Starting phenix.real_space_refine on Sat Mar 7 00:40:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.map" model { file = "/net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uup_64514/03_2026/9uup_64514.cif" } resolution = 4.03 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= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 195 5.16 5 C 22257 2.51 5 N 5844 2.21 5 O 6470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34770 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 6942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6942 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'LLP:plan-1': 1, 'LLP:plan-2': 1, 'LLP:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.23, per 1000 atoms: 0.24 Number of scatterers: 34770 At special positions: 0 Unit cell: (99.6, 174.3, 201.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 195 16.00 P 4 15.00 O 6470 8.00 N 5844 7.00 C 22257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7950 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 39 sheets defined 50.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.157A pdb=" N ASP A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.768A pdb=" N TRP A 40 " --> pdb=" O TRP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.834A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 128 through 145 removed outlier: 3.685A pdb=" N ASP A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.949A pdb=" N THR A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 239 " --> pdb=" O PRO A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 removed outlier: 3.627A pdb=" N LEU A 250 " --> pdb=" O TRP A 246 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 299 through 309 removed outlier: 4.244A pdb=" N LEU A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.709A pdb=" N ARG A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.935A pdb=" N ASN A 404 " --> pdb=" O PRO A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.625A pdb=" N PHE A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET A 436 " --> pdb=" O LYS A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 436' Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.580A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 452 through 482 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.662A pdb=" N ARG A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 604 through 614 removed outlier: 4.057A pdb=" N GLU A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 613 " --> pdb=" O LLP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 645 through 664 Processing helix chain 'A' and resid 665 through 671 Processing helix chain 'A' and resid 678 through 691 removed outlier: 3.531A pdb=" N ILE A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 697 through 708 removed outlier: 3.706A pdb=" N GLN A 701 " --> pdb=" O THR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 741 removed outlier: 6.158A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 745 Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 26 through 35 removed outlier: 4.373A pdb=" N ASP B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.740A pdb=" N TRP B 40 " --> pdb=" O TRP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.813A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 129 through 145 removed outlier: 4.300A pdb=" N GLY B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.644A pdb=" N ILE B 237 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 238 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 239' Processing helix chain 'B' and resid 246 through 265 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.554A pdb=" N LEU B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.687A pdb=" N TRP B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.729A pdb=" N ILE B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 515 through 520 removed outlier: 4.138A pdb=" N LEU B 518 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 520 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 530 removed outlier: 3.633A pdb=" N LEU B 525 " --> pdb=" O ASP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 563 Processing helix chain 'B' and resid 578 through 589 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 645 through 664 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 678 through 692 Processing helix chain 'B' and resid 693 through 696 Processing helix chain 'B' and resid 697 through 709 Processing helix chain 'B' and resid 709 through 721 Processing helix chain 'B' and resid 721 through 741 removed outlier: 5.701A pdb=" N LEU B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 728 " --> pdb=" O ASP B 724 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 740 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG B 741 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.885A pdb=" N MET B 756 " --> pdb=" O CYS B 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 25 No H-bonds generated for 'chain 'C' and resid 23 through 25' Processing helix chain 'C' and resid 26 through 34 removed outlier: 4.103A pdb=" N ASP C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 40 removed outlier: 4.421A pdb=" N TRP C 38 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP C 40 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.620A pdb=" N ARG C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 128 through 145 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.820A pdb=" N THR C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 239 " --> pdb=" O PRO C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 267 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.817A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.819A pdb=" N ARG C 341 " --> pdb=" O GLY C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.981A pdb=" N GLY C 353 " --> pdb=" O PHE C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.593A pdb=" N TRP C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 452 through 482 Processing helix chain 'C' and resid 488 through 496 removed outlier: 3.562A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 520 removed outlier: 3.590A pdb=" N THR C 520 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 Processing helix chain 'C' and resid 549 through 563 Processing helix chain 'C' and resid 578 through 589 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.686A pdb=" N MET C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 629 Processing helix chain 'C' and resid 645 through 664 Processing helix chain 'C' and resid 664 through 670 Processing helix chain 'C' and resid 678 through 692 removed outlier: 3.505A pdb=" N ILE