Starting phenix.real_space_refine on Sat Mar 7 00:12:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.cif Found real_map, /net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20ys_67418/03_2026/20ys_67418.map" } resolution = 2.96 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= -0.000 sd= 0.011 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 22242 2.51 5 N 5829 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 29 residue(s): 0.04s 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: 34740 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 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: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 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: "D" Number of atoms: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 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: 6951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6951 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: 6936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6936 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, '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 Time building chain proxies: 7.40, per 1000 atoms: 0.21 Number of scatterers: 34740 At special positions: 0 Unit cell: (102.09, 177.62, 204.18, 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 5829 7.00 C 22242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 374 " distance=2.03 Simple disulfide: pdb=" SG CYS E 276 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 374 " distance=2.04 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 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: 191 helices and 40 sheets defined 46.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 removed outlier: 3.959A pdb=" N TRP A 38 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 40 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 41 " --> pdb=" O TRP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.001A pdb=" N PHE A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.834A pdb=" N LYS A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.702A pdb=" N VAL A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.632A pdb=" N LYS A 89 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.588A pdb=" N MET A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.054A pdb=" N LEU A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.749A pdb=" N ALA A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.628A pdb=" N TYR A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.023A pdb=" N LYS A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.522A pdb=" N ASN A 404 " --> pdb=" O PRO A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.503A pdb=" N TRP A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.631A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 452 through 482 removed outlier: 3.558A pdb=" N TYR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.628A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.568A pdb=" N ARG A 514 " --> pdb=" O THR A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.848A pdb=" N GLN A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.564A pdb=" N SER A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.719A pdb=" N MET A 612 " --> pdb=" O GLU A 608 " (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 670 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 693 through 696 Processing helix chain 'A' and resid 697 through 709 Processing helix chain 'A' and resid 710 through 741 removed outlier: 3.877A pdb=" N ARG A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 741 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.214A pdb=" N TRP B 38 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 39 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP B 40 " --> pdb=" O TRP B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 40' Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.566A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 71 through 81 Processing helix chain 'B' and resid 81 through 100 Processing helix chain 'B' and resid 128 through 145 Processing helix chain 'B' and resid 245 through 267 removed outlier: 4.700A pdb=" N GLY B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.727A pdb=" N ALA B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 310' Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.720A pdb=" N PHE B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 345 through 352 removed outlier: 3.580A pdb=" N PHE B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.668A pdb=" N TRP B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.890A pdb=" N LYS B 397 " --> pdb=" O ASN B 394 " (cutoff:3.500A) 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 444 through 449 removed outlier: 3.556A pdb=" N ALA B 447 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 449 " --> pdb=" O HIS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 482 removed outlier: 3.605A pdb=" N LEU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.853A pdb=" N VAL B 490 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 492 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 493 