Starting phenix.real_space_refine on Tue Aug 26 07:35:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.map" model { file = "/net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m04_30029/08_2025/6m04_30029.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 22556 2.51 5 N 5746 2.21 5 O 6154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34666 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5773 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5780 Classifications: {'peptide': 714} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 27, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 5773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5773 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 26, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 7.83, per 1000 atoms: 0.23 Number of scatterers: 34666 At special positions: 0 Unit cell: (138.57, 171.35, 184.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6154 8.00 N 5746 7.00 C 22556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 354 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 354 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 354 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 354 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 354 " distance=2.02 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8348 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 30 sheets defined 45.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.184A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.527A pdb=" N LYS A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.543A pdb=" N TYR A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.559A pdb=" N LYS A 163 " --> pdb=" O TRP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 182 removed outlier: 3.525A pdb=" N LEU A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.936A pdb=" N SER A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.226A pdb=" N THR A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.707A pdb=" N LYS A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 390 Processing helix chain 'A' and resid 395 through 408 removed outlier: 4.156A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 4.066A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 removed outlier: 3.900A pdb=" N PHE A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 removed outlier: 4.057A pdb=" N LEU A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.590A pdb=" N LEU A 460 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.070A pdb=" N GLN A 511 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 removed outlier: 4.039A pdb=" N LEU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.509A pdb=" N MET A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.824A pdb=" N ALA A 610 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 4.196A pdb=" N LYS A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.605A pdb=" N ILE A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 655 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 656 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 657 " --> pdb=" O ILE A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 651 through 657' Processing helix chain 'A' and resid 675 through 682 removed outlier: 3.531A pdb=" N PHE A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 removed outlier: 3.942A pdb=" N ILE A 702 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.574A pdb=" N ILE A 748 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 749 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 797 removed outlier: 3.868A pdb=" N GLY A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 removed outlier: 3.534A pdb=" N CYS A 820 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.728A pdb=" N ALA B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.707A pdb=" N VAL B 26 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 Processing helix chain 'B' and resid 164 through 183 removed outlier: 3.518A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.974A pdb=" N VAL B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 4.038A pdb=" N THR B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 303 through 330 removed outlier: 4.322A pdb=" N ASN B 328 " --> pdb=" O CYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 390 removed outlier: 3.539A pdb=" N ILE B 390 " --> pdb=" O TRP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.708A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.573A pdb=" N GLY B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 removed outlier: 3.641A pdb=" N LEU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.754A pdb=" N LEU B 489 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.025A pdb=" N ILE B 509 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 511 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.900A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 576 through 580 removed outlier: 3.591A pdb=" N ILE B 579 " --> pdb=" O ASN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.728A pdb=" N ASP B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 609 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.619A pdb=" N LYS B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 633 " --> pdb=" O ASN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 682 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.717A pdb=" N ILE B 702 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 removed outlier: 4.296A pdb=" N PHE B 726 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 removed outlier: 4.381A pdb=" N LEU B 771 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 772 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 797 removed outlier: 3.592A pdb=" N VAL B 794 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 850 Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.633A pdb=" N VAL C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 157 Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.871A pdb=" N LYS C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 182 removed outlier: 3.909A pdb=" N LEU C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.689A pdb=" N VAL C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.734A pdb=" N THR C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 296 removed outlier: 4.013A pdb=" N ALA C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 328 removed outlier: 3.935A pdb=" N LYS C 318 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 390 removed outlier: 3.891A pdb=" N ILE C 390 " --> pdb=" O TRP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 406 removed outlier: 3.746A pdb=" N GLU C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 427 removed outlier: 3.872A pdb=" N MET C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 426 " --> pdb=" O MET C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 433 through 439 removed outlier: 3.780A pdb=" N PHE C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.363A pdb=" N LEU C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.839A pdb=" N GLN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 removed outlier: 4.310A pdb=" N LEU C 489 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 removed outlier: 3.887A pdb=" N ILE C 509 " --> pdb=" O PRO C 506 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 511 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 Processing helix chain 'C' and resid 576 through 581 removed outlier: 3.825A pdb=" N GLY C 580 " --> pdb=" O ASN C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 610 removed outlier: 4.367A pdb=" N VAL C 609 " --> pdb=" O ILE C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 4.008A pdb=" N ILE C 654 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 655 " --> pdb=" O HIS C 652 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 656 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 657 " --> pdb=" O ILE C 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 651 through 657' Processing helix chain 'C' and resid 677 through 682 Processing helix chain 'C' and resid 769 through 774 removed outlier: 3.551A pdb=" N CYS C 774 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.812A pdb=" N THR C 837 " --> pdb=" O HIS C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 849 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.527A pdb=" N LYS D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 removed outlier: 3.543A pdb=" N TYR D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.560A pdb=" N LYS D 163 " --> pdb=" O TRP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 