20) REVERT: D 552 MET cc_start: 0.4697 (mmt) cc_final: 0.4163 (mmm) REVERT: D 563 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: D 629 MET cc_start: 0.9194 (ptm) cc_final: 0.8990 (ptt) REVERT: D 734 TYR cc_start: 0.8483 (t80) cc_final: 0.8175 (t80) REVERT: D 801 LYS cc_start: 0.7604 (ptmt) cc_final: 0.7169 (ttmt) REVERT: D 805 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: D 823 GLN cc_start: 0.7905 (mt0) cc_final: 0.7555 (mp10) REVERT: B 162 LYS cc_start: 0.8314 (tttm) cc_final: 0.7890 (mtpp) REVERT: B 268 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7646 (mttt) REVERT: B 283 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8051 (ttm) REVERT: B 293 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.5845 (pmt) REVERT: B 551 MET cc_start: 0.7688 (ttp) cc_final: 0.7466 (ttp) REVERT: B 555 GLU cc_start: 0.7444 (tt0) cc_final: 0.7055 (tt0) REVERT: B 558 LYS cc_start: 0.7743 (tttm) cc_final: 0.7189 (ttpp) REVERT: B 560 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 657 GLU cc_start: 0.8111 (mp0) cc_final: 0.7825 (mp0) REVERT: B 776 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7511 (mt0) REVERT: B 832 GLN cc_start: 0.7588 (tt0) cc_final: 0.7011 (tm-30) REVERT: A 256 GLU cc_start: 0.7851 (mp0) cc_final: 0.7457 (mp0) REVERT: A 396 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6213 (mt-10) REVERT: A 551 MET cc_start: 0.1158 (mpp) cc_final: 0.0948 (mmm) REVERT: A 675 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 737 MET cc_start: 0.5809 (mpp) cc_final: 0.5592 (mpp) REVERT: A 752 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 834 LEU cc_start: 0.0773 (OUTLIER) cc_final: 0.0288 (tm) outliers start: 96 outliers final: 38 residues processed: 473 average time/residue: 0.6669 time to fit residues: 365.1321 Evaluate side-chains 436 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 385 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 353 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 718 SER 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 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 793 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 293 MET 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 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 805 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 293 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 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 LEU 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 642 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 2 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 343 optimal weight: 0.5980 chunk 220 optimal weight: 0.1980 chunk 176 optimal weight: 0.5980 chunk 341 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 573 GLN F 703 GLN E 192 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 688 ASN ** 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 719 ASN B 770 HIS B 822 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.211217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153334 restraints weight = 27995.618| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.87 r_work: 0.3553 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28296 Z= 0.148 Angle : 0.595 9.204 38259 Z= 0.293 Chirality : 0.045 0.225 4328 Planarity : 0.004 0.065 4991 Dihedral : 9.163 171.957 3984 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.50 % Allowed : 23.35 % Favored : 73.15 % 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 are not related in a simple way. whole: -1.78 (0.14), residues: 3448 helix: -0.82 (0.13), residues: 1567 sheet: -2.62 (0.29), residues: 274 loop : -1.14 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 852 TYR 0.013 0.001 TYR C 357 PHE 0.014 0.001 PHE E 276 TRP 0.010 0.001 TRP D 543 HIS 0.011 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (28296) covalent geometry : angle 0.59474 / 0.29 (38259) hydrogen bonds : bond 0.03459 / 2.30 ( 719) hydrogen bonds : angle 5.16077 / 3.53 ( 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 497 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 395 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 265 ASP cc_start: 0.8267 (m-30) cc_final: 0.7737 (m-30) REVERT: C 305 ARG cc_start: 0.6631 (mtt-85) cc_final: 0.5429 (mtm-85) REVERT: C 307 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8631 (mt-10) REVERT: C 317 ASP cc_start: 0.8024 (p0) cc_final: 0.7576 (m-30) REVERT: C 555 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6862 (tm-30) REVERT: C 710 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8048 (mtt-85) REVERT: C 731 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: C 784 LYS cc_start: 0.7570 (mptt) cc_final: 0.7234 (mppt) REVERT: C 798 GLU cc_start: 0.8456 (mp0) cc_final: 0.8141 (tp30) REVERT: C 801 LYS cc_start: 0.6811 (ttpp) cc_final: 0.6247 (tptp) REVERT: C 831 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: F 251 TYR cc_start: 0.4719 (m-80) cc_final: 0.4239 (m-80) REVERT: F 264 ASN cc_start: 0.6019 (OUTLIER) cc_final: 0.5665 (t0) REVERT: F 275 LEU cc_start: 0.6010 (tp) cc_final: 0.5572 (tm) REVERT: F 276 PHE cc_start: 0.6846 (m-10) cc_final: 0.6532 (m-10) REVERT: F 300 LYS cc_start: 0.3585 (tptp) cc_final: 0.2760 (mmtt) REVERT: F 320 ARG cc_start: 0.6243 (mtm110) cc_final: 0.5796 (mtt-85) REVERT: F 322 TYR cc_start: 0.5626 (m-10) cc_final: 0.5341 (m-10) REVERT: F 331 ARG cc_start: 0.6719 (tpp-160) cc_final: 0.4842 (ttm-80) REVERT: F 353 LEU cc_start: 0.1025 (OUTLIER) cc_final: 0.0761 (pp) REVERT: F 356 ARG cc_start: 0.2823 (tpt170) cc_final: 0.2260 (tmt-80) REVERT: F 585 ARG cc_start: 0.4994 (mtp85) cc_final: 0.4510 (tpm170) REVERT: F 629 MET cc_start: 0.5223 (ttt) cc_final: 0.4489 (mmt) REVERT: F 638 MET cc_start: -0.2024 (mmp) cc_final: -0.2498 (mpt) REVERT: F 716 MET cc_start: 0.5293 (mtt) cc_final: 0.3248 (tpp) REVERT: F 800 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5627 (pp) REVERT: E 164 TYR cc_start: 0.7703 (m-10) cc_final: 0.6903 (m-10) REVERT: E 167 ASP cc_start: 0.8260 (t70) cc_final: 0.7613 (t0) REVERT: E 217 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6160 (mp0) REVERT: E 252 ARG cc_start: 0.6222 (mpp-170) cc_final: 0.4420 (tpm170) REVERT: E 317 ASP cc_start: 0.7614 (m-30) cc_final: 0.7240 (m-30) REVERT: E 353 LEU cc_start: 0.8033 (tp) cc_final: 0.7614 (mt) REVERT: E 542 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: E 561 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6183 (ptt90) REVERT: E 629 MET cc_start: 0.8851 (ptt) cc_final: 0.8319 (ptp) REVERT: E 638 MET cc_start: 0.8243 (mtm) cc_final: 0.7634 (mtm) REVERT: E 656 TYR cc_start: 0.7649 (p90) cc_final: 0.6946 (p90) REVERT: E 696 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5074 (t0) REVERT: E 698 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7398 (mmm160) REVERT: E 705 ARG cc_start: 0.6523 (mtt180) cc_final: 0.6069 (mtm180) REVERT: E 737 MET cc_start: 0.6999 (tpp) cc_final: 0.6538 (tpt) REVERT: E 752 GLU cc_start: 0.7290 (pm20) cc_final: 0.6858 (pm20) REVERT: E 768 GLU cc_start: 0.7674 (tt0) cc_final: 0.7262 (tp30) REVERT: E 822 GLN cc_start: 0.7448 (mt0) cc_final: 0.6800 (tt0) REVERT: D 163 LYS cc_start: 0.8994 (mtmt) cc_final: 0.7903 (mptt) REVERT: D 230 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8417 (tp30) REVERT: D 260 LYS cc_start: 0.7462 (mttt) cc_final: 0.7050 (mttm) REVERT: D 308 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6899 (mp) REVERT: D 324 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8508 (tt0) REVERT: D 535 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: D 552 MET cc_start: 0.4697 (mmt) cc_final: 0.4161 (mmm) REVERT: D 563 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 780 LYS cc_start: 0.7737 (mttt) cc_final: 0.7516 (mppt) REVERT: D 801 LYS cc_start: 0.7582 (ptmt) cc_final: 0.7136 (ttmt) REVERT: D 805 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: D 823 GLN cc_start: 0.7890 (mt0) cc_final: 0.7543 (mp10) REVERT: D 831 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7087 (tm130) REVERT: B 162 LYS cc_start: 0.8286 (tttm) cc_final: 0.7868 (mtpp) REVERT: B 198 THR cc_start: 0.8574 (t) cc_final: 0.8357 (p) REVERT: B 268 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7649 (mttt) REVERT: B 283 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: B 403 MET cc_start: 0.8111 (mtp) cc_final: 0.7856 (mtm) REVERT: B 555 GLU cc_start: 0.7426 (tt0) cc_final: 0.6996 (tm-30) REVERT: B 558 LYS cc_start: 0.7667 (tttm) cc_final: 0.7178 (ttpt) REVERT: B 560 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 561 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6790 (ptp90) REVERT: B 657 GLU cc_start: 0.8052 (mp0) cc_final: 0.7768 (mp0) REVERT: B 705 ARG cc_start: 0.8095 (tpp-160) cc_final: 0.7120 (ttp-110) REVERT: B 776 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7549 (mt0) REVERT: B 832 GLN cc_start: 0.7533 (tt0) cc_final: 0.6926 (tm-30) REVERT: A 207 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7434 (mp0) REVERT: A 256 GLU cc_start: 0.7843 (mp0) cc_final: 