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 494 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 519 removed outlier: 4.300A pdb=" N LEU B 518 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 548 through 563 Processing helix chain 'B' and resid 584 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 648 through 665 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 712 through 741 removed outlier: 6.359A pdb=" N ASN B 723 " --> pdb=" O LYS B 719 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 726 " --> pdb=" O ALA B 722 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU B 727 " --> pdb=" O ASN B 723 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 728 " --> pdb=" O ASP B 724 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG B 741 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 745 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.729A pdb=" N LYS D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 41 through 50 removed outlier: 3.621A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.571A pdb=" N LEU D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.722A pdb=" N MET D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 removed outlier: 3.595A pdb=" N LEU D 250 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.940A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 288 " --> pdb=" O CYS D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 307 removed outlier: 4.205A pdb=" N GLU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU D 306 " --> pdb=" O GLN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 327 through 336 removed outlier: 3.659A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.640A pdb=" N ILE D 350 " --> pdb=" O TRP D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 Processing helix chain 'D' and resid 381 through 390 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.628A pdb=" N TRP D 445 " --> pdb=" O ASN D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 452 through 482 removed outlier: 3.628A pdb=" N TYR D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.562A pdb=" N LEU D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 563 Processing helix chain 'D' and resid 578 through 589 removed outlier: 3.832A pdb=" N SER D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 610 removed outlier: 3.528A pdb=" N ALA D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 680 through 692 removed outlier: 3.779A pdb=" N ILE D 689 " --> pdb=" O VAL D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 697 through 709 Processing helix chain 'D' and resid 709 through 721 Processing helix chain 'D' and resid 721 through 741 removed outlier: 6.129A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 740 " --> pdb=" O GLU D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 757 removed outlier: 4.067A pdb=" N ALA D 757 " --> pdb=" O CYS D 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 33 Processing helix chain 'E' and resid 35 through 39 removed outlier: 3.858A pdb=" N TRP E 38 " --> pdb=" O ASN E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.793A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 46 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 128 through 144 removed outlier: 3.599A pdb=" N MET E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.512A pdb=" N ILE E 237 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 238' Processing helix chain 'E' and resid 245 through 267 Processing helix chain 'E' and resid 278 through 281 Processing helix chain 'E' and resid 282 through 296 removed outlier: 4.032A pdb=" N LEU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 309 removed outlier: 3.841A 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 335 removed outlier: 3.593A pdb=" N LYS E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 366 through 374 Processing helix chain 'E' and resid 381 through 390 removed outlier: 3.538A pdb=" N TRP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 426 through 431 removed outlier: 3.797A pdb=" N TYR E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.592A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.537A pdb=" N LYS E 450 " --> pdb=" O ALA E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 482 removed outlier: 3.865A pdb=" N TYR E 470 " --> pdb=" O LYS E 466 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU E 473 " --> pdb=" O ALA E 469 " (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 493 Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 548 through 563 removed outlier: 3.772A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 555 " --> pdb=" O GLY E 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 557 " --> pdb=" O GLY E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 589 removed outlier: 3.831A pdb=" N SER E 587 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 614 removed outlier: 3.513A pdb=" N GLY E 614 " --> pdb=" O GLU E 611 " (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 removed outlier: 4.129A pdb=" N VAL E 684 " --> pdb=" O GLU E 680 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 689 " --> pdb=" O VAL E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 696 Processing helix chain 'E' and resid 697 through 