182 removed outlier: 3.525A pdb=" N LEU D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.935A pdb=" N SER D 191 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.224A pdb=" N THR D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 302 through 332 removed outlier: 3.714A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE D 329 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 390 Processing helix chain 'D' and resid 395 through 408 removed outlier: 4.153A pdb=" N ASP D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 427 removed outlier: 4.067A pdb=" N VAL D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 438 removed outlier: 3.900A pdb=" N PHE D 434 " --> pdb=" O TYR D 430 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 455 removed outlier: 4.062A pdb=" N LEU D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.589A pdb=" N LEU D 460 " --> pdb=" O PHE D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 512 removed outlier: 4.070A pdb=" N GLN D 511 " --> pdb=" O LYS D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 537 removed outlier: 4.040A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.509A pdb=" N MET D 578 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 610 removed outlier: 3.825A pdb=" N ALA D 610 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 633 removed outlier: 4.196A pdb=" N LYS D 633 " --> pdb=" O ASN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 657 removed outlier: 3.605A pdb=" N ILE D 654 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 655 " --> pdb=" O HIS D 652 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER D 656 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 657 " --> pdb=" O ILE D 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 651 through 657' Processing helix chain 'D' and resid 675 through 682 removed outlier: 3.531A pdb=" N PHE D 679 " --> pdb=" O GLU D 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 681 " --> pdb=" O ILE D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.942A pdb=" N ILE D 702 " --> pdb=" O PRO D 699 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.575A pdb=" N ILE D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 749 " --> pdb=" O ILE D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 797 removed outlier: 3.870A pdb=" N GLY D 795 " --> pdb=" O PRO D 791 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 820 removed outlier: 3.533A pdb=" N CYS D 820 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 849 Processing helix chain 'E' and resid 4 through 11 removed outlier: 3.683A pdb=" N ALA E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.707A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 157 Processing helix chain 'E' and resid 164 through 183 removed outlier: 3.517A pdb=" N LEU E 168 " --> pdb=" O TYR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.975A pdb=" N VAL E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 214 removed outlier: 4.038A pdb=" N THR E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 298 Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 303 through 330 removed outlier: 4.322A pdb=" N ASN E 328 " --> pdb=" O CYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 390 removed outlier: 3.539A pdb=" N ILE E 390 " --> pdb=" O TRP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 3.717A pdb=" N PHE E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 425 Processing helix chain 'E' and resid 428 through 435 removed outlier: 3.573A pdb=" N GLY E 435 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 454 removed outlier: 3.641A pdb=" N LEU E 446 " --> pdb=" O SER E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 484 through 489 removed outlier: 3.754A pdb=" N LEU E 489 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 511 removed outlier: 4.025A pdb=" N ILE E 509 " --> pdb=" O PRO E 506 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 511 " --> pdb=" O LYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 538 removed outlier: 3.900A pdb=" N LEU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 558 Processing helix chain 'E' and resid 576 through 580 removed outlier: 3.591A pdb=" N ILE E 579 " --> pdb=" O ASN E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 605 through 610 removed outlier: 3.728A pdb=" N ASP E 608 " --> pdb=" O ASN E 605 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL E 609 " --> pdb=" O ILE E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 634 removed outlier: 4.619A pdb=" N LYS E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS E 633 " --> pdb=" O ASN E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 682 Processing helix chain 'E' and resid 699 through 704 removed outlier: 3.717A pdb=" N ILE E 702 " --> pdb=" O PRO E 699 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 703 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 728 removed outlier: 4.298A pdb=" N PHE E 726 " --> pdb=" O VAL E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 773 removed outlier: 4.381A pdb=" N LEU E 771 " --> pdb=" O PRO E 768 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 772 " --> pdb=" O LYS E 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 797 removed outlier: 3.592A pdb=" N VAL E 794 " --> pdb=" O PRO E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 850 Processing helix chain 'F' and resid 4 through 12 removed outlier: 3.563A pdb=" N ALA F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.635A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 157 Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.872A pdb=" N LYS F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 182 removed outlier: 3.910A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.689A pdb=" N VAL F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 removed outlier: 3.734A pdb=" N THR F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 296 removed outlier: 4.014A pdb=" N ALA F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 328 removed outlier: 3.936A pdb=" N LYS F 318 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 390 removed outlier: 3.892A pdb=" N ILE F 390 " --> pdb=" O TRP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 406 removed outlier: 3.746A pdb=" N GLU F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 427 removed outlier: 3.872A pdb=" N MET F 422 " --> pdb=" O PHE F 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 426 " --> pdb=" O MET F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 439 removed outlier: 3.780A pdb=" N PHE F 437 " --> pdb=" O ARG F 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 445 through 455 removed outlier: 4.364A pdb=" N LEU F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 464 removed outlier: 3.839A pdb=" N GLN F 462 " --> pdb=" O GLU F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 485 through 489 removed outlier: 4.310A pdb=" N LEU F 489 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.887A pdb=" N ILE F 509 " --> pdb=" O PRO F 506 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN F 511 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 558 Processing helix chain 'F' and resid 576 through 581 removed outlier: 3.822A pdb=" N GLY F 580 " --> pdb=" O ASN F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 610 removed outlier: 4.367A pdb=" N VAL F 609 " --> pdb=" O ILE F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 657 removed outlier: 4.009A pdb=" N ILE F 654 " --> pdb=" O PRO F 651 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 655 " --> pdb=" O HIS F 652 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER F 656 " --> pdb=" O ALA F 653 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 657 " --> pdb=" O ILE F 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 657' Processing helix chain 'F' and resid 677 through 682 Processing helix chain 'F' and resid 769 through 774 removed outlier: 3.551A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 792 through 797 Processing helix chain 'F' and resid 814 through 819 Processing helix chain 'F' and resid 831 through 837 removed outlier: 3.813A pdb=" N THR F 837 " --> pdb=" O HIS F 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 849 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.823A pdb=" N LEU A 542 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 565 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 593 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 616 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 662 through 664 removed outlier: 5.632A pdb=" N LEU A 663 