0.7433 (mp0) REVERT: A 355 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: A 396 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6361 (mt-10) REVERT: A 639 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6493 (pm20) REVERT: A 668 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.6892 (mtm110) REVERT: A 675 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6774 (mm) REVERT: A 752 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: A 834 LEU cc_start: 0.0771 (OUTLIER) cc_final: 0.0304 (tm) outliers start: 102 outliers final: 46 residues processed: 469 average time/residue: 0.6879 time to fit residues: 373.0068 Evaluate side-chains 440 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 377 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 731 GLU Chi-restraints excluded: chain C residue 741 VAL 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 338 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 718 SER 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 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 793 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 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 805 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 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 689 ILE 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 166 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 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 675 LEU 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: 1.9990 chunk 110 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 339 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 703 GLN E 192 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 361 HIS B 719 ASN B 770 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.207480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151605 restraints weight = 28266.218| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.36 r_work: 0.3446 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28296 Z= 0.222 Angle : 0.662 10.210 38259 Z= 0.327 Chirality : 0.048 0.191 4328 Planarity : 0.005 0.059 4991 Dihedral : 9.304 167.951 3984 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.67 % Allowed : 23.39 % Favored : 72.94 % 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 are not related in a simple way. whole: -1.93 (0.14), residues: 3448 helix: -0.98 (0.13), residues: 1586 sheet: -2.56 (0.27), residues: 315 loop : -1.14 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 852 TYR 0.013 0.002 TYR C 357 PHE 0.023 0.002 PHE E 276 TRP 0.010 0.002 TRP D 543 HIS 0.012 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (28296) covalent geometry : angle 0.66224 / 0.33 (38259) hydrogen bonds : bond 0.03811 / 2.54 ( 719) hydrogen bonds : angle 5.30767 / 3.62 ( 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 499 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 392 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 265 ASP cc_start: 0.8354 (m-30) cc_final: 0.7752 (m-30) REVERT: C 305 ARG cc_start: 0.6747 (mtt-85) cc_final: 0.5473 (mtm-85) REVERT: C 307 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8688 (mt-10) REVERT: C 317 ASP cc_start: 0.8333 (p0) cc_final: 0.7829 (m-30) REVERT: C 555 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 561 ARG cc_start: 0.7307 (mtm110) cc_final: 0.6952 (ptt90) REVERT: C 710 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8164 (mtt-85) REVERT: C 731 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: C 784 LYS cc_start: 0.7664 (mptt) cc_final: 0.7385 (mppt) REVERT: C 798 GLU cc_start: 0.8535 (mp0) cc_final: 0.8212 (tp30) REVERT: C 801 LYS cc_start: 0.6929 (ttpp) cc_final: 0.6299 (tptp) REVERT: C 831 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: F 251 TYR cc_start: 0.4729 (m-80) cc_final: 0.4274 (m-80) REVERT: F 264 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5591 (t0) REVERT: F 275 LEU cc_start: 0.6032 (tp) cc_final: 0.5591 (tm) REVERT: F 276 PHE cc_start: 0.6971 (m-10) cc_final: 0.6675 (m-10) REVERT: F 300 LYS cc_start: 0.3730 (tptp) cc_final: 0.2883 (mmtt) REVERT: F 320 ARG cc_start: 0.6254 (mtm110) cc_final: 0.5684 (mmm-85) REVERT: F 331 ARG cc_start: 0.6749 (tpp-160) cc_final: 0.4803 (ttm-80) REVERT: F 353 LEU cc_start: 0.1204 (OUTLIER) cc_final: 0.0934 (pp) REVERT: F 356 ARG cc_start: 0.2963 (tpt170) cc_final: 0.2370 (tmt-80) REVERT: F 585 ARG cc_start: 0.5072 (mtp85) cc_final: 0.4521 (tpm170) REVERT: F 629 MET cc_start: 0.5538 (ttt) cc_final: 0.4797 (mmt) REVERT: F 638 MET cc_start: -0.1872 (mmp) cc_final: -0.2411 (mpt) REVERT: F 716 MET cc_start: 0.5329 (mtt) cc_final: 0.3378 (tpp) REVERT: F 800 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5477 (pp) REVERT: E 164 TYR cc_start: 0.7796 (m-10) cc_final: 0.7052 (m-10) REVERT: E 167 ASP cc_start: 0.8192 (t70) cc_final: 0.7513 (t0) REVERT: E 252 ARG cc_start: 0.6319 (mpp-170) cc_final: 0.4470 (tpm170) REVERT: E 405 ILE cc_start: 0.8185 (mt) cc_final: 0.7981 (mp) REVERT: E 629 MET cc_start: 0.8966 (ptt) cc_final: 0.8371 (ptp) REVERT: E 638 MET cc_start: 0.8354 (mtm) cc_final: 0.7725 (mtm) REVERT: E 643 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8022 (p) REVERT: E 656 TYR cc_start: 0.7692 (p90) cc_final: 0.7006 (p90) REVERT: E 696 ASP cc_start: 0.5639 (OUTLIER) cc_final: 0.5099 (t0) REVERT: E 698 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7524 (mmm160) REVERT: E 705 ARG cc_start: 0.6596 (mtt180) cc_final: 0.6124 (mtm180) REVERT: E 737 MET cc_start: 0.7028 (tpp) cc_final: 0.6560 (tpt) REVERT: E 752 GLU cc_start: 0.7376 (pm20) cc_final: 0.6930 (pm20) REVERT: E 768 GLU cc_start: 0.7712 (tt0) cc_final: 0.7277 (tp30) REVERT: E 822 GLN cc_start: 0.7635 (mt0) cc_final: 0.6902 (tt0) REVERT: D 163 LYS cc_start: 0.9052 (mtmt) cc_final: 0.7954 (mptt) REVERT: D 230 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8439 (tp30) REVERT: D 260 LYS cc_start: 0.7546 (mttt) cc_final: 0.7147 (mttm) REVERT: D 308 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7175 (mp) REVERT: D 535 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7527 (pp20) REVERT: D 552 MET cc_start: 0.4807 (mmt) cc_final: 0.4264 (mmm) REVERT: D 769 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: D 780 LYS cc_start: 0.7810 (mttt) cc_final: 0.7595 (mppt) REVERT: D 801 LYS cc_start: 0.7695 (ptmt) cc_final: 0.7296 (ttmt) REVERT: D 805 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: D 831 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7230 (tm130) REVERT: B 188 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7115 (ttp-110) REVERT: B 232 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (mp) REVERT: B 268 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7777 (mttt) REVERT: B 283 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8295 (ttm) REVERT: B 403 MET cc_start: 0.8171 (mtp) cc_final: 0.7912 (mtm) REVERT: B 551 MET cc_start: 0.7930 (ttp) cc_final: 0.7677 (ttp) REVERT: B 552 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4838 (mpp) REVERT: B 555 GLU cc_start: 0.7536 (tt0) cc_final: 0.7131 (tt0) REVERT: B 558 LYS cc_start: 0.7742 (tttm) cc_final: 0.7227 (ttpt) REVERT: B 561 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6714 (ptp90) REVERT: B 615 CYS cc_start: 0.8416 (m) cc_final: 0.8182 (m) REVERT: B 657 GLU cc_start: 0.7983 (mp0) cc_final: 0.7729 (mp0) REVERT: B 768 GLU cc_start: 0.8067 (mp0) cc_final: 0.7825 (mp0) REVERT: B 776 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7594 (mt0) REVERT: B 832 GLN cc_start: 0.7547 (tt0) cc_final: 0.6901 (tm-30) REVERT: A 256 GLU cc_start: 0.7960 (mp0) cc_final: 0.7582 (mp0) REVERT: A 355 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: A 396 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6337 (mt-10) REVERT: A 551 MET cc_start: 0.0848 (mmm) cc_final: -0.0404 (mmt) REVERT: A 664 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 668 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.6792 (mtm110) REVERT: A 675 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6846 (mm) REVERT: A 684 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8204 (Cg_endo) REVERT: A 737 MET cc_start: 0.5804 (mpp) cc_final: 0.5555 (mpp) REVERT: A 752 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 834 LEU cc_start: 0.0864 (OUTLIER) cc_final: 0.0424 (tm) outliers start: 107 outliers final: 51 residues processed: 461 average time/residue: 0.6813 time to fit residues: 364.4088 Evaluate side-chains 438 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 368 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 731 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 338 VAL Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 654 VAL Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 718 SER 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 192 GLN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU 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 793 ILE 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 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 