C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 Processing helix chain 'C' and resid 697 through 709 Processing helix chain 'C' and resid 709 through 745 removed outlier: 6.387A pdb=" N ASN C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP C 724 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 727 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 794 removed outlier: 3.563A pdb=" N GLY C 793 " --> pdb=" O PRO C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.508A pdb=" N ASP C 844 " --> pdb=" O HIS C 841 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 845 " --> pdb=" O ARG C 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 841 through 845' Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.507A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 3.715A pdb=" N TRP D 40 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.556A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.866A pdb=" N MET D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 4.545A pdb=" N TYR D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.733A pdb=" N ILE D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 Processing helix chain 'D' and resid 282 through 297 removed outlier: 4.028A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 327 through 336 removed outlier: 3.765A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.864A pdb=" N ARG D 341 " --> pdb=" O GLY D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.903A pdb=" N GLY D 353 " --> pdb=" O PHE D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 414 through 419 removed outlier: 3.549A pdb=" N TRP D 418 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 432 through 436 removed outlier: 4.469A pdb=" N MET D 436 " --> pdb=" O LYS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 482 Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 488 through 495 removed outlier: 3.794A pdb=" N ARG D 495 " --> pdb=" O SER D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.622A pdb=" N PHE D 519 " --> pdb=" O HIS D 516 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 520 " --> pdb=" O LEU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 520' Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 548 through 564 removed outlier: 3.524A pdb=" N ARG D 564 " --> pdb=" O GLU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.820A pdb=" N GLU D 611 " --> pdb=" O GLU D 608 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET D 612 " --> pdb=" O LLP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 629 removed outlier: 4.268A pdb=" N GLU D 627 " --> pdb=" O GLY D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 664 removed outlier: 3.550A pdb=" N GLN D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 671 Processing helix chain 'D' and resid 678 through 692 removed outlier: 3.524A pdb=" N ILE D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 697 through 709 removed outlier: 3.767A pdb=" N GLN D 701 " --> pdb=" O THR D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 721 Processing helix chain 'D' and resid 721 through 742 removed outlier: 5.981A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 757 removed outlier: 3.628A pdb=" N MET D 756 " --> pdb=" O ASP D 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 757 " --> pdb=" O CYS D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 752 through 757' Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 26 through 35 removed outlier: 4.062A pdb=" N ASP E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.648A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'E' and resid 81 through 101 removed outlier: 3.675A pdb=" N MET E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 142 Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 245 through 267 Processing helix chain 'E' and resid 282 through 297 removed outlier: 4.070A pdb=" N LEU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 310 removed outlier: 3.664A pdb=" N LEU E 306 " --> pdb=" O GLN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 345 through 353 Processing helix chain 'E' and resid 366 through 374 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 432 through 436 removed outlier: 4.385A pdb=" N MET E 436 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.618A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 452 through 482 removed outlier: 3.622A pdb=" N ILE E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 488 through 494 Processing helix chain 'E' and resid 516 through 520 Processing helix chain 'E' and resid 521 through 531 Processing helix chain 'E' and resid 548 through 564 removed outlier: 3.619A pdb=" N GLN E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 564 " --> pdb=" O GLU E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 589 Processing helix chain 'E' and resid 604 through 612 removed outlier: 4.518A pdb=" N GLU E 608 " --> pdb=" O GLY E 604 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET E 612 " --> pdb=" O GLU E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 629 Processing helix chain 'E' and resid 645 through 664 Processing helix chain 'E' and resid 664 through 670 Processing helix chain 'E' and resid 678 through 692 Processing helix chain 'E' and resid 693 through 696 Processing helix chain 'E' and resid 697 through 709 removed outlier: 3.977A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 742 removed outlier: 6.079A pdb=" N ASN E 723 " --> pdb=" O LYS E 719 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP E 724 " --> pdb=" O LEU E 720 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU E 727 " --> pdb=" O ASN E 723 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA E 728 " --> pdb=" O ASP E 724 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 9.104A pdb=" N SER B 825 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 788 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS B 787 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ALA B 798 " --> pdb=" O LYS B 787 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N GLN B 789 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL B 796 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 18 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 4.066A pdb=" N PHE A 113 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 153 removed outlier: 6.507A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 185 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 153 removed outlier: 6.507A pdb=" N ALA A 150 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N LEU A 223 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY A 152 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 571 through 573 removed outlier: 