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 688 " --> pdb=" O TYR A 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 757 removed outlier: 6.695A pdb=" N LEU A 757 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 803 " --> pdb=" O LYS A 825 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.735A pdb=" N GLN B 472 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU B 498 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 495 " --> pdb=" O HIS B 519 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N CYS B 521 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 497 " --> pdb=" O CYS B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 592 through 595 removed outlier: 6.113A pdb=" N LEU B 593 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 616 " --> pdb=" O GLU B 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 687 through 688 removed outlier: 3.524A pdb=" N LEU B 688 " --> pdb=" O SER B 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 removed outlier: 7.594A pdb=" N VAL B 736 " --> pdb=" O THR B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 779 through 781 removed outlier: 5.979A pdb=" N LEU B 780 " --> pdb=" O GLU B 804 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 803 " --> pdb=" O LYS B 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 56 removed outlier: 3.744A pdb=" N GLU C 353 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 471 through 473 removed outlier: 6.621A pdb=" N GLN C 472 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU C 498 " --> pdb=" O GLN C 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 541 through 543 removed outlier: 6.510A pdb=" N LEU C 542 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 565 " --> pdb=" O HIS C 594 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 593 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 616 " --> pdb=" O GLU C 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 759 through 760 removed outlier: 6.763A pdb=" N ILE C 759 " --> pdb=" O GLY C 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB8, first strand: chain 'D' and resid 471 through 472 Processing sheet with id=AB9, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.823A pdb=" N LEU D 542 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU D 565 " --> pdb=" O HIS D 594 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU D 593 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 616 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 662 through 664 removed outlier: 5.632A pdb=" N LEU D 663 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU D 688 " --> pdb=" O TYR D 712 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 756 through 757 removed outlier: 6.695A pdb=" N LEU D 757 " --> pdb=" O ASN D 781 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 803 " --> pdb=" O LYS D 825 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'E' and resid 471 through 472 removed outlier: 6.735A pdb=" N GLN E 472 " --> pdb=" O LYS E 496 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU E 498 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU E 495 " --> pdb=" O HIS E 519 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N CYS E 521 " --> pdb=" O LEU E 495 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 497 " --> pdb=" O CYS E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 592 through 595 removed outlier: 6.113A pdb=" N LEU E 593 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU E 616 " --> pdb=" O GLU E 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 687 through 688 removed outlier: 3.525A pdb=" N LEU E 688 " --> pdb=" O SER E 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 736 through 737 removed outlier: 7.594A pdb=" N VAL E 736 " --> pdb=" O THR E 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 779 through 781 removed outlier: 5.979A pdb=" N LEU E 780 " --> pdb=" O GLU E 804 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU E 803 " --> pdb=" O LYS E 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 52 through 56 removed outlier: 3.744A pdb=" N GLU F 353 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 471 through 473 removed outlier: 6.622A pdb=" N GLN F 472 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU F 498 " --> pdb=" O GLN F 472 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 541 through 543 removed outlier: 6.509A pdb=" N LEU F 542 " --> pdb=" O TYR F 566 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU F 565 " --> pdb=" O HIS F 594 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 593 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU F 616 " --> pdb=" O GLU F 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 759 through 760 removed outlier: 6.763A pdb=" N ILE F 759 " --> pdb=" O GLY F 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 1182 hydrogen bonds defined for protein. 3330 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: 6.36 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9364 1.33 - 1.45: 5915 1.45 - 1.57: 19845 1.57 - 1.69: 2 1.69 - 1.81: 306 Bond restraints: 35432 Sorted by residual: bond pdb=" CA LEU D 782 " pdb=" CB LEU D 782 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.53e-02 4.27e+03 5.81e+00 bond pdb=" CA LEU A 782 " pdb=" CB LEU A 782 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.53e-02 4.27e+03 5.81e+00 bond pdb=" C LYS A 185 " pdb=" N TYR A 186 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.93e+00 bond pdb=" C LYS D 185 " pdb=" N TYR D 186 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.93e+00 bond pdb=" CB PHE E 294 " pdb=" CG PHE E 294 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.71e+00 ... (remaining 35427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 46569 3.13 - 6.27: 1162 6.27 - 9.40: 227 9.40 - 12.54: 34 12.54 - 15.67: 26 Bond angle restraints: 48018 Sorted by residual: angle pdb=" N THR F 686 " pdb=" CA THR F 686 " pdb=" C THR F 686 " ideal model delta sigma weight residual 114.56 108.46 6.10 1.27e+00 6.20e-01 2.31e+01 angle pdb=" N THR C 686 " pdb=" CA THR C 686 " pdb=" C THR C 686 " ideal model delta sigma weight residual 114.56 108.52 6.04 1.27e+00 6.20e-01 2.26e+01 angle pdb=" C PHE E 352 " pdb=" N GLU E 353 " pdb=" CA GLU E 353 " ideal model delta sigma weight residual 121.85 113.59 8.26 1.77e+00 3.19e-01 2.18e+01 angle pdb=" C PHE B 352 " pdb=" N GLU B 353 " pdb=" CA GLU B 353 " ideal model delta sigma weight residual 121.85 113.59 8.26 1.77e+00 3.19e-01 2.18e+01 angle pdb=" CA TYR F 30 " pdb=" CB TYR F 30 " pdb=" CG TYR F 30 " ideal model delta sigma weight residual 113.90 122.05 -8.15 1.80e+00 3.09e-01 2.05e+01 ... (remaining 48013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 19005 15.78 - 31.56: 1914 31.56 - 47.34: 473 47.34 - 63.13: 36 63.13 - 78.91: 28 Dihedral angle restraints: 21456 sinusoidal: 8712 harmonic: 12744 Sorted by residual: dihedral pdb=" CA PHE B 182 " pdb=" C PHE B 182 " pdb=" N TRP B 183 " pdb=" CA TRP B 183 " ideal model delta harmonic sigma weight residual 180.00 143.88 36.12 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA PHE E 182 " pdb=" C PHE E 182 " pdb=" N TRP E 183 " pdb=" CA TRP E 183 " ideal model delta harmonic sigma weight residual 180.00 143.90 36.10 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA LYS F 504 " pdb=" C LYS F 504 " pdb=" N ILE F 505 " pdb=" CA ILE F 505 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.50e+01 ... (remaining 21453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4800 0.088 - 0.177: 736 0.177 - 0.265: 70 0.265 - 0.353: 6 0.353 - 0.441: 8 Chirality restraints: 5620 Sorted by residual: chirality pdb=" CB ILE D 759 " pdb=" CA ILE D 759 " pdb=" CG1 ILE D 759 " pdb=" CG2 ILE D 759 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE E 746 " pdb=" CA ILE E 746 " pdb=" CG1 ILE E 746 " pdb=" CG2 ILE E 746 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.31e+00 ... (remaining 5617 not shown) Planarity restraints: 5960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 500 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO F 501 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO F 501 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 501 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 500 " 0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO C 501 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 501 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 501 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 505 " 0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO C 506 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 