769 GLN Chi-restraints excluded: chain D residue 805 GLU Chi-restraints excluded: chain D residue 837 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 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 632 ILE Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE 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 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 675 LEU 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: 6.9990 chunk 110 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 310 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 688 ASN ** 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** A 362 HIS A 595 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.211601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153873 restraints weight = 28095.355| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.90 r_work: 0.3558 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3319 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= 0.127 Angle : 0.603 9.527 38259 Z= 0.296 Chirality : 0.045 0.203 4328 Planarity : 0.004 0.075 4991 Dihedral : 9.084 169.770 3984 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.74 % Allowed : 24.86 % 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 are not related in a simple way. whole: -1.62 (0.14), residues: 3448 helix: -0.67 (0.13), residues: 1560 sheet: -2.56 (0.28), residues: 296 loop : -1.04 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 561 TYR 0.013 0.001 TYR B 783 PHE 0.015 0.001 PHE E 276 TRP 0.008 0.001 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (28296) covalent geometry : angle 0.60252 / 0.30 (38259) hydrogen bonds : bond 0.03456 / 2.32 ( 719) hydrogen bonds : angle 5.13241 / 3.50 ( 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 466 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 386 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 188 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7974 (ttm110) REVERT: C 242 MET cc_start: 0.8265 (mmt) cc_final: 0.8063 (mmm) REVERT: C 265 ASP cc_start: 0.8227 (m-30) cc_final: 0.7610 (m-30) REVERT: C 305 ARG cc_start: 0.6685 (mtt-85) cc_final: 0.5505 (mtm-85) REVERT: C 307 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8661 (mt-10) REVERT: C 317 ASP cc_start: 0.8174 (p0) cc_final: 0.7748 (m-30) REVERT: C 555 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6387 (tm-30) REVERT: C 569 ARG cc_start: 0.8914 (ttt-90) cc_final: 0.8588 (mtp180) REVERT: C 710 ARG cc_start: 0.8327 (mtt90) cc_final: 0.7920 (mtt-85) REVERT: C 728 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7037 (mtp85) REVERT: C 784 LYS cc_start: 0.7562 (mptt) cc_final: 0.7251 (mppt) REVERT: C 798 GLU cc_start: 0.8456 (mp0) cc_final: 0.8108 (tp30) REVERT: C 801 LYS cc_start: 0.6783 (ttpp) cc_final: 0.6222 (tptp) REVERT: F 251 TYR cc_start: 0.4687 (m-80) cc_final: 0.4225 (m-80) REVERT: F 275 LEU cc_start: 0.5948 (tp) cc_final: 0.5506 (tm) REVERT: F 276 PHE cc_start: 0.6851 (m-10) cc_final: 0.6533 (m-10) REVERT: F 300 LYS cc_start: 0.3648 (tptp) cc_final: 0.2785 (mmtt) REVERT: F 320 ARG cc_start: 0.6245 (mtm110) cc_final: 0.5734 (mmm-85) REVERT: F 331 ARG cc_start: 0.6677 (tpp-160) cc_final: 0.4748 (ttm-80) REVERT: F 353 LEU cc_start: 0.0986 (OUTLIER) cc_final: 0.0680 (pp) REVERT: F 356 ARG cc_start: 0.2943 (tpt170) cc_final: 0.2355 (tmt-80) REVERT: F 538 GLU cc_start: 0.7000 (tp30) cc_final: 0.6144 (tp30) REVERT: F 585 ARG cc_start: 0.5022 (mtp85) cc_final: 0.4502 (tpm170) REVERT: F 629 MET cc_start: 0.5426 (ttt) cc_final: 0.4751 (mmt) REVERT: F 638 MET cc_start: -0.2001 (mmp) cc_final: -0.2548 (mpt) REVERT: F 716 MET cc_start: 0.5304 (mtt) cc_final: 0.3331 (tpp) REVERT: F 763 PHE cc_start: 0.2161 (OUTLIER) cc_final: 0.1249 (t80) REVERT: E 164 TYR cc_start: 0.7707 (m-10) cc_final: 0.6940 (m-10) REVERT: E 167 ASP cc_start: 0.8216 (t70) cc_final: 0.7562 (t0) REVERT: E 252 ARG cc_start: 0.6215 (mpp-170) cc_final: 0.4435 (tpm170) REVERT: E 317 ASP cc_start: 0.7458 (m-30) cc_final: 0.6726 (p0) REVERT: E 318 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6290 (tm-30) REVERT: E 405 ILE cc_start: 0.8241 (mt) cc_final: 0.8033 (mp) REVERT: E 542 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: E 561 ARG cc_start: 0.6701 (mtm110) cc_final: 0.5967 (ptt90) REVERT: E 629 MET cc_start: 0.8850 (ptt) cc_final: 0.8354 (ptp) REVERT: E 638 MET cc_start: 0.8264 (mtm) cc_final: 0.7710 (mtm) REVERT: E 643 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7877 (p) REVERT: E 656 TYR cc_start: 