3.548A pdb=" N SER A 541 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 593 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 746 through 749 removed outlier: 4.378A pdb=" N VAL A 748 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N HIS A 807 " --> pdb=" O ASN A 811 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 813 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 800 through 801 Processing sheet with id=AB2, first strand: chain 'C' and resid 758 through 759 removed outlier: 3.993A pdb=" N ALA C 758 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 19 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 824 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 829 " --> pdb=" O VAL C 784 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 784 " --> pdb=" O GLY C 829 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 831 " --> pdb=" O GLU C 782 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 782 " --> pdb=" O ARG C 831 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS C 787 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL C 796 " --> pdb=" O LYS C 787 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 196 through 200 removed outlier: 3.597A pdb=" N LEU B 220 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET B 148 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR B 221 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY B 152 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B 274 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR B 314 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 276 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 377 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 574 removed outlier: 6.455A pdb=" N LEU B 501 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE B 539 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 503 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER B 541 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE B 505 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET B 593 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N CYS B 506 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TRP B 592 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL B 620 " --> pdb=" O TRP B 592 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN B 594 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 746 through 751 removed outlier: 3.566A pdb=" N HIS B 746 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 750 " --> pdb=" O GLN B 767 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN B 767 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 811 " --> pdb=" O HIS B 807 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS B 807 " --> pdb=" O ASN B 811 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR B 813 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 805 " --> pdb=" O THR B 813 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 14 through 17 removed outlier: 8.914A pdb=" N SER D 825 " --> pdb=" O GLU D 788 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 788 " --> pdb=" O SER D 825 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 831 " --> pdb=" O GLU D 782 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS D 787 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 796 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN D 789 " --> pdb=" O LYS D 794 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS D 794 " --> pdb=" O GLN D 789 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.597A pdb=" N MET D 832 " --> pdb=" O LYS D 849 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 849 " --> pdb=" O MET D 832 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AC1, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.685A pdb=" N TYR C 209 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 224 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 220 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET C 148 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N TYR C 221 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA C 150 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU C 223 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 152 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR C 274 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS C 276 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU C 376 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 378 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 377 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AC3, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AC4, first strand: chain 'C' and resid 572 through 574 removed outlier: 7.938A pdb=" N ILE C 572 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE C 538 " --> pdb=" O ILE C 572 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU C 574 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 540 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 501 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 539 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 503 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER C 541 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASN C 617 " --> pdb=" O TRP C 635 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU C 637 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER C 619 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 767 through 769 removed outlier: 6.970A pdb=" N ASN C 811 " --> pdb=" O HIS C 807 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS C 807 " --> pdb=" O ASN C 811 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR C 813 " --> pdb=" O VAL C 805 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 16 through 17 removed outlier: 8.260A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL E 785 " --> pdb=" O TYR E 800 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR E 800 " --> pdb=" O VAL E 785 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LYS E 787 " --> pdb=" O ALA E 798 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ALA E 798 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N GLN E 789 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N VAL E 796 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AC8, first strand: chain 'D' and resid 185 through 186 removed outlier: 6.946A pdb=" N MET D 148 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR D 221 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA D 150 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 223 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY D 152 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS D 149 