506 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 506 " 0.048 5.00e-02 4.00e+02 ... (remaining 5957 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6737 2.78 - 3.31: 34116 3.31 - 3.84: 59340 3.84 - 4.37: 66372 4.37 - 4.90: 108567 Nonbonded interactions: 275132 Sorted by model distance: nonbonded pdb=" O LEU C 803 " pdb=" OG SER C 826 " model vdw 2.245 3.040 nonbonded pdb=" O LEU F 803 " pdb=" OG SER F 826 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR D 17 " pdb=" OE1 GLU D 194 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 17 " pdb=" OE1 GLU A 194 " model vdw 2.281 3.040 nonbonded pdb=" O MET A 177 " pdb=" OG SER A 180 " model vdw 2.288 3.040 ... (remaining 275127 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 58 or resid 135 through 850)) selection = (chain 'B' and (resid 2 through 58 or resid 135 through 850)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 58 or resid 135 through 850)) selection = (chain 'E' and (resid 2 through 58 or resid 135 through 850)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.450 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.006 0.078 35438 Z= 0.271 Angle : 1.279 15.669 48030 Z= 0.639 Chirality : 0.065 0.441 5620 Planarity : 0.008 0.090 5960 Dihedral : 13.634 78.907 13090 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.51 % Favored : 87.49 % Rotamer: Outliers : 1.93 % Allowed : 9.50 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.02 (0.10), residues: 4246 helix: -2.94 (0.09), residues: 1768 sheet: -3.15 (0.27), residues: 262 loop : -3.79 (0.10), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 433 TYR 0.031 0.004 TYR C 146 PHE 0.048 0.003 PHE B 182 TRP 0.045 0.004 TRP A 208 HIS 0.019 0.003 HIS E 543 Details of bonding type rmsd covalent geometry : bond 0.00587 (35432) covalent geometry : angle 1.27932 (48018) SS BOND : bond 0.01404 ( 6) SS BOND : angle 0.51523 ( 12) hydrogen bonds : bond 0.14096 ( 1182) hydrogen bonds : angle 7.06584 ( 3330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 815 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.8782 (t) cc_final: 0.8361 (p) REVERT: A 28 MET cc_start: 0.8564 (mtt) cc_final: 0.8288 (mtt) REVERT: A 329 PHE cc_start: 0.8290 (p90) cc_final: 0.8014 (p90) REVERT: A 358 MET cc_start: 0.8090 (mmt) cc_final: 0.7866 (mmm) REVERT: A 420 LEU cc_start: 0.8741 (tp) cc_final: 0.8527 (tp) REVERT: A 478 MET cc_start: 0.6139 (tpt) cc_final: 0.5526 (tpp) REVERT: A 480 SER cc_start: 0.8200 (p) cc_final: 0.7940 (t) REVERT: A 628 LEU cc_start: 0.7572 (mm) cc_final: 0.6958 (pp) REVERT: A 632 LYS cc_start: 0.7934 (pttp) cc_final: 0.7622 (mmtt) REVERT: A 743 MET cc_start: 0.5606 (tpt) cc_final: 0.5312 (mtp) REVERT: B 152 MET cc_start: 0.8203 (tpp) cc_final: 0.7931 (tpp) REVERT: B 171 ILE cc_start: 0.9088 (mm) cc_final: 0.8811 (mm) REVERT: B 184 PHE cc_start: 0.7718 (t80) cc_final: 0.7468 (t80) REVERT: B 351 VAL cc_start: 0.8425 (t) cc_final: 0.7971 (p) REVERT: B 367 ILE cc_start: 0.9204 (pt) cc_final: 0.8980 (tt) REVERT: B 542 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6797 (pt) REVERT: B 558 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7692 (pt) REVERT: B 568 ILE cc_start: 0.8514 (pp) cc_final: 0.7775 (pt) REVERT: B 617 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 152 MET cc_start: 0.8584 (tpp) cc_final: 0.8264 (tpp) REVERT: C 453 HIS cc_start: 0.8426 (t70) cc_final: 0.8060 (m170) REVERT: C 458 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8204 (tm-30) REVERT: C 462 GLN cc_start: 0.8745 (mp10) cc_final: 0.8379 (mp10) REVERT: C 464 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6786 (mp) REVERT: C 511 GLN cc_start: 0.8380 (pt0) cc_final: 0.7820 (tm-30) REVERT: C 567 LEU cc_start: 0.9342 (tm) cc_final: 0.9097 (tt) REVERT: C 665 LEU cc_start: 0.2226 (OUTLIER) cc_final: 0.1997 (pt) REVERT: C 782 LEU cc_start: 0.7516 (pp) cc_final: 0.7239 (mp) REVERT: D 26 VAL cc_start: 0.8784 (t) cc_final: 0.8373 (p) REVERT: D 28 MET cc_start: 0.8572 (mtt) cc_final: 0.8282 (mtt) REVERT: D 329 PHE cc_start: 0.8290 (p90) cc_final: 0.8016 (p90) REVERT: D 358 MET cc_start: 0.8103 (mmt) cc_final: 0.7879 (mmm) REVERT: D 420 LEU cc_start: 0.8740 (tp) cc_final: 0.8516 (tp) REVERT: D 478 MET cc_start: 0.6152 (tpt) cc_final: 0.5535 (tpp) REVERT: D 480 SER cc_start: 0.8186 (p) cc_final: 0.7946 (t) REVERT: D 628 LEU cc_start: 0.7563 (mm) cc_final: 0.6957 (pp) REVERT: D 632 LYS cc_start: 0.7884 (pttp) cc_final: 0.7553 (mmtt) REVERT: D 743 MET cc_start: 0.5603 (tpt) cc_final: 0.5305 (mtp) REVERT: E 152 MET cc_start: 0.8209 (tpp) cc_final: 0.7937 (tpp) REVERT: E 171 ILE cc_start: 0.9088 (mm) cc_final: 0.8813 (mm) REVERT: E 184 PHE cc_start: 0.7719 (t80) cc_final: 0.7475 (t80) REVERT: E 351 VAL cc_start: 0.8429 (t) cc_final: 0.7981 (p) REVERT: E 367 ILE cc_start: 0.9201 (pt) cc_final: 0.8975 (tt) REVERT: E 542 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6789 (pt) REVERT: E 558 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7691 (pt) REVERT: E 568 ILE cc_start: 0.8512 (pp) cc_final: 0.7777 (pt) REVERT: E 617 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.7752 (p) REVERT: F 152 MET cc_start: 0.8591 (tpp) cc_final: 0.8255 (tpp) REVERT: F 453 HIS cc_start: 0.8424 (t70) cc_final: 0.8056 (m170) REVERT: F 464 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6392 (mp) REVERT: F 491 ASP cc_start: 0.7815 (p0) cc_final: 0.7275 (p0) REVERT: F 511 GLN cc_start: 0.8380 (pt0) cc_final: 0.7815 (tm-30) REVERT: F 567 LEU cc_start: 0.9343 (tm) cc_final: 0.9097 (tt) REVERT: F 665 LEU cc_start: 0.2154 (OUTLIER) cc_final: 0.1946 (pt) REVERT: F 782 LEU cc_start: 0.7518 (pp) cc_final: 0.7239 (mp) outliers start: 76 outliers final: 12 residues processed: 883 average time/residue: 0.1835 time to fit residues: 264.0985 Evaluate side-chains 478 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 456 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 283 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN B 605 ASN ** B 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN B 692 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 337 HIS C 463 HIS ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 HIS ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS D 195 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 715 ASN D 755 GLN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS E 283 GLN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 HIS ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 ASN E 605 ASN ** E 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN E 692 HIS E 752 GLN ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 337 HIS F 463 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 612 HIS ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN F 784 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.114120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089085 restraints weight = 117536.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088531 restraints weight = 85186.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088505 restraints weight = 67147.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088847 restraints weight = 60025.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089010 restraints weight = 54013.397| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 35438 Z= 0.280 Angle : 0.921 11.465 48030 Z= 0.474 Chirality : 0.051 0.238 5620 Planarity : 0.006 0.072 5960 Dihedral : 7.748 33.205 4522 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.61 % Favored : 88.34 % Rotamer: Outliers : 0.46 % Allowed : 9.27 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.11), residues: 4246 helix: -1.88 (0.11), residues: 1786 sheet: -2.83 (0.29), residues: 270 loop : -3.44 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 295 TYR 0.038 0.003 TYR F 30 PHE 0.036 0.003 PHE E 321 TRP 0.034 0.003 TRP D 208 HIS 0.013 0.002 HIS D 758 Details of bonding type rmsd covalent geometry : bond 0.00618 (35432) covalent geometry : angle 0.92118 (48018) SS BOND : bond 0.01623 ( 6) SS BOND : angle 1.51574 ( 12) hydrogen bonds : bond 0.06341 ( 1182) hydrogen bonds : angle 5.88054 ( 3330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 541 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6690 (pp30) cc_final: 0.6380 (pp30) REVERT: A 28 MET cc_start: 0.8256 (mtt) cc_final: 0.8019 (mtt) REVERT: A 35 MET cc_start: 0.8910 (tmm) cc_final: 0.8660 (tmm) REVERT: A 37 MET cc_start: 0.8491 (tmm) cc_final: 0.8172 (tmm) REVERT: A 325 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.5391 (m-10) REVERT: A 329 PHE cc_start: 0.8528 (p90) cc_final: 0.8014 (p90) REVERT: A 