709 Processing helix chain 'E' and resid 709 through 721 removed outlier: 3.785A pdb=" N LYS E 719 " --> pdb=" O ALA E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 740 Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 35 through 40 removed outlier: 4.009A pdb=" N TRP C 38 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 40 " --> pdb=" O TRP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 52 removed outlier: 4.040A pdb=" N ARG C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.569A pdb=" N GLU C 57 " --> pdb=" O PRO C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.574A pdb=" N LEU C 182 " --> pdb=" O PHE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 239 removed outlier: 4.022A pdb=" N THR C 238 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 239 " --> pdb=" O PRO C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 239' Processing helix chain 'C' and resid 245 through 267 removed outlier: 3.731A pdb=" N LEU C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.263A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 309 removed outlier: 3.821A pdb=" N GLU C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 381 through 392 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: 3.689A 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 495 removed outlier: 3.646A pdb=" N ARG C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 removed outlier: 3.741A pdb=" N LEU C 518 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 530 removed outlier: 3.518A pdb=" N LEU C 525 " --> pdb=" O ASP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 563 removed outlier: 3.806A pdb=" N GLN C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 589 removed outlier: 3.572A pdb=" N SER C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 4.185A pdb=" N GLU C 608 " --> pdb=" O GLY C 604 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 627 Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' 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 691 Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 697 through 709 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 721 through 742 removed outlier: 5.731A pdb=" N LEU C 727 " --> pdb=" O ASN C 723 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA C 728 " --> pdb=" O ASP C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 845 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.112A pdb=" N TYR A 7 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TRP B 850 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA B 758 " --> pdb=" O THR A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.112A pdb=" N TYR A 7 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N TRP B 850 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N SER B 825 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 788 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 827 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS B 787 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 796 " --> pdb=" O LYS B 787 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLN B 789 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS B 794 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186 removed outlier: 4.406A pdb=" N LYS A 219 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 376 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 377 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 571 through 574 removed outlier: 8.377A pdb=" N ILE A 572 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 538 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 574 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 540 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 501 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE A 539 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 503 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N SER A 541 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 505 " --> pdb=" O SER A 541 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N CYS A 506 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TRP A 592 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A 620 " --> pdb=" O TRP A 592 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN A 594 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN A 617 " --> pdb=" O TRP A 635 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A 637 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER A 619 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 747 through 750 removed outlier: 6.611A pdb=" N VAL A 769 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A 750 " --> pdb=" O GLN A 767 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 767 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS A 807 " --> pdb=" O ASN A 811 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 813 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 15 removed outlier: 3.738A pdb=" N VAL C 784 " --> pdb=" O GLY C 829 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N GLN C 789 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 796 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.075A pdb=" N ALA B 111 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASN B 277 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 113 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 377 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.875A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 209 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.875A pdb=" N ALA B 150 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N LEU B 223 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 209 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.507A pdb=" N SER B 163 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 571 through 574 removed outlier: 8.495A pdb=" N ILE B 572 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 538 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU B 574 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE B 540 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 501 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE B 539 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 503 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N SER B 541 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE B 505 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS B 506 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN B 617 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 637 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER B 619 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 746 through 750 removed outlier: 3.930A pdb=" N HIS B 746 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 769 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASN B 811 " --> pdb=" O HIS B 807 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N HIS B 807 " --> pdb=" O ASN B 811 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 813 " --> pdb=" O VAL B 805 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 764 through 765 Processing sheet with id=AC1, first strand: chain 'E' and resid 758 through 759 removed outlier: 4.075A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA E 798 " --> pdb=" O VAL E 785 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS E 787 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 796 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN E 789 " --> pdb=" O LYS E 794 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS E 794 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.716A pdb=" N TYR D 204 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 185 through 186 removed outlier: 7.187A pdb=" N MET D 148 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TYR D 221 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 150 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU D 223 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY D 152 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 277 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AC5, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AC6, first strand: chain 'D' and resid 571 through 574 removed outlier: 8.590A pdb=" N ILE D 572 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE D 538 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU D 574 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE D 540 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 501 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE D 539 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 503 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER D 541 " --> pdb=" O ILE D 503 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE D 505 " --> pdb=" O SER D 541 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS D 506 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN D 617 " --> pdb=" O TRP D 635 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU D 637 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER D 619 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 747 through 750 removed outlier: 6.800A pdb=" N VAL D 769 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS D 750 " --> pdb=" O GLN D 767 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 767 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN D 811 " --> pdb=" O HIS D 807 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS D 807 " --> pdb=" O ASN D 811 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR D 813 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU D 817 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN D 795 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 785 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 799 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU D 783 " --> pdb=" O VAL D 799 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 781 " --> pdb=" O PRO D 801 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LYS D 803 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N VAL D 779 " --> pdb=" O LYS D 803 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL D 830 " --> pdb=" O LEU D 851 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 758 through 759 removed outlier: 7.198A pdb=" N ALA D 758 " --> pdb=" O LYS C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 846 through 847 removed outlier: 7.041A pdb=" N CYS D 846 " --> pdb=" O TYR C 