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 111 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN D 277 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE D 113 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AD1, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AD2, first strand: chain 'D' and resid 571 through 574 removed outlier: 9.039A pdb=" N ILE D 572 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE D 538 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU D 574 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE D 540 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU D 501 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE D 539 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 503 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N SER D 541 " --> pdb=" O ILE D 503 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE D 505 " --> pdb=" O SER D 541 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N CYS D 506 " --> pdb=" O MET D 593 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 746 through 751 removed outlier: 3.781A pdb=" N HIS D 746 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 769 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS D 750 " --> pdb=" O GLN D 767 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN D 767 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY D 806 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU D 815 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N MET D 804 " --> pdb=" O GLU D 815 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 764 through 765 removed outlier: 3.654A pdb=" N ILE D 818 " --> pdb=" O ILE D 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 110 through 113 Processing sheet with id=AD6, first strand: chain 'E' and resid 150 through 153 removed outlier: 6.330A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 222 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AD8, first strand: chain 'E' and resid 199 through 201 Processing sheet with id=AD9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.789A pdb=" N TYR E 313 " --> pdb=" O ASN E 378 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE2, first strand: chain 'E' and resid 571 through 573 removed outlier: 6.553A pdb=" N LEU E 501 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE E 539 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 503 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER E 541 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE E 505 " --> pdb=" O SER E 541 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 591 " --> pdb=" O MET E 502 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N CYS E 506 " --> pdb=" O MET E 593 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 746 through 751 removed outlier: 3.661A pdb=" N HIS E 746 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 769 " --> pdb=" O VAL E 748 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS E 750 " --> pdb=" O GLN E 767 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN E 767 " --> pdb=" O LYS E 750 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) 1566 hydrogen bonds defined for protein. 4344 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: 8.27 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6413 1.32 - 1.45: 9554 1.45 - 1.57: 19368 1.57 - 1.70: 4 1.70 - 1.82: 325 Bond restraints: 35664 Sorted by residual: bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.609 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.613 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" OP4 LLP B 609 " pdb=" P LLP B 609 " ideal model delta sigma weight residual 1.726 1.618 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C ALA D 636 " pdb=" N LEU D 637 " ideal model delta sigma weight residual 1.327 1.259 0.068 1.39e-02 5.18e+03 2.36e+01 ... (remaining 35659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 46992 2.45 - 4.90: 1137 4.90 - 7.35: 126 7.35 - 9.79: 19 9.79 - 12.24: 7 Bond angle restraints: 48281 Sorted by residual: angle pdb=" N ILE A 125 " pdb=" CA ILE A 125 " pdb=" C ILE A 125 " ideal model delta sigma weight residual 113.10 104.52 8.58 9.70e-01 1.06e+00 7.82e+01 angle pdb=" N PRO B 320 " pdb=" CA PRO B 320 " pdb=" C PRO B 320 " ideal model delta sigma weight residual 113.86 103.49 10.37 1.25e+00 6.40e-01 6.88e+01 angle pdb=" N THR E 459 " pdb=" CA THR E 459 " pdb=" C THR E 459 " ideal model delta sigma weight residual 111.07 102.90 8.17 1.07e+00 8.73e-01 5.84e+01 angle pdb=" C ASN D 9 " pdb=" CA ASN D 9 " pdb=" CB ASN D 9 " ideal model delta sigma weight residual 117.07 107.15 9.92 1.44e+00 4.82e-01 4.75e+01 angle pdb=" N ASP B 167 " pdb=" CA ASP B 167 " pdb=" C ASP B 167 " ideal model delta sigma weight residual 112.54 104.34 8.20 1.22e+00 6.72e-01 4.52e+01 ... (remaining 48276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 19978 25.51 - 51.02: 992 51.02 - 76.53: 110 76.53 - 102.05: 20 102.05 - 127.56: 1 Dihedral angle restraints: 21101 sinusoidal: 8646 harmonic: 12455 Sorted by residual: dihedral pdb=" CA PHE A 677 " pdb=" C PHE A 677 " pdb=" N SER A 678 " pdb=" CA SER A 678 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL E 848 " pdb=" C VAL E 848 " pdb=" N LYS E 849 " pdb=" CA LYS E 849 " ideal model delta harmonic sigma weight residual 180.00 155.21 24.79 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASN C 617 " pdb=" C ASN C 617 " pdb=" N LEU C 618 " pdb=" CA LEU C 618 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 21098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4014 0.059 - 0.117: 842 0.117 - 0.176: 108 0.176 - 0.235: 21 0.235 - 0.294: 5 Chirality restraints: 4990 Sorted by residual: chirality pdb=" CA LEU B 130 " pdb=" N LEU B 130 " pdb=" C LEU B 130 " pdb=" CB LEU B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ILE E 18 " pdb=" N ILE E 18 " pdb=" C ILE E 18 " pdb=" CB ILE E 18 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA GLU B 608 " pdb=" N GLU B 608 " pdb=" C GLU B 608 " pdb=" CB GLU B 608 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4987 not shown) Planarity restraints: 6243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 609 " 0.017 2.00e-02 2.50e+03 2.65e-01 7.00e+02 pdb=" NZ LLP A 609 " -0.258 2.00e-02 2.50e+03 pdb=" C4 LLP A 609 " -0.182 2.00e-02 2.50e+03 pdb=" C4' LLP A 609 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP D 609 " 0.135 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" NZ LLP D 609 " -0.120 2.00e-02 2.50e+03 pdb=" C4 LLP D 609 " 0.143 2.00e-02 2.50e+03 pdb=" C4' LLP D 609 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 609 " -0.118 2.00e-02 2.50e+03 1.24e-01 1.54e+02 pdb=" NZ LLP B 609 " 0.099 2.00e-02 2.50e+03 pdb=" C4 