0.7656 (p90) cc_final: 0.7035 (p90) REVERT: E 696 ASP cc_start: 0.5590 (OUTLIER) cc_final: 0.4963 (t0) REVERT: E 698 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7325 (mmm160) REVERT: E 705 ARG cc_start: 0.6689 (mtt180) cc_final: 0.6163 (mtm180) REVERT: E 752 GLU cc_start: 0.7304 (pm20) cc_final: 0.6847 (pm20) REVERT: E 768 GLU cc_start: 0.7666 (tt0) cc_final: 0.7250 (tp30) REVERT: E 822 GLN cc_start: 0.7456 (mt0) cc_final: 0.6811 (tt0) REVERT: D 163 LYS cc_start: 0.8998 (mtmt) cc_final: 0.7901 (mptt) REVERT: D 174 GLN cc_start: 0.9106 (mt0) cc_final: 0.8845 (mt0) REVERT: D 230 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8389 (tp30) REVERT: D 260 LYS cc_start: 0.7534 (mttt) cc_final: 0.7196 (mttm) REVERT: D 535 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: D 552 MET cc_start: 0.4800 (mmt) cc_final: 0.4312 (mmm) REVERT: D 563 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: D 627 GLU cc_start: 0.7661 (mp0) cc_final: 0.7406 (mp0) REVERT: D 780 LYS cc_start: 0.7740 (mttt) cc_final: 0.7521 (mppt) REVERT: D 801 LYS cc_start: 0.7553 (ptmt) cc_final: 0.7065 (ttmt) REVERT: D 805 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 831 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7158 (tm130) REVERT: D 857 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5415 (mp10) REVERT: B 188 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7057 (ttp-110) REVERT: B 232 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8616 (mp) REVERT: B 235 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7530 (mtm180) REVERT: B 268 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7620 (mttt) REVERT: B 283 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8045 (ttm) REVERT: B 317 ASP cc_start: 0.7600 (p0) cc_final: 0.7204 (m-30) REVERT: B 551 MET cc_start: 0.7825 (ttp) cc_final: 0.7491 (ttp) REVERT: B 552 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4801 (mpp) REVERT: B 555 GLU cc_start: 0.7439 (tt0) cc_final: 0.6912 (tt0) REVERT: B 558 LYS cc_start: 0.7666 (tttm) cc_final: 0.7172 (ttpt) REVERT: B 561 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6866 (ptp90) REVERT: B 615 CYS cc_start: 0.8271 (m) cc_final: 0.8034 (m) REVERT: B 657 GLU cc_start: 0.7936 (mp0) cc_final: 0.7658 (mp0) REVERT: B 705 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7038 (ttp-110) REVERT: B 768 GLU cc_start: 0.7961 (mp0) cc_final: 0.7728 (mp0) REVERT: B 776 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7474 (mt0) REVERT: B 832 GLN cc_start: 0.7434 (tt0) cc_final: 0.6858 (tm-30) REVERT: A 207 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 256 GLU cc_start: 0.7825 (mp0) cc_final: 0.7588 (mp0) REVERT: A 317 ASP cc_start: 0.7409 (p0) cc_final: 0.7153 (p0) REVERT: A 355 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: A 396 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6314 (mt-10) REVERT: A 551 MET cc_start: 0.0957 (mmm) cc_final: -0.0427 (mmt) REVERT: A 664 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 668 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.6893 (mtm110) REVERT: A 675 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6771 (mm) REVERT: A 737 MET cc_start: 0.5800 (mpp) cc_final: 0.5508 (mpp) REVERT: A 752 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: A 834 LEU cc_start: 0.0897 (OUTLIER) cc_final: 0.0458 (tm) outliers start: 80 outliers final: 43 residues processed: 443 average time/residue: 0.6993 time to fit residues: 357.5116 Evaluate side-chains 429 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 353 LEU Chi-restraints excluded: chain F residue 533 ASP 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 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU 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 793 ILE 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 563 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 805 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 235 ARG 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 552 MET Chi-restraints excluded: chain B residue 604 LEU 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 166 ILE Chi-restraints excluded: chain A residue 232 LEU 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: 0.6980 chunk 27 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 152 optimal weight: 0.0030 chunk 67 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 142 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 180 optimal weight: 0.0170 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 