353 GLU cc_start: 0.8277 (pp20) cc_final: 0.7964 (pp20) REVERT: A 420 LEU cc_start: 0.9103 (tp) cc_final: 0.8751 (tp) REVERT: A 446 LEU cc_start: 0.9073 (mt) cc_final: 0.8869 (mt) REVERT: A 529 GLN cc_start: 0.7912 (mm-40) cc_final: 0.6708 (pm20) REVERT: A 564 GLU cc_start: 0.4628 (pm20) cc_final: 0.4422 (pm20) REVERT: A 628 LEU cc_start: 0.7664 (mm) cc_final: 0.6965 (pp) REVERT: A 635 MET cc_start: 0.7896 (mtp) cc_final: 0.7312 (tpp) REVERT: A 642 LEU cc_start: 0.6406 (mp) cc_final: 0.6094 (pp) REVERT: A 717 LYS cc_start: 0.7849 (pttm) cc_final: 0.7572 (mmtm) REVERT: A 743 MET cc_start: 0.4697 (tpt) cc_final: 0.4415 (mtp) REVERT: A 832 ASP cc_start: 0.8335 (m-30) cc_final: 0.7933 (t0) REVERT: B 28 MET cc_start: 0.8016 (mmp) cc_final: 0.7814 (mmt) REVERT: B 35 MET cc_start: 0.8530 (tmm) cc_final: 0.8285 (tmm) REVERT: B 40 ILE cc_start: 0.9538 (tp) cc_final: 0.9327 (tt) REVERT: B 173 THR cc_start: 0.8858 (m) cc_final: 0.8174 (m) REVERT: B 204 PHE cc_start: 0.8457 (t80) cc_final: 0.8240 (t80) REVERT: B 418 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: B 471 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8116 (ptmt) REVERT: B 478 MET cc_start: 0.8134 (tpt) cc_final: 0.7316 (tpt) REVERT: B 499 LEU cc_start: 0.9130 (mm) cc_final: 0.8929 (mt) REVERT: B 545 LYS cc_start: 0.8761 (ptmt) cc_final: 0.8523 (ptmt) REVERT: B 657 LEU cc_start: 0.4191 (OUTLIER) cc_final: 0.3710 (pp) REVERT: C 26 VAL cc_start: 0.9587 (t) cc_final: 0.9383 (p) REVERT: C 152 MET cc_start: 0.9064 (tpp) cc_final: 0.8766 (tpp) REVERT: C 165 PHE cc_start: 0.8027 (t80) cc_final: 0.7815 (t80) REVERT: C 422 MET cc_start: 0.8917 (tmm) cc_final: 0.8601 (tmm) REVERT: C 453 HIS cc_start: 0.8597 (t70) cc_final: 0.8310 (m-70) REVERT: C 458 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8268 (tm-30) REVERT: C 478 MET cc_start: 0.8109 (tmm) cc_final: 0.7771 (tmm) REVERT: C 484 ASP cc_start: 0.8468 (m-30) cc_final: 0.7839 (m-30) REVERT: C 567 LEU cc_start: 0.9274 (tt) cc_final: 0.8977 (tt) REVERT: C 743 MET cc_start: 0.7925 (tmm) cc_final: 0.7435 (pmm) REVERT: C 782 LEU cc_start: 0.8079 (pp) cc_final: 0.7848 (mp) REVERT: C 822 MET cc_start: 0.4819 (ppp) cc_final: 0.4572 (ppp) REVERT: D 28 MET cc_start: 0.8206 (mtt) cc_final: 0.8002 (mtt) REVERT: D 35 MET cc_start: 0.8912 (tmm) cc_final: 0.8673 (tmm) REVERT: D 37 MET cc_start: 0.8483 (tmm) cc_final: 0.8166 (tmm) REVERT: D 185 LYS cc_start: 0.9351 (mmmt) cc_final: 0.8556 (pttp) REVERT: D 325 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5431 (m-10) REVERT: D 329 PHE cc_start: 0.8558 (p90) cc_final: 0.8029 (p90) REVERT: D 353 GLU cc_start: 0.8298 (pp20) cc_final: 0.7969 (pp20) REVERT: D 420 LEU cc_start: 0.9091 (tp) cc_final: 0.8749 (tp) REVERT: D 446 LEU cc_start: 0.9094 (mt) cc_final: 0.8881 (mt) REVERT: D 564 GLU cc_start: 0.4674 (pm20) cc_final: 0.4433 (pm20) REVERT: D 628 LEU cc_start: 0.7658 (mm) cc_final: 0.6958 (pp) REVERT: D 635 MET cc_start: 0.7892 (mtp) cc_final: 0.7314 (tpp) REVERT: D 642 LEU cc_start: 0.6404 (mp) cc_final: 0.6087 (pp) REVERT: D 717 LYS cc_start: 0.7862 (pttm) cc_final: 0.7584 (mmtm) REVERT: D 743 MET cc_start: 0.4666 (tpt) cc_final: 0.4411 (mtp) REVERT: D 832 ASP cc_start: 0.8345 (m-30) cc_final: 0.7933 (t0) REVERT: E 28 MET cc_start: 0.8022 (mmp) cc_final: 0.7821 (mmt) REVERT: E 35 MET cc_start: 0.8539 (tmm) cc_final: 0.8302 (tmm) REVERT: E 40 ILE cc_start: 0.9538 (tp) cc_final: 0.9330 (tt) REVERT: E 173 THR cc_start: 0.8857 (m) cc_final: 0.8176 (m) REVERT: E 204 PHE cc_start: 0.8505 (t80) cc_final: 0.8262 (t80) REVERT: E 418 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: E 471 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8139 (ptmt) REVERT: E 478 MET cc_start: 0.8157 (tpt) cc_final: 0.7341 (tpt) REVERT: E 499 LEU cc_start: 0.9154 (mm) cc_final: 0.8948 (mt) REVERT: E 511 GLN cc_start: 0.8915 (pt0) cc_final: 0.8696 (pp30) REVERT: E 512 MET cc_start: 0.6543 (mmm) cc_final: 0.6318 (tpp) REVERT: E 545 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8550 (ptmt) REVERT: E 657 LEU cc_start: 0.4152 (OUTLIER) cc_final: 0.3656 (pp) REVERT: E 717 LYS cc_start: 0.8922 (pttm) cc_final: 0.8568 (tppt) REVERT: F 152 MET cc_start: 0.9025 (tpp) cc_final: 0.8713 (tpp) REVERT: F 165 PHE cc_start: 0.8037 (t80) cc_final: 0.7829 (t80) REVERT: F 422 MET cc_start: 0.8912 (tmm) cc_final: 0.8592 (tmm) REVERT: F 453 HIS cc_start: 0.8604 (t70) cc_final: 0.8312 (m-70) REVERT: F 466 ARG cc_start: 0.8353 (mmt-90) cc_final: 0.8077 (mmm-85) REVERT: F 478 MET cc_start: 0.8100 (tmm) cc_final: 0.7771 (tmm) REVERT: F 484 ASP cc_start: 0.8492 (m-30) cc_final: 0.7861 (m-30) REVERT: F 567 LEU cc_start: 0.9330 (tt) cc_final: 0.9025 (tt) REVERT: F 634 MET cc_start: 0.8499 (mtm) cc_final: 0.8256 (mtt) REVERT: F 743 MET cc_start: 0.7931 (tmm) cc_final: 0.7450 (pmm) REVERT: F 782 LEU cc_start: 0.8084 (pp) cc_final: 0.7867 (mp) outliers start: 18 outliers final: 8 residues processed: 555 average time/residue: 0.1884 time to fit residues: 172.0072 Evaluate side-chains 397 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 383 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 389 optimal weight: 0.2980 chunk 205 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 241 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 576 ASN A 598 ASN A 715 ASN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 576 ASN D 598 ASN D 715 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.116830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090444 restraints weight = 116468.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091721 restraints weight = 75177.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092171 restraints weight = 47976.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092387 restraints weight = 42265.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.092674 restraints weight = 38905.907| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 35438 Z= 0.175 Angle : 0.829 12.794 48030 Z= 0.413 Chirality : 0.048 0.209 5620 Planarity : 0.005 0.060 5960 Dihedral : 7.142 31.111 4522 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.60 (0.12), residues: 4246 helix: -1.42 (0.11), residues: 1820 sheet: -2.59 (0.33), residues: 230 loop : -3.32 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 295 TYR 0.033 0.002 TYR F 30 PHE 0.026 0.002 PHE D 321 TRP 0.025 0.002 TRP A 208 HIS 0.011 0.002 HIS D 758 Details of bonding type rmsd covalent geometry : bond 0.00392 (35432) covalent geometry : angle 0.82861 (48018) SS BOND : bond 0.02082 ( 6) SS BOND : angle 1.20586 ( 12) hydrogen bonds : bond 0.05524 ( 1182) hydrogen bonds : angle 5.52860 ( 3330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 515 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6705 (pp30) cc_final: 0.6316 (pp30) REVERT: A 19 ILE cc_start: 0.8696 (tp) cc_final: 0.8199 (mm) REVERT: A 185 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8629 (pttp) REVERT: A 420 LEU cc_start: 0.9153 (tp) cc_final: 0.8806 (tp) REVERT: A 446 LEU cc_start: 0.8965 (mt) cc_final: 0.8712 (mt) REVERT: A 512 MET cc_start: 0.6550 (mmm) cc_final: 0.5742 (tpp) REVERT: A 529 GLN cc_start: 0.7781 (mm-40) cc_final: 0.6663 (pm20) REVERT: A 543 HIS cc_start: 0.7882 (m170) cc_final: 0.7632 (m-70) REVERT: A 575 ASN cc_start: 0.7578 (m-40) cc_final: 0.7198 (p0) REVERT: A 628 LEU cc_start: 0.7564 (mm) cc_final: 0.6879 (pp) REVERT: A 642 LEU cc_start: 0.6641 (mp) cc_final: 0.6366 (pp) REVERT: A 717 LYS cc_start: 0.7898 (pttm) cc_final: 0.7647 (mmtm) REVERT: A 743 MET cc_start: 0.4631 (tpt) cc_final: 0.4376 (ttp) REVERT: A 832 ASP cc_start: 0.8289 (m-30) cc_final: 0.7889 (t0) REVERT: B 28 MET cc_start: 0.8016 (mmp) cc_final: 0.7772 (mmp) REVERT: B 35 MET cc_start: 0.8522 (tmm) cc_final: 0.8286 (tmm) REVERT: B 37 MET cc_start: 0.8624 (tpp) cc_final: 0.8321 (tpp) REVERT: B 289 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8104 (mm-30) REVERT: B 340 LYS cc_start: 0.8569 (mmmt) cc_final: 0.7477 (mmmm) REVERT: B 422 MET cc_start: 0.8661 (tmm) cc_final: 0.8453 (tmm) REVERT: B 471 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7888 (pttm) REVERT: B 478 MET cc_start: 0.7456 (tpt) cc_final: 0.7061 (tpt) REVERT: B 499 LEU cc_start: 0.9203 (mm) cc_final: 0.8915 (mt) REVERT: B 512 MET cc_start: 0.6776 (tpt) cc_final: 0.6273 (tpp) REVERT: B 545 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8508 (ptmt) REVERT: C 453 HIS cc_start: 0.8515 (t70) cc_final: 0.8182 (m90) REVERT: C 458 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8203 (tm-30) REVERT: C 478 MET cc_start: 0.8106 (tmm) cc_final: 0.7788 (tmm) REVERT: C 484 ASP cc_start: 0.8356 (m-30) cc_final: 0.7709 (m-30) REVERT: C 512 MET cc_start: 0.5947 (mpp) cc_final: 0.5472 (mpp) REVERT: C 567 LEU cc_start: 0.9360 (tt) cc_final: 0.9098 (tt) REVERT: C 743 MET cc_start: 0.7698 (tmm) cc_final: 0.7443 (pmm) REVERT: C 782 LEU cc_start: 0.8186 (pp) cc_final: 0.7964 (mp) REVERT: D 14 GLN cc_start: 0.6972 (pp30) cc_final: 0.6737 (pp30) REVERT: D 19 ILE cc_start: 0.8650 (tp) cc_final: 0.8166 (mm) REVERT: D 185 LYS cc_start: 0.9345 (mmmt) cc_final: 0.8611 (pttp) REVERT: D 329 PHE cc_start: 0.8436 (p90) cc_final: 0.8223 (p90) REVERT: D 420 LEU cc_start: 0.9151 (tp) cc_final: 0.8801 (tp) REVERT: D 446 LEU cc_start: 0.8981 (mt) cc_final: 0.8721 (mt) REVERT: D 512 MET cc_start: 0.6536 (mmm) cc_final: 0.5724 (tpp) REVERT: D 543 HIS cc_start: 0.7851 (m170) cc_final: 0.7600 (m-70) REVERT: D 628 LEU cc_start: 0.7550 (mm) cc_final: 0.6862 (pp) REVERT: D 642 LEU cc_start: 0.6627 (mp) cc_final: 0.6356 (pp) REVERT: D 717 LYS cc_start: 0.7892 (pttm) cc_final: 0.7646 (mmtm) REVERT: D 743 MET cc_start: 0.4669 (tpt) cc_final: 0.4388 (mtp) REVERT: D 832 ASP cc_start: 0.8285 (m-30) cc_final: 0.7889 (t0) REVERT: E 28 MET cc_start: 0.7929 (mmp) cc_final: 0.7690 (mmp) REVERT: E 35 MET cc_start: 0.8462 (tmm) cc_final: 0.8233 (tmm) REVERT: E 37 MET cc_start: 0.8674 (tpp) cc_final: 0.8373 (tpp) REVERT: E 289 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8106 (mm-30) REVERT: E 340 LYS cc_start: 0.8640 (mmmt) cc_final: 0.7454 (mmmm) REVERT: E 471 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7897 (pttm) REVERT: E 478 MET cc_start: 0.7480 (tpt) cc_final: 0.7085 (tpt) REVERT: E 499 LEU cc_start: 0.9223 (mm) cc_final: 0.8932 (mt) REVERT: E 545 LYS cc_start: 0.8786 (ptmt) cc_final: 0.8530 (ptmt) REVERT: E 717 LYS cc_start: 0.9128 (pttm) cc_final: 0.8768 (tppt) REVERT: F 453 HIS cc_start: 0.8571 (t70) cc_final: 0.8207 (m90) REVERT: F 466 ARG cc_start: 0.8383 (mmt-90) cc_final: 0.8041 (mmm-85) REVERT: F 478 MET cc_start: 0.8113 (tmm) cc_final: 0.7807 (tmm) REVERT: F 484 ASP cc_start: 0.8337 (m-30) cc_final: 0.7694 (m-30) REVERT: F 567 LEU cc_start: 0.9393 (tt) cc_final: 0.9127 (tt) REVERT: F 634 MET cc_start: 0.8551 (mtm) cc_final: 0.8016 (mtt) REVERT: F 743 MET cc_start: 0.7702 (tmm) cc_final: 0.7464 (pmm) outliers start: 5 outliers final: 0 residues processed: 520 average time/residue: 0.1804 time to fit residues: 157.3399 Evaluate side-chains 380 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 387 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 319 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 20.0000 chunk 332 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 576 ASN A 715 ASN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN ** B 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 HIS ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 HIS ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 576 ASN D 715 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 HIS ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 681 HIS ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 ASN F 612 HIS ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.115126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087819 restraints weight = 118368.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.089887 restraints weight = 76699.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090286 restraints weight = 50430.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090634 restraints weight = 40893.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090931 restraints weight = 40384.970| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35438 Z= 0.208 Angle : 0.842 16.238 48030 Z= 0.418 Chirality : 0.049 0.251 5620 Planarity : 0.005 0.057 5960 Dihedral : 6.951 31.098 4522 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 0.13 % Allowed : 7.33 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.12), residues: 4246 helix: -1.19 (0.12), residues: 1810 sheet: -2.33 (0.37), residues: 176 loop : -3.30 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 433 TYR 0.036 0.002 TYR C 30 PHE 0.038 0.002 PHE B 182 TRP 0.032 0.002 TRP E 23 HIS 0.013 0.002 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00468 (35432) covalent geometry : angle 0.84152 (48018) SS BOND : bond 0.01420 ( 6) SS BOND : angle 1.47024 ( 12) hydrogen bonds : bond 0.05522 ( 1182) hydrogen bonds : angle 5.50550 ( 3330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 496 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.6955 (pp30) cc_final: 0.6416 (pp30) REVERT: A 35 MET cc_start: 0.8966 (tmm) cc_final: 0.8692 (tmm) REVERT: A 37 MET cc_start: 0.8425 (tmm) cc_final: 0.8190 (tmm) REVERT: A 185 LYS cc_start: 0.9370 (mmmt) cc_final: 0.8720 (pttp) REVERT: A 329 PHE cc_start: 0.8504 (p90) cc_final: 0.8091 (p90) REVERT: A 420 LEU cc_start: 0.9155 (tp) cc_final: 0.8631 (tp) REVERT: A 512 MET cc_start: 0.6597 (mmm) cc_final: 0.5852 (tpp) REVERT: A 529 GLN cc_start: 0.7627 (mm-40) cc_final: 0.6586 (pm20) REVERT: A 543 HIS cc_start: 0.7948 (m170) cc_final: 0.7703 (m-70) REVERT: A 576 ASN cc_start: 0.5912 (m110) cc_final: 0.5386 (m-40) REVERT: A 628 LEU cc_start: 0.7650 (mm) cc_final: 0.6936 (pp) REVERT: A 642 LEU cc_start: 0.6723 (mp) cc_final: 0.6441 (pp) REVERT: A 717 LYS cc_start: 0.7939 (pttm) cc_final: 0.7649 (mmtm) REVERT: A 743 MET cc_start: 0.4756 (tpt) cc_final: 0.4495 (ttp) REVERT: A 832 ASP cc_start: 0.8088 (m-30) cc_final: 0.7702 (t0) REVERT: B 28 MET cc_start: 0.7980 (mmp) cc_final: 0.7718 (mmp) REVERT: B 37 MET cc_start: 0.8579 (tpp) cc_final: 0.8339 (tpp) REVERT: B 289 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8058 (mm-30) REVERT: B 471 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7835 (pttm) REVERT: B 478 MET cc_start: 0.7080 (tpt) cc_final: 0.6840 (tpt) REVERT: B 492 LEU cc_start: 0.8080 (mt) cc_final: 0.7827 (mt) REVERT: B 499 LEU cc_start: 0.9176 (mm) cc_final: 0.8925 (mt) REVERT: B 512 MET cc_start: 0.7291 (tpt) cc_final: 0.6696 (tpp) REVERT: B 545 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8501 (ptmt) REVERT: C 149 ILE cc_start: 0.9183 (mm) cc_final: 0.8884 (mm) REVERT: C 152 MET cc_start: 0.9011 (tpp) cc_final: 0.8769 (tpp) REVERT: C 453 HIS cc_start: 0.8493 (t70) cc_final: 0.8249 (m90) REVERT: C 478 MET cc_start: 0.8183 (tmm) cc_final: 0.7870 (tmm) REVERT: C 567 LEU cc_start: 0.9311 (tt) cc_final: 0.9035 (tt) REVERT: C 634 MET cc_start: 0.8114 (mtt) cc_final: 0.7400 (mtt) REVERT: C 743 MET cc_start: 0.7842 (tmm) cc_final: 0.7375 (pmm) REVERT: D 14 GLN cc_start: 0.6936 (pp30) cc_final: 0.6613 (pp30) REVERT: D 19 ILE cc_start: 0.8845 (tp) cc_final: 0.8519 (mm) REVERT: D 35 MET cc_start: 0.8948 (tmm) cc_final: 0.8683 (tmm) REVERT: D 37 MET cc_start: 0.8433 (tmm) cc_final: 0.8182 (tmm) REVERT: D 185 LYS cc_start: 0.9366 (mmmt) cc_final: 0.8708 (pttp) REVERT: D 329 PHE cc_start: 0.8509 (p90) cc_final: 0.8299 (p90) REVERT: D 420 LEU cc_start: 0.9161 (tp) cc_final: 0.8638 (tp) REVERT: D 512 MET cc_start: 0.6619 (mmm) cc_final: 0.5863 (tpp) REVERT: D 543 HIS cc_start: 0.7901 (m170) cc_final: 0.7667 (m-70) REVERT: D 628 LEU cc_start: 0.7641 (mm) cc_final: 0.6927 (pp) REVERT: D 642 LEU cc_start: 0.6728 (mp) cc_final: 0.6452 (pp) REVERT: D 717 LYS cc_start: 0.7950 (pttm) cc_final: 0.7642 (mmtm) REVERT: D 743 MET cc_start: 0.4692 (tpt) cc_final: 0.4435 (ttp) REVERT: D 832 ASP cc_start: 0.8083 (m-30) cc_final: 0.7704 (t0) REVERT: E 28 MET cc_start: 0.7975 (mmp) cc_final: 0.7715 (mmp) REVERT: E 37 MET cc_start: 0.8578 (tpp) cc_final: 0.8341 (tpp) REVERT: E 289 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8079 (mm-30) REVERT: E 471 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7880 (pttm) REVERT: E 478 MET cc_start: 0.7105 (tpt) cc_final: 0.6861 (tpt) REVERT: E 499 LEU cc_start: 0.9200 (mm) cc_final: 0.8948 (mt) REVERT: E 512 MET cc_start: 0.7160 (tpp) cc_final: 0.6536 (tpp) REVERT: E 545 LYS cc_start: 0.8746 (ptmt) cc_final: 0.8507 (ptmt) REVERT: F 149 ILE cc_start: 0.9171 (mm) cc_final: 0.8874 (mm) REVERT: F 152 MET cc_start: 0.8975 (tpp) cc_final: 0.8721 (tpp) REVERT: F 453 HIS cc_start: 0.8487 (t70) cc_final: 0.8247 (m90) REVERT: F 466 ARG cc_start: 0.8277 (mmt-90) cc_final: 0.8027 (tpm170) REVERT: F 478 MET cc_start: 0.8196 (tmm) cc_final: 0.7834 (tmm) REVERT: F 567 LEU cc_start: 0.9356 (tt) cc_final: 0.9081 (tt) REVERT: F 743 MET cc_start: 0.7808 (tmm) cc_final: 0.7402 (pmm) outliers start: 5 outliers final: 1 residues processed: 501 average time/residue: 0.1734 time to fit residues: 144.1946 Evaluate side-chains 358 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN B 785 ASN C 151 GLN C 561 ASN C 598 ASN C 612 HIS C 620 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 HIS ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 785 ASN F 151 GLN F 561 ASN ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.119209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092300 restraints weight = 116503.