LLP B 609 " -0.128 2.00e-02 2.50e+03 pdb=" C4' LLP B 609 " 0.146 2.00e-02 2.50e+03 ... (remaining 6240 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 3663 2.74 - 3.28: 37075 3.28 - 3.82: 59769 3.82 - 4.36: 69516 4.36 - 4.90: 116964 Nonbonded interactions: 286987 Sorted by model distance: nonbonded pdb=" OG1 THR D 202 " pdb=" N ASN D 203 " model vdw 2.194 3.120 nonbonded pdb=" O PRO A 535 " pdb=" OH TYR A 670 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASN C 659 " pdb=" ND2 ASN C 663 " model vdw 2.202 3.120 nonbonded pdb=" O LEU B 518 " pdb=" OH TYR B 658 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU E 611 " pdb=" OG SER E 688 " model vdw 2.211 3.040 ... (remaining 286982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = (chain 'B' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) selection = (chain 'E' and (resid 1 through 608 or (resid 609 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 610 through 852)) } 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: 15.780 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: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.710 Find NCS groups from input model: 0.730 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 0.117 35664 Z= 0.324 Angle : 0.877 12.243 48281 Z= 0.534 Chirality : 0.050 0.294 4990 Planarity : 0.006 0.265 6243 Dihedral : 14.401 127.557 13151 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.10 % Favored : 91.10 % Rotamer: Outliers : 1.06 % Allowed : 0.79 % Favored : 98.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 4235 helix: 0.56 (0.13), residues: 1772 sheet: -1.18 (0.21), residues: 615 loop : -1.76 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 507 TYR 0.034 0.002 TYR A 239 PHE 0.026 0.002 PHE B 364 TRP 0.030 0.002 TRP D 625 HIS 0.008 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00601 (35664) covalent geometry : angle 0.87689 (48281) hydrogen bonds : bond 0.18729 ( 1544) hydrogen bonds : angle 7.69504 ( 4344) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 1.464 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: A 6 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (t0) REVERT: A 132 MET cc_start: 0.8964 (tpp) cc_final: 0.8582 (mmm) REVERT: C 335 MET cc_start: 0.8345 (ppp) cc_final: 0.7739 (ppp) REVERT: C 629 TYR cc_start: 0.7500 (t80) cc_final: 0.7245 (t80) REVERT: D 20 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8343 (p) REVERT: D 660 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9249 (mm) REVERT: E 106 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7979 (mtmm) REVERT: E 692 ILE cc_start: 0.9175 (tt) cc_final: 0.8922 (tp) REVERT: E 832 MET cc_start: 0.8088 (ppp) cc_final: 0.7750 (ppp) outliers start: 39 outliers final: 14 residues processed: 239 average time/residue: 0.2112 time to fit residues: 86.0869 Evaluate side-chains 187 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 316 HIS ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN B 360 HIS B 482 ASN C 207 HIS C 545 HIS C 613 ASN C 746 HIS D 9 ASN D 12 GLN D 162 GLN D 170 GLN D 404 ASN D 446 HIS ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 ASN E 649 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.043616 restraints weight = 180540.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044957 restraints weight = 99167.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045836 restraints weight = 66947.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046409 restraints weight = 51827.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046783 restraints weight = 43836.449| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35664 Z= 0.204 Angle : 0.635 10.454 48281 Z= 0.332 Chirality : 0.043 0.229 4990 Planarity : 0.004 0.053 6243 Dihedral : 5.873 84.878 4716 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.73 % Favored : 93.13 % Rotamer: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4235 helix: 0.73 (0.12), residues: 1826 sheet: -0.98 (0.20), residues: 634 loop : -1.73 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 354 TYR 0.019 0.002 TYR E 112 PHE 0.019 0.002 PHE E 160 TRP 0.018 0.001 TRP A 850 HIS 0.008 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00452 (35664) covalent geometry : angle 0.63543 (48281) hydrogen bonds : bond 0.04854 ( 1544) hydrogen bonds : angle 5.61740 ( 4344) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8804 (mmm) cc_final: 0.8554 (tmm) REVERT: C 195 LEU cc_start: 0.8690 (mt) cc_final: 0.8469 (mt) REVERT: C 335 MET cc_start: 0.8371 (ppp) cc_final: 0.7576 (ppp) REVERT: C 742 TRP cc_start: 0.5194 (p-90) cc_final: 0.4761 (p-90) REVERT: C 770 ILE cc_start: 0.8899 (mm) cc_final: 0.8611 (tp) REVERT: E 132 MET cc_start: 0.8885 (mmp) cc_final: 0.8674 (mmt) REVERT: E 804 MET cc_start: 0.7808 (tmm) cc_final: 0.7523 (tmm) REVERT: E 832 MET cc_start: 0.8158 (ppp) cc_final: 0.7889 (ppp) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2033 time to fit residues: 73.6944 Evaluate side-chains 179 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 373 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 378 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 613 ASN C 207 HIS C 613 ASN D 458 ASN E 212 GLN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.043705 restraints weight = 179542.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.045041 restraints weight = 99348.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045900 restraints weight = 67392.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046502 restraints weight = 52458.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046891 restraints weight = 44159.457| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 35664 Z= 0.174 Angle : 0.593 9.994 48281 Z= 0.308 Chirality : 0.042 0.162 4990 Planarity : 0.004 0.066 6243 Dihedral : 5.688 79.506 4716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.45 % Favored : 93.41 % Rotamer: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4235 helix: 0.99 (0.13), residues: 1793 sheet: -0.90 (0.20), residues: 639 loop : -1.52 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 488 TYR 0.030 0.002 TYR D 239 PHE 0.031 0.002 PHE A 677 TRP 0.018 0.001 TRP A 850 HIS 0.007 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00389 (35664) covalent geometry : angle 0.59276 (48281) hydrogen bonds : bond 0.04271 ( 1544) hydrogen bonds : angle 5.19993 ( 4344) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8794 (mmm) cc_final: 0.8590 (tmm) REVERT: A 612 MET cc_start: 0.8915 (mmm) cc_final: 0.8623 (mmm) REVERT: C 335 MET cc_start: 0.8359 (ppp) cc_final: 0.8110 (ppp) REVERT: C 698 MET cc_start: 0.8944 (mmm) cc_final: 0.8680 (mmm) REVERT: C 742 TRP cc_start: 0.5533 (p-90) cc_final: 0.5214 (p-90) REVERT: C 770 ILE cc_start: 0.8940 (mm) cc_final: 0.8664 (tp) REVERT: D 335 MET cc_start: 0.8209 (mmm) cc_final: 0.7695 (mmm) REVERT: E 579 MET cc_start: 0.7391 (ttp) cc_final: 0.7188 (ttp) REVERT: E 832 MET cc_start: 0.8146 (ppp) cc_final: 0.7879 (ppp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2093 time to fit residues: 75.4934 Evaluate side-chains 164 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 87 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 420 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 387 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 299 ASN A 482 ASN A 613 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN C 207 HIS C 613 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN D 683 GLN ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043037 restraints weight = 181123.