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'E' and resid 185 through 186 removed outlier: 7.202A pdb=" N MET E 148 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N TYR E 221 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E 109 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N HIS E 275 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA E 111 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR E 314 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU E 376 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL E 377 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AD4, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AD5, first strand: chain 'E' and resid 571 through 574 removed outlier: 6.292A pdb=" N LEU E 501 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE E 539 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE E 503 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER E 541 " --> pdb=" O ILE E 503 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE E 505 " --> pdb=" O SER E 541 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET E 502 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N MET E 593 " --> pdb=" O MET E 502 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY E 504 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN E 617 " --> pdb=" O TRP E 635 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU E 637 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER E 619 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 747 through 750 removed outlier: 6.536A pdb=" N VAL E 769 " --> pdb=" O VAL E 748 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 750 " --> pdb=" O GLN E 767 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN E 767 " --> pdb=" O LYS E 750 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AD8, first strand: chain 'C' and resid 185 through 186 removed outlier: 7.500A pdb=" N MET C 148 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N TYR C 221 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 150 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU C 223 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY C 152 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 110 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL C 151 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR C 112 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N PHE C 153 " --> pdb=" O TYR C 112 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR C 274 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS C 276 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 313 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AE1, first strand: chain 'C' and resid 571 through 574 removed outlier: 8.445A pdb=" N ILE C 572 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 538 " --> pdb=" O ILE C 572 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU C 574 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE C 540 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU C 501 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE C 539 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 503 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N SER C 541 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 620 removed outlier: 7.458A pdb=" N SER C 619 " --> pdb=" O LEU C 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 746 through 747 removed outlier: 4.042A pdb=" N HIS C 746 " --> pdb=" O ASP C 771 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 803 through 804 1427 hydrogen bonds defined for protein. 3957 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: 8.33 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11222 1.34 - 1.48: 9209 1.48 - 1.61: 14877 1.61 - 1.75: 2 1.75 - 1.88: 324 Bond restraints: 35634 Sorted by residual: bond pdb=" OP4 LLP B 609 " pdb=" P LLP B 609 " ideal model delta sigma weight residual 1.726 1.539 0.187 2.00e-02 2.50e+03 8.71e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" OP4 LLP A 609 " pdb=" P LLP A 609 " ideal model delta sigma weight residual 1.726 1.543 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" NZ LLP E 609 " pdb=" C4' LLP E 609 " ideal model delta sigma weight residual 1.273 1.425 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 35629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 47604 2.70 - 5.41: 568 5.41 - 8.11: 50 8.11 - 10.82: 17 10.82 - 13.52: 7 Bond angle restraints: 48246 Sorted by residual: angle pdb=" N LYS E 787 " pdb=" CA LYS E 787 " pdb=" C LYS E 787 " ideal model delta sigma weight residual 110.53 99.77 10.76 1.29e+00 6.01e-01 6.96e+01 angle pdb=" N GLU B 305 " pdb=" CA GLU B 305 " pdb=" C GLU B 305 " ideal model delta sigma weight residual 114.75 104.95 9.80 1.26e+00 6.30e-01 6.05e+01 angle pdb=" C VAL E 101 " pdb=" N LYS E 102 " pdb=" CA LYS E 102 " ideal model delta sigma weight residual 120.49 130.51 -10.02 1.42e+00 4.96e-01 4.98e+01 angle pdb=" N ASP A 30 " pdb=" CA ASP A 30 " pdb=" C ASP A 30 " ideal model delta sigma weight residual 114.75 106.89 7.86 1.26e+00 6.30e-01 3.90e+01 angle pdb=" CA LEU E 283 " pdb=" C LEU E 283 " pdb=" N CYS E 284 " ideal model delta sigma weight residual 118.43 110.27 8.16 1.33e+00 5.65e-01 3.77e+01 ... (remaining 