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.094099 restraints weight = 72115.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.094538 restraints weight = 46984.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095318 restraints weight = 37713.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095427 restraints weight = 32291.385| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35438 Z= 0.136 Angle : 0.790 14.697 48030 Z= 0.384 Chirality : 0.047 0.234 5620 Planarity : 0.005 0.051 5960 Dihedral : 6.484 28.094 4522 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.12), residues: 4246 helix: -0.89 (0.12), residues: 1826 sheet: -2.19 (0.35), residues: 196 loop : -3.22 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 292 TYR 0.024 0.002 TYR F 30 PHE 0.027 0.002 PHE D 321 TRP 0.028 0.002 TRP F 23 HIS 0.013 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00299 (35432) covalent geometry : angle 0.79023 (48018) SS BOND : bond 0.01198 ( 6) SS BOND : angle 1.22125 ( 12) hydrogen bonds : bond 0.04826 ( 1182) hydrogen bonds : angle 5.23962 ( 3330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 546 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7355 (pp30) cc_final: 0.6840 (pp30) REVERT: A 35 MET cc_start: 0.9038 (tmm) cc_final: 0.8746 (tmm) REVERT: A 185 LYS cc_start: 0.9348 (mmmt) cc_final: 0.8712 (pttp) REVERT: A 420 LEU cc_start: 0.9171 (tp) cc_final: 0.8542 (tp) REVERT: A 512 MET cc_start: 0.6876 (mmm) cc_final: 0.6053 (tpp) REVERT: A 529 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6619 (pm20) REVERT: A 628 LEU cc_start: 0.7513 (mm) cc_final: 0.6829 (pp) REVERT: A 743 MET cc_start: 0.4551 (tpt) cc_final: 0.4242 (ttp) REVERT: B 28 MET cc_start: 0.7877 (mmp) cc_final: 0.7535 (mmp) REVERT: B 152 MET cc_start: 0.8209 (tpp) cc_final: 0.7879 (tpp) REVERT: B 195 HIS cc_start: 0.7971 (t-90) cc_final: 0.7580 (t-90) REVERT: B 340 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8460 (mmmm) REVERT: B 373 ILE cc_start: 0.9468 (mm) cc_final: 0.9011 (tp) REVERT: B 471 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7749 (pttm) REVERT: B 478 MET cc_start: 0.6907 (tpt) cc_final: 0.6625 (tpt) REVERT: B 499 LEU cc_start: 0.9186 (mm) cc_final: 0.8961 (mt) REVERT: B 512 MET cc_start: 0.6921 (tpt) cc_final: 0.6573 (tpp) REVERT: B 545 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8533 (ptmt) REVERT: B 591 LYS cc_start: 0.7613 (mtpt) cc_final: 0.6652 (mppt) REVERT: C 149 ILE cc_start: 0.9017 (mm) cc_final: 0.8688 (mm) REVERT: C 205 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 358 MET cc_start: 0.7282 (mmt) cc_final: 0.7067 (mmt) REVERT: C 453 HIS cc_start: 0.8383 (t70) cc_final: 0.8161 (m90) REVERT: C 458 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7947 (tm-30) REVERT: C 478 MET cc_start: 0.8046 (tmm) cc_final: 0.7781 (tmm) REVERT: C 562 LEU cc_start: 0.8754 (mm) cc_final: 0.8104 (tp) REVERT: C 567 LEU cc_start: 0.9198 (tt) cc_final: 0.8978 (tt) REVERT: C 634 MET cc_start: 0.7976 (mtt) cc_final: 0.7220 (mtt) REVERT: C 743 MET cc_start: 0.7741 (tmm) cc_final: 0.7356 (pmm) REVERT: D 14 GLN cc_start: 0.7092 (pp30) cc_final: 0.6591 (pp30) REVERT: D 19 ILE cc_start: 0.8733 (tp) cc_final: 0.8333 (mm) REVERT: D 35 MET cc_start: 0.9022 (tmm) cc_final: 0.8762 (tmm) REVERT: D 185 LYS cc_start: 0.9335 (mmmt) cc_final: 0.8660 (pttp) REVERT: D 372 ILE cc_start: 0.8755 (mm) cc_final: 0.8550 (tt) REVERT: D 420 LEU cc_start: 0.9158 (tp) cc_final: 0.8562 (tp) REVERT: D 512 MET cc_start: 0.6801 (mmm) cc_final: 0.6051 (tpp) REVERT: D 628 LEU cc_start: 0.7514 (mm) cc_final: 0.6831 (pp) REVERT: D 743 MET cc_start: 0.4523 (tpt) cc_final: 0.4236 (ttp) REVERT: E 28 MET cc_start: 0.7867 (mmp) cc_final: 0.7548 (mmp) REVERT: E 152 MET cc_start: 0.8193 (tpp) cc_final: 0.7878 (tpp) REVERT: E 195 HIS cc_start: 0.7953 (t-90) cc_final: 0.7545 (t-90) REVERT: E 373 ILE cc_start: 0.9466 (mm) cc_final: 0.8999 (tp) REVERT: E 471 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7808 (pttm) REVERT: E 478 MET cc_start: 0.6951 (tpt) cc_final: 0.6668 (tpt) REVERT: E 499 LEU cc_start: 0.9204 (mm) cc_final: 0.8908 (mt) REVERT: E 512 MET cc_start: 0.7152 (tpp) cc_final: 0.6494 (tpp) REVERT: E 545 LYS cc_start: 0.8795 (ptmt) cc_final: 0.8531 (ptmt) REVERT: E 578 MET cc_start: 0.5112 (mpp) cc_final: 0.4528 (mpp) REVERT: F 44 THR cc_start: 0.9511 (t) cc_final: 0.9303 (t) REVERT: F 149 ILE cc_start: 0.9021 (mm) cc_final: 0.8696 (mm) REVERT: F 205 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7485 (mt-10) REVERT: F 453 HIS cc_start: 0.8369 (t70) cc_final: 0.8156 (m90) REVERT: F 466 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7933 (tpm170) REVERT: F 478 MET cc_start: 0.8057 (tmm) cc_final: 0.7780 (tmm) REVERT: F 562 LEU cc_start: 0.8764 (mm) cc_final: 0.8268 (mm) REVERT: F 567 LEU cc_start: 0.9232 (tt) cc_final: 0.9007 (tt) REVERT: F 743 MET cc_start: 0.7710 (tmm) cc_final: 0.7393 (pmm) outliers start: 3 outliers final: 0 residues processed: 549 average time/residue: 0.1797 time to fit residues: 166.3730 Evaluate side-chains 375 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 213 optimal weight: 1.9990 chunk 189 optimal weight: 0.0770 chunk 158 optimal weight: 0.9980 chunk 317 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN C 612 HIS C 620 ASN ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 HIS ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 GLN ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 GLN E 752 GLN ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 785 ASN ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.120521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092471 restraints weight = 116007.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094592 restraints weight = 68796.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095993 restraints weight = 45462.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.096966 restraints weight = 33434.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.097530 restraints weight = 26705.584| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35438 Z= 0.131 Angle : 0.777 15.541 48030 Z= 0.374 Chirality : 0.046 0.252 5620 Planarity : 0.004 0.052 5960 Dihedral : 6.191 27.321 4522 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.12), residues: 4246 helix: -0.71 (0.12), residues: 1818 sheet: -1.90 (0.37), residues: 176 loop : -3.18 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 821 TYR 0.020 0.002 TYR F 30 PHE 0.031 0.002 PHE E 182 TRP 0.023 0.002 TRP C 23 HIS 0.029 0.002 HIS D 543 Details of bonding type rmsd covalent geometry : bond 0.00283 (35432) covalent geometry : angle 0.77677 (48018) SS BOND : bond 0.01176 ( 6) SS BOND : angle 0.94914 ( 12) hydrogen bonds : bond 0.04539 ( 1182) hydrogen bonds : angle 5.09802 ( 3330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7120 (pp30) cc_final: 0.6622 (pp30) REVERT: A 19 ILE cc_start: 0.8633 (tp) cc_final: 0.8253 (mm) REVERT: A 28 MET cc_start: 0.8792 (mtm) cc_final: 0.8578 (ttm) REVERT: A 35 MET cc_start: 0.8972 (tmm) cc_final: 0.8632 (tmm) REVERT: A 185 LYS cc_start: 0.9306 (mmmt) cc_final: 0.8707 (pttp) REVERT: A 420 LEU cc_start: 0.9102 (tp) cc_final: 0.8561 (tp) REVERT: A 446 LEU cc_start: 0.8976 (mt) cc_final: 0.8760 (mt) REVERT: A 512 MET cc_start: 0.7421 (mmm) cc_final: 0.6709 (tpp) REVERT: A 529 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6567 (pm20) REVERT: A 628 LEU cc_start: 0.7391 (mm) cc_final: 0.6534 (pp) REVERT: A 632 LYS cc_start: 0.7509 (pttp) cc_final: 0.7302 (mmtt) REVERT: B 55 LEU cc_start: 0.8932 (pp) cc_final: 0.8635 (pp) REVERT: B 168 LEU cc_start: 0.9455 (pp) cc_final: 0.9191 (pp) REVERT: B 195 HIS cc_start: 0.8240 (t-90) cc_final: 0.7741 (t-90) REVERT: B 340 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8665 (mmmm) REVERT: B 373 ILE cc_start: 0.9429 (mm) cc_final: 0.8985 (tp) REVERT: B 471 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7701 (pttm) REVERT: B 545 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8423 (ptmt) REVERT: C 313 VAL cc_start: 0.9074 (t) cc_final: 0.8706 (p) REVERT: C 429 LEU cc_start: 0.7781 (tp) cc_final: 0.7459 (tp) REVERT: C 511 GLN cc_start: 0.8731 (pt0) cc_final: 0.8036 (tm-30) REVERT: C 634 MET cc_start: 0.7771 (mtt) cc_final: 0.7033 (mtt) REVERT: C 743 MET cc_start: 0.8009 (tmm) cc_final: 0.7571 (pmm) REVERT: D 14 GLN