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044353 restraints weight = 101110.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045227 restraints weight = 68911.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045802 restraints weight = 53463.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046139 restraints weight = 45297.827| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 35664 Z= 0.200 Angle : 0.610 14.714 48281 Z= 0.317 Chirality : 0.043 0.178 4990 Planarity : 0.004 0.057 6243 Dihedral : 5.520 64.775 4716 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4235 helix: 1.05 (0.13), residues: 1774 sheet: -0.83 (0.20), residues: 618 loop : -1.49 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 508 TYR 0.032 0.002 TYR E 155 PHE 0.028 0.002 PHE A 677 TRP 0.016 0.001 TRP A 850 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00448 (35664) covalent geometry : angle 0.60988 (48281) hydrogen bonds : bond 0.04145 ( 1544) hydrogen bonds : angle 5.08112 ( 4344) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.8172 (mtm) cc_final: 0.7881 (ttp) REVERT: A 612 MET cc_start: 0.8796 (mmm) cc_final: 0.8149 (mmm) REVERT: B 391 MET cc_start: 0.8545 (ttp) cc_final: 0.8311 (ttp) REVERT: B 843 GLN cc_start: 0.9021 (mp10) cc_final: 0.8606 (mp10) REVERT: C 335 MET cc_start: 0.8370 (ppp) cc_final: 0.7698 (ppp) REVERT: C 629 TYR cc_start: 0.8374 (t80) cc_final: 0.7789 (t80) REVERT: C 698 MET cc_start: 0.9031 (mmm) cc_final: 0.8701 (mmm) REVERT: C 742 TRP cc_start: 0.5557 (p-90) cc_final: 0.5244 (p-90) REVERT: C 754 MET cc_start: 0.7851 (ppp) cc_final: 0.7521 (ppp) REVERT: C 770 ILE cc_start: 0.8966 (mm) cc_final: 0.8675 (tp) REVERT: D 15 GLU cc_start: 0.8654 (tp30) cc_final: 0.8270 (tm-30) REVERT: D 335 MET cc_start: 0.8131 (mmm) cc_final: 0.7551 (mmm) REVERT: D 668 MET cc_start: 0.9123 (tpp) cc_final: 0.8899 (tpp) REVERT: E 213 MET cc_start: 0.8309 (tpp) cc_final: 0.8074 (tpp) REVERT: E 668 MET cc_start: 0.8841 (tmm) cc_final: 0.8402 (tmm) REVERT: E 832 MET cc_start: 0.8196 (ppp) cc_final: 0.7871 (ppp) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2019 time to fit residues: 69.6933 Evaluate side-chains 168 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 150 optimal weight: 9.9990 chunk 354 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS C 405 HIS C 613 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 ASN E 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042595 restraints weight = 181452.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.043906 restraints weight = 100620.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044759 restraints weight = 68261.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045327 restraints weight = 52996.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045703 restraints weight = 44880.102| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35664 Z= 0.219 Angle : 0.626 18.022 48281 Z= 0.325 Chirality : 0.043 0.159 4990 Planarity : 0.004 0.053 6243 Dihedral : 5.473 64.182 4716 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4235 helix: 0.99 (0.12), residues: 1790 sheet: -0.82 (0.21), residues: 593 loop : -1.51 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 186 TYR 0.033 0.002 TYR D 239 PHE 0.027 0.002 PHE A 677 TRP 0.017 0.001 TRP A 423 HIS 0.008 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00489 (35664) covalent geometry : angle 0.62575 (48281) hydrogen bonds : bond 0.04184 ( 1544) hydrogen bonds : angle 5.07417 ( 4344) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 612 MET cc_start: 0.8640 (mmm) cc_final: 0.8054 (mmm) REVERT: A 832 MET cc_start: 0.8417 (mmm) cc_final: 0.8199 (mmt) REVERT: B 391 MET cc_start: 0.8519 (ttp) cc_final: 0.8300 (ttp) REVERT: B 843 GLN cc_start: 0.9018 (mp10) cc_final: 0.8613 (mp10) REVERT: C 335 MET cc_start: 0.8167 (ppp) cc_final: 0.7901 (ppp) REVERT: C 629 TYR cc_start: 0.8396 (t80) cc_final: 0.7894 (t80) REVERT: C 742 TRP cc_start: 0.5499 (p-90) cc_final: 0.5155 (p-90) REVERT: C 770 ILE cc_start: 0.8999 (mm) cc_final: 0.8741 (tp) REVERT: D 15 GLU cc_start: 0.8642 (tp30) cc_final: 0.8355 (tm-30) REVERT: D 335 MET cc_start: 0.8111 (mmm) cc_final: 0.7521 (mmm) REVERT: E 668 MET cc_start: 0.8913 (tmm) cc_final: 0.8349 (tmm) REVERT: E 832 MET cc_start: 0.8234 (ppp) cc_final: 0.7877 (ppp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2009 time to fit residues: 65.7498 Evaluate side-chains 162 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 97 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 228 optimal weight: 8.9990 chunk 296 optimal weight: 0.8980 chunk 87 optimal weight: 0.0370 chunk 173 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 323 HIS A 613 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.044395 restraints weight = 177992.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045742 restraints weight = 99013.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046634 restraints weight = 67175.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047222 restraints weight = 51878.