48241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 19134 17.73 - 35.46: 1575 35.46 - 53.18: 260 53.18 - 70.91: 95 70.91 - 88.64: 21 Dihedral angle restraints: 21085 sinusoidal: 8630 harmonic: 12455 Sorted by residual: dihedral pdb=" CA CYS B 374 " pdb=" C CYS B 374 " pdb=" N GLN B 375 " pdb=" CA GLN B 375 " ideal model delta harmonic sigma weight residual 180.00 131.12 48.88 0 5.00e+00 4.00e-02 9.56e+01 dihedral pdb=" CA CYS B 371 " pdb=" C CYS B 371 " pdb=" N ASN B 372 " pdb=" CA ASN B 372 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CB CYS C 371 " pdb=" SG CYS C 371 " pdb=" SG CYS C 374 " pdb=" CB CYS C 374 " ideal model delta sinusoidal sigma weight residual 93.00 21.36 71.64 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 21082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3795 0.052 - 0.103: 1024 0.103 - 0.155: 157 0.155 - 0.207: 12 0.207 - 0.258: 2 Chirality restraints: 4990 Sorted by residual: chirality pdb=" CA GLU E 791 " pdb=" N GLU E 791 " pdb=" C GLU E 791 " pdb=" CB GLU E 791 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL D 685 " pdb=" CA VAL D 685 " pdb=" CG1 VAL D 685 " pdb=" CG2 VAL D 685 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA GLN E 789 " pdb=" N GLN E 789 " pdb=" C GLN E 789 " pdb=" CB GLN E 789 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 4987 not shown) Planarity restraints: 6238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 609 " -0.064 2.00e-02 2.50e+03 6.11e-02 3.74e+01 pdb=" NZ LLP A 609 " 0.062 2.00e-02 2.50e+03 pdb=" C4 LLP A 609 " -0.059 2.00e-02 2.50e+03 pdb=" C4' LLP A 609 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 508 " -0.437 9.50e-02 1.11e+02 1.96e-01 2.35e+01 pdb=" NE ARG E 508 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG E 508 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 508 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 508 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 609 " -0.038 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" NZ LLP B 609 " 0.035 2.00e-02 2.50e+03 pdb=" C4 LLP B 609 " -0.036 2.00e-02 2.50e+03 pdb=" C4' LLP B 609 " 0.039 2.00e-02 2.50e+03 ... (remaining 6235 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 806 2.68 - 3.24: 32973 3.24 - 3.79: 53904 3.79 - 4.35: 77927 4.35 - 4.90: 128250 Nonbonded interactions: 293860 Sorted by model distance: nonbonded pdb=" O THR A 760 " pdb=" OG SER E 21 " model vdw 2.129 3.040 nonbonded pdb=" O GLY C 353 " pdb=" OG1 THR C 368 " model vdw 2.134 3.040 nonbonded pdb=" OE2 GLU C 247 " pdb=" OH TYR C 334 " model vdw 2.177 3.040 nonbonded pdb=" O MET C 352 " pdb=" ND2 ASN C 372 " model vdw 2.184 3.120 nonbonded pdb=" OE2 GLU C 116 " pdb=" OH TYR C 242 " model vdw 2.187 3.040 ... (remaining 293855 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.590 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 0.187 35637 Z= 0.316 Angle : 0.808 13.523 48252 Z= 0.479 Chirality : 0.046 0.258 4990 Planarity : 0.006 0.196 6238 Dihedral : 13.736 88.638 13126 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.16 % Allowed : 0.46 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 4235 helix: -0.41 (0.13), residues: 1702 sheet: -0.54 (0.22), residues: 611 loop : -1.78 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 249 TYR 0.030 0.002 TYR A 239 PHE 0.029 0.002 PHE C 331 TRP 0.051 0.002 TRP D 734 HIS 0.007 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00650 (35634) covalent geometry : angle 0.80243 (48246) SS BOND : bond 0.00886 ( 3) SS BOND : angle 8.41349 ( 6) hydrogen bonds : bond 0.18139 ( 1410) hydrogen bonds : angle 7.46364 ( 3957) *********************** 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 456 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 450 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7691 (pttp) REVERT: A 325 TYR cc_start: 0.6439 (m-10) cc_final: 0.6233 (m-80) REVERT: A 734 TRP cc_start: 0.7854 (t60) cc_final: 0.7603 (t60) REVERT: A 763 LYS cc_start: 0.8730 (mppt) cc_final: 0.8306 (mmmt) REVERT: B 1 MET cc_start: 0.4670 (ttt) cc_final: 0.2921 (tmm) REVERT: B 512 TYR cc_start: 0.7727 (p90) cc_final: 0.7311 (p90) REVERT: B 593 MET cc_start: 0.8503 (ttp) cc_final: 0.8263 (ttp) REVERT: D 42 TYR cc_start: 0.7278 (p90) cc_final: 0.7032 (p90) REVERT: D 209 TYR cc_start: 0.7775 (m-80) cc_final: 0.7520 (m-80) REVERT: D 523 GLU cc_start: 0.7627 (tp30) cc_final: 0.7420 (tp30) REVERT: D 764 ILE cc_start: 0.7471 (mp) cc_final: 0.7156 (mt) REVERT: E 249 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7543 (mmm160) REVERT: E 347 ASP cc_start: 0.7788 (t70) cc_final: 0.7572 (t0) REVERT: E 512 TYR cc_start: 0.8649 (p90) cc_final: 0.8197 (p90) REVERT: E 671 ASN cc_start: 0.8042 (t0) cc_final: 0.7841 (t0) REVERT: C 148 MET cc_start: 0.8231 (ttt) cc_final: 0.7997 (ttp) REVERT: C 756 MET cc_start: 0.2497 (ppp) cc_final: 0.2016 (pmt) outliers start: 6 outliers final: 2 residues processed: 454 average time/residue: 0.8615 time to fit residues: 457.5920 Evaluate side-chains 306 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain D residue 688 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 277 ASN A 356 ASN A 767 GLN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 HIS D 545 HIS ** E 