192 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 688 ASN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 703 GLN D 794 HIS D 822 GLN B 568 HIS B 719 ASN B 822 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.214565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156711 restraints weight = 28167.854| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.92 r_work: 0.3606 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28296 Z= 0.107 Angle : 0.595 9.801 38259 Z= 0.292 Chirality : 0.044 0.197 4328 Planarity : 0.004 0.081 4991 Dihedral : 8.942 169.434 3984 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.26 % Allowed : 25.38 % Favored : 72.36 % 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 are not related in a simple way. whole: -1.39 (0.14), residues: 3448 helix: -0.44 (0.13), residues: 1574 sheet: -2.57 (0.28), residues: 288 loop : -0.95 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 852 TYR 0.018 0.001 TYR B 783 PHE 0.010 0.001 PHE D 729 TRP 0.010 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (28296) covalent geometry : angle 0.59486 / 0.29 (38259) hydrogen bonds : bond 0.03317 / 2.21 ( 719) hydrogen bonds : angle 5.01970 / 3.43 ( 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 463 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 397 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 265 ASP cc_start: 0.8157 (m-30) cc_final: 0.7532 (m-30) REVERT: C 305 ARG cc_start: 0.6628 (mtt-85) cc_final: 0.5631 (mtt180) REVERT: C 307 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 317 ASP cc_start: 0.8087 (p0) cc_final: 0.7658 (m-30) REVERT: C 555 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6688 (tm-30) REVERT: C 569 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8567 (mtp180) REVERT: C 728 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7145 (mtp85) REVERT: C 784 LYS cc_start: 0.7541 (mptt) cc_final: 0.7196 (mppt) REVERT: C 801 LYS cc_start: 0.6712 (ttpp) cc_final: 0.6201 (tptp) REVERT: F 251 TYR cc_start: 0.4655 (m-80) cc_final: 0.4161 (m-80) REVERT: F 275 LEU cc_start: 0.6149 (tp) cc_final: 0.5713 (tm) REVERT: F 276 PHE cc_start: 0.6747 (m-10) cc_final: 0.6416 (m-10) REVERT: F 300 LYS cc_start: 0.3638 (tptp) cc_final: 0.2773 (mmtt) REVERT: F 320 ARG cc_start: 0.6202 (mtm110) cc_final: 0.5801 (mtt-85) REVERT: F 330 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6472 (tm-30) REVERT: F 331 ARG cc_start: 0.6705 (tpp-160) cc_final: 0.4872 (ttm-80) REVERT: F 333 PHE cc_start: 0.5476 (m-80) cc_final: 0.5108 (m-80) REVERT: F 353 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0660 (pp) REVERT: F 356 ARG cc_start: 0.2983 (tpt170) cc_final: 0.2442 (tmt-80) REVERT: F 538 GLU cc_start: 0.7016 (tp30) cc_final: 0.6145 (tp30) REVERT: F 585 ARG cc_start: 0.4951 (mtp85) cc_final: 0.4459 (tpm170) REVERT: F 629 MET cc_start: 0.5366 (ttt) cc_final: 0.4780 (mmt) REVERT: F 638 MET cc_start: -0.1877 (mmp) cc_final: -0.2524 (mpt) REVERT: F 716 MET cc_start: 0.5272 (mtt) cc_final: 0.3313 (tpp) REVERT: F 763 PHE cc_start: 0.2323 (OUTLIER) cc_final: 0.1424 (t80) REVERT: E 164 TYR cc_start: 0.7717 (m-10) cc_final: 0.6850 (m-10) REVERT: E 167 ASP cc_start: 0.8271 (t70) cc_final: 0.7630 (t0) REVERT: E 217 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6173 (mp0) REVERT: E 252 ARG cc_start: 0.6184 (mpp-170) cc_final: 0.4443 (tpm170) REVERT: E 317 ASP cc_start: 0.7191 (m-30) cc_final: 0.6564 (p0) REVERT: E 318 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6162 (tm-30) REVERT: E 542 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: E 561 ARG cc_start: 0.6570 (mtm110) cc_final: 0.5805 (ptt90) REVERT: E 629 MET cc_start: 0.8817 (ptt) cc_final: 0.8326 (ptp) REVERT: E 638 MET cc_start: 0.8213 (mtm) cc_final: 0.7713 (mtm) REVERT: E 656 TYR cc_start: 0.7643 (p90) cc_final: 0.7026 (p90) REVERT: E 698 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7144 (mmm160) REVERT: E 705 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6071 (mtm180) REVERT: E 752 GLU cc_start: 0.7237 (pm20) cc_final: 0.6795 (pm20) REVERT: E 768 GLU cc_start: 0.7657 (tt0) cc_final: 0.7290 (tp30) REVERT: E 822 GLN cc_start: 0.7449 (mt0) cc_final: 0.6827 (tt0) REVERT: D 163 LYS cc_start: 0.8949 (mtmt) cc_final: 0.7869 (mptt) REVERT: D 174 GLN cc_start: 0.9067 (mt0) cc_final: 0.8823 (mt0) REVERT: D 260 LYS cc_start: 0.7538 (mttt) cc_final: 0.7243 (mttm) REVERT: D 535 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: D 552 MET cc_start: 0.4809 (mmt) cc_final: 0.4282 (mmm) REVERT: D 627 GLU cc_start: 0.7555 (mp0) cc_final: 0.7262 (mp0) REVERT: D 696 ASP cc_start: 0.7287 (t70) cc_final: 0.7004 (p0) REVERT: D 780 LYS cc_start: 0.7746 (mttt) cc_final: 0.7515 (mppt) REVERT: D 801 LYS cc_start: 0.7558 (ptmt) cc_final: 0.7033 (ttmt) REVERT: D 805 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: D 823 GLN cc_start: 0.7827 (mt0) cc_final: 0.7542 (mp10) REVERT: B 162 LYS cc_start: 0.8108 (tttm) cc_final: 0.7736 (mtpp) REVERT: B 188 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7033 (ttp-110) REVERT: B 197 ARG cc_start: 0.8461 (ttt-90) cc_final: 0.8114 (ttt-90) REVERT: B 232 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 235 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7465 (mtm180) REVERT: B 268 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7602 (mttt) REVERT: B 283 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7876 (ttm) REVERT: B 317 ASP cc_start: 0.7494 (p0) cc_final: 0.7094 (m-30) REVERT: B 325 LYS cc_start: 0.8260 (mttm) cc_final: 0.7934 (mptt) REVERT: B 403 MET cc_start: 0.8265 (mtp) cc_final: 0.7913 (mtm) REVERT: B 558 LYS cc_start: 0.7666 (tttm) cc_final: 0.7176 (ttpt) REVERT: B 560 LEU cc_start: 0.8578 (mm) cc_final: 0.8208 (mm) REVERT: B 615 CYS cc_start: 0.8216 (m) cc_final: 0.8005 (m) REVERT: B 657 GLU cc_start: 0.8025 (mp0) cc_final: 0.7750 (mp0) REVERT: B 768 GLU cc_start: 0.7933 (mp0) cc_final: 0.7702 (mp0) REVERT: B 832 GLN cc_start: 0.7479 (tt0) cc_final: 0.6886 (tm-30) REVERT: A 207 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7374 (mp0) REVERT: A 242 MET cc_start: 0.7971 (mmt) cc_final: 0.7656 (mmt) REVERT: A 256 GLU cc_start: 0.7818 (mp0) cc_final: 0.7598 (mp0) REVERT: A 317 ASP cc_start: 0.7402 (p0) cc_final: 0.7123 (p0) REVERT: A 355 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: A 396 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6326 (mt-10) REVERT: A 551 MET cc_start: 0.0746 (mmm) cc_final: -0.0497 (mmt) REVERT: A 639 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6494 (pm20) REVERT: A 668 ARG cc_start: 0.7443 (mmt-90) cc_final: 0.6898 (mtm110) REVERT: A 675 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6777 (mm) REVERT: A 737 MET cc_start: 0.5731 (mpp) cc_final: 0.5473 (mpp) REVERT: A 752 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: A 834 LEU cc_start: 0.1040 (OUTLIER) cc_final: 0.0597 (tm) outliers start: 66 outliers final: 34 residues processed: 444 average time/residue: 0.6982 time to fit residues: 356.9191 Evaluate side-chains 419 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 569 ARG Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain F residue 353 LEU 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 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain D residue 293 MET 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 805 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 ARG 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 604 LEU 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 757 ILE Chi-restraints excluded: chain A residue 232 LEU 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: 2.9990 chunk 322 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 178 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 192 GLN ** 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 B 822 GLN B 823 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.208978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152205 restraints weight = 28146.829| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.36 r_work: 0.3469 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 28296 Z= 0.224 Angle : 0.675 10.778 38259 Z= 0.330 Chirality : 0.048 0.215 4328 Planarity : 0.005 0.069 4991 Dihedral : 9.135 170.768 3984 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.30 % Allowed : 25.51 % Favored : 72.19 % 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 are not related in a simple way. whole: -1.60 (0.14), residues: 3448 helix: -0.65 (0.13), residues: 1588 sheet: -2.62 (0.28), residues: 300 loop : -1.01 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 852 TYR 0.012 0.002 TYR B 783 PHE 0.020 0.002 PHE E 276 TRP 0.010 0.002 TRP D 543 HIS 0.009 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.22 (28296) covalent geometry : angle 0.67459 / 0.33 (38259) hydrogen bonds : bond 0.03772 / 2.53 ( 719) hydrogen bonds : angle 5.15489 / 3.50 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11029.64 seconds wall clock time: 188 minutes 4.35 seconds (11284.35 seconds total)