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047611 restraints weight = 43697.726| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35664 Z= 0.119 Angle : 0.554 16.553 48281 Z= 0.287 Chirality : 0.042 0.234 4990 Planarity : 0.004 0.051 6243 Dihedral : 5.343 62.253 4716 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4235 helix: 1.20 (0.13), residues: 1775 sheet: -0.69 (0.21), residues: 627 loop : -1.32 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 741 TYR 0.024 0.001 TYR A 705 PHE 0.024 0.001 PHE A 677 TRP 0.021 0.001 TRP B 625 HIS 0.014 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00266 (35664) covalent geometry : angle 0.55399 (48281) hydrogen bonds : bond 0.03773 ( 1544) hydrogen bonds : angle 4.80658 ( 4344) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 HIS cc_start: 0.6119 (m-70) cc_final: 0.5872 (m-70) REVERT: A 612 MET cc_start: 0.8785 (mmm) cc_final: 0.8049 (mmm) REVERT: B 383 LEU cc_start: 0.9081 (tp) cc_final: 0.8781 (tt) REVERT: B 391 MET cc_start: 0.8575 (ttp) cc_final: 0.8368 (ttp) REVERT: B 612 MET cc_start: 0.8999 (mmm) cc_final: 0.8707 (mmm) REVERT: B 843 GLN cc_start: 0.8930 (mp10) cc_final: 0.8599 (mp10) REVERT: C 335 MET cc_start: 0.8446 (ppp) cc_final: 0.7500 (ppp) REVERT: C 629 TYR cc_start: 0.8387 (t80) cc_final: 0.7958 (t80) REVERT: C 698 MET cc_start: 0.8930 (mmm) cc_final: 0.8596 (tpp) REVERT: C 742 TRP cc_start: 0.5644 (p-90) cc_final: 0.5318 (p-90) REVERT: C 770 ILE cc_start: 0.8899 (mm) cc_final: 0.8629 (tp) REVERT: D 15 GLU cc_start: 0.8598 (tp30) cc_final: 0.8355 (tm-30) REVERT: D 335 MET cc_start: 0.8110 (mmm) cc_final: 0.7605 (mmm) REVERT: D 391 MET cc_start: 0.8830 (tpp) cc_final: 0.8627 (tpt) REVERT: D 668 MET cc_start: 0.9089 (tpp) cc_final: 0.8844 (tpp) REVERT: E 148 MET cc_start: 0.9354 (tpp) cc_final: 0.8999 (tpt) REVERT: E 608 GLU cc_start: 0.8402 (mp0) cc_final: 0.7673 (mp0) REVERT: E 668 MET cc_start: 0.8864 (tmm) cc_final: 0.8430 (tmm) REVERT: E 832 MET cc_start: 0.8234 (ppp) cc_final: 0.8010 (ppp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2060 time to fit residues: 75.5838 Evaluate side-chains 169 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 331 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 482 ASN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.042162 restraints weight = 183564.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.043449 restraints weight = 102575.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044299 restraints weight = 70122.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044868 restraints weight = 54605.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045190 restraints weight = 46278.668| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 35664 Z= 0.263 Angle : 0.669 19.216 48281 Z= 0.345 Chirality : 0.044 0.187 4990 Planarity : 0.004 0.052 6243 Dihedral : 5.545 62.986 4716 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.13 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 4235 helix: 1.01 (0.12), residues: 1784 sheet: -0.75 (0.22), residues: 576 loop : -1.40 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 354 TYR 0.024 0.002 TYR D 239 PHE 0.026 0.002 PHE A 677 TRP 0.018 0.002 TRP B 625 HIS 0.007 0.001 HIS C 746 Details of bonding type rmsd covalent geometry : bond 0.00582 (35664) covalent geometry : angle 0.66854 (48281) hydrogen bonds : bond 0.04203 ( 1544) hydrogen bonds : angle 5.09527 ( 4344) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8949 (mmm) cc_final: 0.8599 (mmm) REVERT: A 323 HIS cc_start: 0.6517 (m-70) cc_final: 0.6149 (m-70) REVERT: A 391 MET cc_start: 0.9458 (ttt) cc_final: 0.9221 (ttt) REVERT: A 612 MET cc_start: 0.8844 (mmm) cc_final: 0.8164 (mmm) REVERT: B 331 PHE cc_start: 0.6899 (t80) cc_final: 0.6661 (t80) REVERT: B 612 MET cc_start: 0.9014 (mmm) cc_final: 0.8715 (mmm) REVERT: B 843 GLN cc_start: 0.9015 (mp10) cc_final: 0.8646 (mp10) REVERT: C 502 MET cc_start: 0.8561 (mpp) cc_final: 0.8319 (mpp) REVERT: C 698 MET cc_start: 0.8977 (mmm) cc_final: 0.8744 (mmm) REVERT: C 742 TRP cc_start: 0.5480 (p-90) cc_final: 0.5155 (p-90) REVERT: C 770 ILE cc_start: 0.8969 (mm) cc_final: 0.8726 (tp) REVERT: D 335 MET cc_start: 0.8139 (mmm) cc_final: 0.7628 (mmm) REVERT: D 391 MET cc_start: 0.8857 (tpp) cc_final: 0.8391 (tpt) REVERT: E 99 MET cc_start: 0.8621 (mtt) cc_final: 0.8374 (mtt) REVERT: E 461 MET cc_start: 0.8929 (mmp) cc_final: 0.8486 (mmp) REVERT: E 668 MET cc_start: 0.8933 (tmm) cc_final: 0.8516 (tmm) REVERT: E 832 MET cc_start: 0.8371 (ppp) cc_final: 0.8138 (ppp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1959 time to fit residues: 63.7145 Evaluate side-chains 159 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 125 optimal weight: 4.9990 chunk 368 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 355 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043430 restraints weight = 181357.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.044753 restraints weight = 100752.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045623 restraints weight = 68492.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046207 restraints weight = 53182.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046589 restraints weight = 44906.636| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35664 Z= 0.154 Angle : 0.588 17.415 48281 Z= 0.303 Chirality : 0.043 0.177 4990 Planarity : 0.004 0.052 6243 Dihedral : 5.437 69.183 4716 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4235 helix: 1.11 (0.13), residues: 1784 sheet: -0.74 (0.21), residues: 582 loop : -1.32 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 831 TYR 0.036 0.001 TYR D 239 PHE 0.023 0.001 PHE A 677 TRP 0.018 0.001 TRP A 850 HIS 0.013 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00346 (35664) covalent geometry : angle 0.58751 (48281) hydrogen bonds : bond 0.03894 ( 1544) hydrogen bonds : angle 4.90282 ( 4344) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8932 (mmm) cc_final: 0.8594 (mmm) REVERT: A 323 HIS cc_start: 0.6415 (m-70) cc_final: 0.6167 (m-70) REVERT: A 391 MET cc_start: 0.9465 (ttt) cc_final: 0.9224 (ttt) REVERT: A 612 MET cc_start: 0.8867 (mmm) cc_final: 0.8064 (mmm) REVERT: B 612 MET cc_start: 0.8915 (mmm) cc_final: 0.8615 (mmm) REVERT: B 843 GLN cc_start: 0.8926 (mp10) cc_final: 0.8617 (mp10) REVERT: C 99 MET cc_start: 0.8198 (tpt) cc_final: 0.7953 (tpt) REVERT: C 335 MET cc_start: 0.8470 (ppp) cc_final: 0.7397 (ppp) REVERT: C 593 MET cc_start: 0.8612 (tpp) cc_final: 0.7986 (tpp) REVERT: C 698 MET cc_start: 0.8904 (mmm) cc_final: 0.8694 (mmm) REVERT: C 742 TRP cc_start: 0.5632 (p-90) cc_final: 0.5329 (p-90) REVERT: C 770 ILE cc_start: 0.8932 (mm) cc_final: 0.8709 (tp) REVERT: D 335 MET cc_start: 0.8082 (mmm) cc_final: 0.7551 (mmm) REVERT: D 391 MET cc_start: 0.8840 (tpp) cc_final: 0.8344 (tpt) REVERT: D 668 MET cc_start: 0.9031 (tpp) cc_final: 0.8827 (tpp) REVERT: E 99 MET cc_start: 0.8558 (mtt) cc_final: 0.8320 (mtt) REVERT: E 148 MET cc_start: 0.9424 (tpp) cc_final: 0.9215 (tpt) REVERT: E 608 GLU cc_start: 0.8408 (mp0) cc_final: 0.7744 (mp0) REVERT: E 668 MET cc_start: 0.8865 (tmm) cc_final: 0.8433 (tmm) REVERT: E 832 MET cc_start: 0.8296 (ppp) cc_final: 0.8084 (ppp) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.2032 time to fit residues: 68.0782 Evaluate side-chains 161 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 417 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 87 optimal weight: 0.0270 chunk 263 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 325 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 319 optimal weight: 8.