cc_start: 0.7381 (pp30) cc_final: 0.6718 (pp30) REVERT: D 19 ILE cc_start: 0.8667 (tp) cc_final: 0.8329 (mm) REVERT: D 28 MET cc_start: 0.8771 (mtm) cc_final: 0.8462 (mtt) REVERT: D 35 MET cc_start: 0.8971 (tmm) cc_final: 0.8544 (tmm) REVERT: D 185 LYS cc_start: 0.9284 (mmmt) cc_final: 0.8670 (pttp) REVERT: D 384 LEU cc_start: 0.8447 (mm) cc_final: 0.8233 (mm) REVERT: D 420 LEU cc_start: 0.9122 (tp) cc_final: 0.8544 (tp) REVERT: D 512 MET cc_start: 0.7415 (mmm) cc_final: 0.6755 (tpp) REVERT: D 628 LEU cc_start: 0.7317 (mm) cc_final: 0.6520 (pp) REVERT: E 168 LEU cc_start: 0.9442 (pp) cc_final: 0.9165 (pp) REVERT: E 195 HIS cc_start: 0.8244 (t-90) cc_final: 0.7741 (t-90) REVERT: E 373 ILE cc_start: 0.9430 (mm) cc_final: 0.8982 (tp) REVERT: E 471 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7747 (pttm) REVERT: E 512 MET cc_start: 0.7319 (tpp) cc_final: 0.6802 (tpp) REVERT: E 545 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8428 (ptmt) REVERT: E 578 MET cc_start: 0.5024 (mpp) cc_final: 0.4766 (mpp) REVERT: F 149 ILE cc_start: 0.9017 (mm) cc_final: 0.8796 (mm) REVERT: F 429 LEU cc_start: 0.7796 (tp) cc_final: 0.7462 (tp) REVERT: F 478 MET cc_start: 0.8024 (tmm) cc_final: 0.7743 (tmm) REVERT: F 511 GLN cc_start: 0.8749 (pt0) cc_final: 0.8049 (tm-30) REVERT: F 743 MET cc_start: 0.7968 (tmm) cc_final: 0.7586 (pmm) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1778 time to fit residues: 160.3587 Evaluate side-chains 379 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 270 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 366 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN ** C 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN D 715 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 472 GLN ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 GLN ** E 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 GLN ** E 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 ASN ** F 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 785 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.117229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.090261 restraints weight = 118474.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091314 restraints weight = 82304.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092476 restraints weight = 52383.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.092946 restraints weight = 39591.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093026 restraints weight = 36285.471| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35438 Z= 0.186 Angle : 0.827 15.956 48030 Z= 0.405 Chirality : 0.048 0.273 5620 Planarity : 0.005 0.049 5960 Dihedral : 6.311 28.144 4522 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.12), residues: 4246 helix: -0.81 (0.12), residues: 1838 sheet: -1.86 (0.37), residues: 176 loop : -3.17 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 433 TYR 0.029 0.002 TYR F 30 PHE 0.029 0.002 PHE E 329 TRP 0.027 0.002 TRP D 208 HIS 0.025 0.002 HIS A 543 Details of bonding type rmsd covalent geometry : bond 0.00423 (35432) covalent geometry : angle 0.82683 (48018) SS BOND : bond 0.01256 ( 6) SS BOND : angle 1.23419 ( 12) hydrogen bonds : bond 0.05144 ( 1182) hydrogen bonds : angle 5.25408 ( 3330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8492 Ramachandran restraints generated. 4246 Oldfield, 0 Emsley, 4246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7108 (pp30) cc_final: 0.6669 (pp30) REVERT: A 19 ILE cc_start: 0.8770 (tp) cc_final: 0.8523 (mm) REVERT: A 28 MET cc_start: 0.8805 (mtm) cc_final: 0.8431 (mtt) REVERT: A 185 LYS cc_start: 0.9344 (mmmt) cc_final: 0.8766 (pttp) REVERT: A 420 LEU cc_start: 0.9250 (tp) cc_final: 0.8620 (tp) REVERT: A 446 LEU cc_start: 0.9019 (mt) cc_final: 0.8719 (mt) REVERT: A 512 MET cc_start: 0.7787 (mmm) cc_final: 0.7012 (tpp) REVERT: A 628 LEU cc_start: 0.7472 (mm) cc_final: 0.6691 (pp) REVERT: B 340 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8680 (mmmm) REVERT: B 350 GLU cc_start: 0.6101 (pp20) cc_final: 0.5786 (tm-30) REVERT: B 471 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7788 (pttm) REVERT: B 545 LYS cc_start: 0.8795 (ptmt) cc_final: 0.8542 (ptmt) REVERT: C 149 ILE cc_start: 0.9169 (mm) cc_final: 0.8796 (tt) REVERT: C 371 SER cc_start: 0.8589 (m) cc_final: 0.8368 (p) REVERT: C 429 LEU cc_start: 0.7809 (tp) cc_final: 0.7539 (tp) REVERT: C 458 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8246 (tm-30) REVERT: C 473 GLU cc_start: 0.5928 (mt-10) cc_final: 0.5669 (mp0) REVERT: C 478 MET cc_start: 0.7486 (ppp) cc_final: 0.7249 (ppp) REVERT: C 542 LEU cc_start: 0.9452 (pp) cc_final: 0.9138 (pt) REVERT: C 567 LEU cc_start: 0.9381 (tt) cc_final: 0.9078 (tt) REVERT: C 634 MET cc_start: 0.7889 (mtt) cc_final: 0.7195 (mtt) REVERT: C 743 MET cc_start: 0.7790 (tmm) cc_final: 0.7494 (pmm) REVERT: D 14 GLN cc_start: 0.7370 (pp30) cc_final: 0.6723 (pp30) REVERT: D 19 ILE cc_start: 0.8711 (tp) cc_final: 0.8493 (mm) REVERT: D 28 MET cc_start: 0.8846 (mtm) cc_final: 0.8353 (mtt) REVERT: D 35 MET cc_start: 0.8923 (tmm) cc_final: 0.8633 (tmm) REVERT: D 185 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8737 (pttp) REVERT: D 420 LEU cc_start: 0.9232 (tp) cc_final: 0.8625 (tp) REVERT: D 512 MET cc_start: 0.7683 (mmm) cc_final: 0.6891 (tpp) REVERT: D 628 LEU cc_start: 0.7459 (mm) cc_final: 0.6679 (pp) REVERT: E 471 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7816 (pttm) REVERT: E 478 MET cc_start: 0.6746 (tpt) cc_final: 0.6544 (tpt) REVERT: E 512 MET cc_start: 0.7155 (tpp) cc_final: 0.6850 (tpp) REVERT: E 545 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8580 (ptmt) REVERT: E 578 MET cc_start: 0.5041 (mpp) cc_final: 0.4824 (mpp) REVERT: F 429 LEU cc_start: 0.7781 (tp) cc_final: 0.7522 (tp) REVERT: F 542 LEU cc_start: 0.9470 (pp) cc_final: 0.9163 (pt) REVERT: F 562 LEU cc_start: 0.8641 (mm) cc_final: 0.8358 (mm) REVERT: F 567 LEU cc_start: 0.9423 (tt) cc_final: 0.9133 (tt) REVERT: F 634 MET cc_start: 0.8290 (mtt) cc_final: 0.7853 (mtt) REVERT: F 743 MET cc_start: 0.7816 (tmm) cc_final: 0.7553 (pmm) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.1709 time to fit residues: 142.6920 Evaluate side-chains 372 residues out of total 3994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.427 > 50: distance: 45 - 50: 35.488 distance: 50 - 51: 50.184 distance: 51 - 52: 30.051 distance: 51 - 54: 52.770 distance: 52 - 53: 65.831 distance: 52 - 58: 6.587 distance: 54 - 55: 26.085 distance: 54 - 56: 10.431 distance: 55 - 57: 26.268 distance: 58 - 59: 40.295 distance: 59 - 60: 60.437 distance: 59 - 62: 42.360 distance: 60 - 61: 63.172 distance: 60 - 66: 8.192 distance: 62 - 63: 47.817 distance: 63 - 64: 45.559 distance: 63 - 65: 47.033 distance: 66 - 67: 44.872 distance: 66 - 72: 31.825 distance: 67 - 68: 24.523 distance: 67 - 70: 50.280 distance: 68 - 69: 39.892 distance: 68 - 73: 13.966 distance: 70 - 71: 48.355 distance: 71 - 72: 19.812 distance: 73 - 74: 40.100 distance: 74 - 75: 16.904 distance: 74 - 77: 47.083 distance: 75 - 76: 18.839 distance: 75 - 82: 37.052 distance: 77 - 78: 43.822 distance: 78 - 79: 27.310 distance: 79 - 80: 32.734 distance: 80 - 81: 39.429 distance: 82 - 83: 21.089 distance: 83 - 84: 17.715 distance: 83 - 86: 19.121 distance: 84 - 85: 24.017 distance: 84 - 91: 31.966 distance: 85 - 110: 31.187 distance: 86 - 87: 16.577 distance: 87 - 88: 12.216 distance: 88 - 89: 13.532 distance: 88 - 90: 19.993 distance: 91 - 92: 29.996 distance: 92 - 93: 26.714 distance: 92 - 95: 53.162 distance: 93 - 94: 5.533 distance: 93 - 99: 39.244 distance: 95 - 96: 26.866 distance: 96 - 97: 30.949 distance: 96 - 98: 3.516 distance: 99 - 100: 28.487 distance: 100 - 101: 48.127 distance: 100 - 103: 32.956 distance: 101 - 102: 41.782 distance: 101 - 110: 49.361 distance: 103 - 104: 7.009 distance: 104 - 105: 25.660 distance: 104 - 106: 16.556 distance: 105 - 107: 8.329 distance: 106 - 108: 11.629 distance: 107 - 109: 8.515 distance: 108 - 109: 10.715 distance: 110 - 111: 9.557 distance: 111 - 112: 36.929 distance: 111 - 114: 49.738 distance: 112 - 113: 35.087 distance: 112 - 119: 41.533 distance: 114 - 115: 44.645 distance: 115 - 116: 30.480 distance: 116 - 117: 27.431 distance: 117 - 118: 15.857 distance: 119 - 120: 21.945 distance: 120 - 121: 28.460 distance: 120 - 123: 25.311 distance: 121 - 122: 16.993 distance: 121 - 125: 29.059 distance: 123 - 124: 24.894 distance: 125 - 126: 14.985 distance: 126 - 127: 36.506 distance: 126 - 129: 38.060 distance: 127 - 128: 31.150 distance: 127 - 133: 11.161 distance: 129 - 130: 40.240 distance: 129 - 131: 39.221 distance: 130 - 132: 25.084