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 746 HIS E 762 GLN E 852 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044039 restraints weight = 180002.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045388 restraints weight = 99830.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046275 restraints weight = 67482.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046869 restraints weight = 52202.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047255 restraints weight = 43900.495| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35664 Z= 0.123 Angle : 0.566 16.712 48281 Z= 0.290 Chirality : 0.042 0.172 4990 Planarity : 0.004 0.051 6243 Dihedral : 5.269 73.316 4716 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4235 helix: 1.19 (0.13), residues: 1778 sheet: -0.62 (0.21), residues: 598 loop : -1.19 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 45 TYR 0.032 0.001 TYR D 239 PHE 0.025 0.001 PHE A 677 TRP 0.011 0.001 TRP A 850 HIS 0.010 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00277 (35664) covalent geometry : angle 0.56625 (48281) hydrogen bonds : bond 0.03716 ( 1544) hydrogen bonds : angle 4.78514 ( 4344) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8891 (mmm) cc_final: 0.8584 (mmm) REVERT: A 323 HIS cc_start: 0.6353 (m-70) cc_final: 0.6144 (m-70) REVERT: A 391 MET cc_start: 0.9477 (ttt) cc_final: 0.9155 (ttt) REVERT: A 612 MET cc_start: 0.8816 (mmm) cc_final: 0.8017 (mmm) REVERT: B 383 LEU cc_start: 0.9088 (tp) cc_final: 0.8781 (tt) REVERT: B 612 MET cc_start: 0.8925 (mmm) cc_final: 0.8585 (mmm) REVERT: B 843 GLN cc_start: 0.8908 (mp10) cc_final: 0.8586 (mp10) REVERT: C 335 MET cc_start: 0.8445 (ppp) cc_final: 0.7365 (ppp) REVERT: C 593 MET cc_start: 0.8636 (tpp) cc_final: 0.7992 (tpp) REVERT: C 698 MET cc_start: 0.8805 (mmm) cc_final: 0.8599 (mmm) REVERT: C 742 TRP cc_start: 0.5631 (p-90) cc_final: 0.5344 (p-90) REVERT: C 770 ILE cc_start: 0.8884 (mm) cc_final: 0.8648 (tp) REVERT: D 335 MET cc_start: 0.8042 (mmm) cc_final: 0.7436 (mmm) REVERT: D 668 MET cc_start: 0.9034 (tpp) cc_final: 0.8787 (tpp) REVERT: E 99 MET cc_start: 0.8510 (mtt) cc_final: 0.8287 (mtt) REVERT: E 148 MET cc_start: 0.9403 (tpp) cc_final: 0.9172 (tpt) REVERT: E 608 GLU cc_start: 0.8370 (mp0) cc_final: 0.7736 (mp0) REVERT: E 668 MET cc_start: 0.8832 (tmm) cc_final: 0.8233 (tmm) outliers start: 2 outliers final: 0 residues processed: 196 average time/residue: 0.1905 time to fit residues: 64.5868 Evaluate side-chains 164 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 6 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 274 optimal weight: 0.0010 chunk 21 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 405 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 ASN ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 852 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.043507 restraints weight = 181744.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044821 restraints weight = 101038.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045700 restraints weight = 68846.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046280 restraints weight = 53340.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046667 restraints weight = 45054.158| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35664 Z= 0.161 Angle : 0.591 17.853 48281 Z= 0.303 Chirality : 0.042 0.181 4990 Planarity : 0.004 0.052 6243 Dihedral : 5.295 71.439 4716 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4235 helix: 1.14 (0.13), residues: 1788 sheet: -0.63 (0.22), residues: 582 loop : -1.22 (0.15), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 700 TYR 0.034 0.001 TYR E 155 PHE 0.025 0.001 PHE A 677 TRP 0.014 0.001 TRP A 850 HIS 0.009 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00362 (35664) covalent geometry : angle 0.59139 (48281) hydrogen bonds : bond 0.03793 ( 1544) hydrogen bonds : angle 4.81032 ( 4344) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8894 (mmm) cc_final: 0.8613 (mmm) REVERT: A 132 MET cc_start: 0.8768 (mmm) cc_final: 0.8445 (mmm) REVERT: A 391 MET cc_start: 0.9490 (ttt) cc_final: 0.9146 (ttt) REVERT: A 612 MET cc_start: 0.8861 (mmm) cc_final: 0.8016 (mmm) REVERT: A 815 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6163 (pp20) REVERT: B 612 MET cc_start: 0.8982 (mmm) cc_final: 0.8680 (mmm) REVERT: B 843 GLN cc_start: 0.8936 (mp10) cc_final: 0.8618 (mp10) REVERT: C 335 MET cc_start: 0.8459 (ppp) cc_final: 0.7350 (ppp) REVERT: C 593 MET cc_start: 0.8517 (tpp) cc_final: 0.8068 (tpp) REVERT: C 742 TRP cc_start: 0.5628 (p-90) cc_final: 0.5356 (p-90) REVERT: C 770 ILE cc_start: 0.8904 (mm) cc_final: 0.8692 (tp) REVERT: D 335 MET cc_start: 0.8039 (mmm) cc_final: 0.7486 (mmm) REVERT: D 668 MET cc_start: 0.9063 (tpp) cc_final: 0.8799 (tpp) REVERT: E 148 MET cc_start: 0.9427 (tpp) cc_final: 0.9199 (tpt) REVERT: E 608 GLU cc_start: 0.8449 (mp0) cc_final: 0.7780 (mp0) REVERT: E 668 MET cc_start: 0.8861 (tmm) cc_final: 0.8441 (tmm) REVERT: E 832 MET cc_start: 0.8145 (ppp) cc_final: 0.7730 (ppp) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1988 time to fit residues: 65.6469 Evaluate side-chains 163 residues out of total 3685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 156 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 218 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 852 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.042179 restraints weight = 182864.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.043459 restraints weight = 102486.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.044301 restraints weight = 70093.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044865 restraints weight = 54564.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045232 restraints weight = 46236.661| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 35664 Z= 0.255 Angle : 0.672 17.404 48281 Z= 0.346 Chirality : 0.045 0.189 4990 Planarity : 0.004 0.051 6243 Dihedral : 5.571 72.144 4716 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4235 helix: 0.97 (0.12), residues: 1788 sheet: -0.77 (0.22), residues: 573 loop : -1.28 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 700 TYR 0.034 0.002 TYR D 239 PHE 0.024 0.002 PHE A 677 TRP 0.022 0.002 TRP D 37 HIS 0.007 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00568 (35664) covalent geometry : angle 0.67211 (48281) hydrogen bonds : bond 0.04204 ( 1544) hydrogen bonds : angle 5.03043 ( 4344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4697.18 seconds wall clock time: 83 minutes 26.43 seconds (5006.43 seconds total)