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 810 ASN C 90 ASN C 104 ASN C 301 ASN C 687 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102377 restraints weight = 45493.001| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.06 r_work: 0.3078 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 35637 Z= 0.141 Angle : 0.576 11.503 48252 Z= 0.303 Chirality : 0.043 0.296 4990 Planarity : 0.005 0.063 6238 Dihedral : 5.573 80.761 4714 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.49 % Allowed : 7.88 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4235 helix: -0.01 (0.13), residues: 1740 sheet: -0.36 (0.22), residues: 627 loop : -1.67 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 363 TYR 0.023 0.001 TYR B 696 PHE 0.017 0.001 PHE A 160 TRP 0.026 0.001 TRP D 734 HIS 0.004 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00329 (35634) covalent geometry : angle 0.57102 (48246) SS BOND : bond 0.00547 ( 3) SS BOND : angle 6.71160 ( 6) hydrogen bonds : bond 0.04108 ( 1410) hydrogen bonds : angle 5.24311 ( 3957) *********************** 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 412 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8117 (tt0) cc_final: 0.7845 (pt0) REVERT: A 325 TYR cc_start: 0.6240 (m-10) cc_final: 0.5984 (m-80) REVERT: A 734 TRP cc_start: 0.7877 (t60) cc_final: 0.7667 (t60) REVERT: A 763 LYS cc_start: 0.8754 (mppt) cc_final: 0.8119 (ttmm) REVERT: A 792 ASP cc_start: 0.7552 (t0) cc_final: 0.7339 (t0) REVERT: B 300 PHE cc_start: 0.8127 (t80) cc_final: 0.7897 (t80) REVERT: B 502 MET cc_start: 0.9045 (mtp) cc_final: 0.8747 (mtm) REVERT: B 508 ARG cc_start: 0.8205 (ttp-110) cc_final: 0.7993 (ttp80) REVERT: B 512 TYR cc_start: 0.8296 (p90) cc_final: 0.7551 (p90) REVERT: B 645 ASN cc_start: 0.9069 (t0) cc_final: 0.8719 (t0) REVERT: B 724 ASP cc_start: 0.7368 (t0) cc_final: 0.7101 (t0) REVERT: B 741 ARG cc_start: 0.6419 (ttp-110) cc_final: 0.6018 (mtm110) REVERT: D 1 MET cc_start: 0.6161 (tmm) cc_final: 0.5471 (tpt) REVERT: D 19 LYS cc_start: 0.7307 (mmtt) cc_final: 0.7020 (mmtt) REVERT: D 24 LYS cc_start: 0.8303 (mmpt) cc_final: 0.8057 (tptp) REVERT: D 42 TYR cc_start: 0.7570 (p90) cc_final: 0.7291 (p90) REVERT: D 247 GLU cc_start: 0.8253 (tt0) cc_final: 0.8007 (tp30) REVERT: D 764 ILE cc_start: 0.7331 (mp) cc_final: 0.6995 (mt) REVERT: E 49 LYS cc_start: 0.8402 (tttt) cc_final: 0.8166 (tttm) REVERT: E 249 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7756 (mmm160) REVERT: E 512 TYR cc_start: 0.8762 (p90) cc_final: 0.8348 (p90) REVERT: E 671 ASN cc_start: 0.8326 (t0) cc_final: 0.7951 (t0) REVERT: E 756 MET cc_start: 0.7836 (pmm) cc_final: 0.7573 (pmm) REVERT: C 148 MET cc_start: 0.8176 (ttt) cc_final: 0.7953 (ttp) REVERT: C 328 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6855 (pm20) REVERT: C 360 HIS cc_start: 0.6148 (m90) cc_final: 0.5910 (m90) REVERT: C 698 MET cc_start: 0.8780 (tpp) cc_final: 0.8491 (tpt) REVERT: C 756 MET cc_start: 0.3024 (ppp) cc_final: 0.2671 (pmt) REVERT: C 771 ASP cc_start: 0.7410 (t0) cc_final: 0.7170 (p0) outliers start: 55 outliers final: 15 residues processed: 387 average time/residue: 0.7739 time to fit residues: 356.1760 Evaluate side-chains 319 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 304 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 253 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 402 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 412 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 356 ASN A 360 HIS A 725 ASN B 285 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 207 HIS ** E 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095145 restraints weight = 45976.194| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.07 r_work: 0.2965 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.162 35637 Z= 0.404 Angle : 0.747 10.414 48252 Z= 0.391 Chirality : 0.051 0.312 4990 Planarity : 0.006 0.070 6238 Dihedral : 5.890 72.892 4714 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.02 % Allowed : 10.41 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.12), residues: 4235 helix: -0.31 (0.12), residues: 1690 sheet: -0.49 (0.21), residues: 637 loop : -1.79 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 495 TYR 0.034 0.003 TYR E 705 PHE 0.030 0.003 PHE A 160 TRP 0.023 0.003 TRP D 734 HIS 0.008 0.002 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00982 (35634) covalent geometry : angle 0.74559 (48246) SS BOND : bond 0.02431 ( 3) SS BOND : angle 4.78303 ( 6) hydrogen bonds : bond 0.05614 ( 1410) hydrogen bonds : angle 5.47556 ( 3957) *********************** 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 430 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 319 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: A 507 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: A 734 TRP cc_start: 0.7895 (t60) cc_final: 0.7682 (t60) REVERT: A 763 LYS cc_start: 0.8827 (mppt) cc_final: 0.8230 (ttmm) REVERT: A 773 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 792 ASP cc_start: 0.7698 (t0) cc_final: 0.7374 (OUTLIER) REVERT: A 804 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6272 (tmm) REVERT: A 822 ASN cc_start: 0.8284 (m-40) cc_final: 0.8063 (m-40) REVERT: B 300 PHE cc_start: 0.8200 (t80) cc_final: 0.7998 (t80) REVERT: B 363 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6834 (mmm-85) REVERT: B 512 TYR cc_start: 0.8366 (p90) cc_final: 0.7655 (p90) REVERT: B 593 MET cc_start: 0.9079 (ttp) cc_final: 0.8858 (ttp) REVERT: B 631 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: D 229 MET cc_start: 0.7467 (mtp) cc_final: 0.7067 (mtt) REVERT: D 502 MET cc_start: 0.8968 (mtp) cc_final: 0.8527 (mtp) REVERT: D 523 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: D 724 ASP cc_start: 0.8470 (m-30) cc_final: 0.7852 (t0) REVERT: D 764 ILE cc_start: 0.7375 (mp) cc_final: 0.7133 (mt) REVERT: E 249 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7799 (mmm160) REVERT: E 671 ASN cc_start: 0.8486 (t0) cc_final: 0.8121 (t0) REVERT: E 815 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: C 65 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6847 (mp) REVERT: C 148 MET cc_start: 0.8490 (ttt) cc_final: 0.8252 (ttp) REVERT: C 612 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6830 (mmt) REVERT: C 698 MET cc_start: 0.8849 (tpp) cc_final: 0.8624 (tpt) REVERT: C 756 MET cc_start: 0.2693 (ppp) cc_final: 0.2466 (pmm) outliers start: 111 outliers final: 38 residues processed: 390 average time/residue: 0.7729 time to fit residues: 359.3884 Evaluate side-chains 342 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 323 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 300 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 530 ASN E 773 GLN C 301 ASN C 617 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111286 restraints weight = 45503.313| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.12 r_work: 0.3062 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35637 Z= 0.117 Angle : 0.528 12.606 48252 Z= 0.277 Chirality : 0.042 0.207 4990 Planarity : 0.004 0.056 6238 Dihedral : 5.400 77.656 4714 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.15 % Allowed : 12.20 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.00 (0.13), residues: 4235 helix: 0.15 (0.13), residues: 1761 sheet: -0.26 (0.21), residues: 629 loop : -1.57 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 741 TYR 0.029 0.001 TYR A 209 PHE 0.015 0.001 PHE A 160 TRP 0.023 0.001 TRP D 734 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00270 (35634) covalent geometry : angle 0.52262 (48246) SS BOND : bond 0.00792 ( 3) SS BOND : angle 6.53755 ( 6) hydrogen bonds : bond 0.03621 ( 1410) hydrogen bonds : angle 4.92733 ( 3957) *********************** 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 426 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 347 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.8157 (m) cc_final: 0.7833 (p) REVERT: A 31 GLU cc_start: 0.8155 (tt0) cc_final: 0.7855 (pt0) REVERT: A 325 TYR cc_start: 0.6387 (m-80) cc_final: 0.6005 (m-80) REVERT: A 751 ASP cc_start: 0.7243 (t0) cc_final: 0.6694 (t0) REVERT: A 763 LYS cc_start: 0.8727 (mppt) cc_final: 0.8164 (ttmm) REVERT: A 773 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7477 (mm-40) REVERT: A 792 ASP cc_start: 0.7506 (t0) cc_final: 0.7072 (OUTLIER) REVERT: A 804 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.5942 (tmm) REVERT: A 822 ASN cc_start: 0.8220 (m-40) cc_final: 0.8005 (m-40) REVERT: B 132 MET cc_start: 0.8654 (mpp) cc_final: 0.8445 (mpp) REVERT: B 246 TRP cc_start: 0.6326 (t-100) cc_final: 0.6073 (t-100) REVERT: B 363 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6270 (mmm-85) REVERT: B 502 MET cc_start: 0.9059 (mtp) cc_final: 0.8737 (mtm) REVERT: B 512 TYR cc_start: 0.8266 (p90) cc_final: 0.7540 (p90) REVERT: D 24 LYS cc_start: 0.8464 (tptp) cc_final: 0.7966 (mmpt) REVERT: D 115 MET cc_start: 0.9117 (tpp) cc_final: 0.8913 (tpp) REVERT: D 229 MET cc_start: 0.7250 (mtp) cc_final: 0.6864 (mtt) REVERT: D 247 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7688 (tp30) REVERT: D 438 ASP cc_start: 0.8307 (t70) cc_final: 0.8092 (t0) REVERT: D 502 MET cc_start: 0.8742 (mtp) cc_final: 0.8181 (mtp) REVERT: D 764 ILE cc_start: 0.7435 (mp) cc_final: 0.7210 (mt) REVERT: D 789 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5840 (mp10) REVERT: E 42 TYR cc_start: 0.8447 (p90) cc_final: 0.8070 (p90) REVERT: E 249 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7612 (mmm160) REVERT: E 671 ASN cc_start: 0.8266 (t0) cc_final: 0.7879 (t0) REVERT: C 74 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6224 (mmt180) REVERT: C 560 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 643 TYR cc_start: 0.5311 (OUTLIER) cc_final: 0.4330 (t80) REVERT: C 698 MET cc_start: 0.8745 (tpp) cc_final: 0.8514 (tpt) REVERT: C 773 GLN cc_start: 0.5298 (tm-30) cc_final: 0.5025 (mm-40) outliers start: 79 outliers final: 29 residues processed: 401 average time/residue: 0.7562 time to fit residues: 360.4779 Evaluate side-chains 345 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 312 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 150 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 276 optimal weight: 0.0980 chunk 199 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 152 optimal weight: 0.0030 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100272 restraints weight = 45524.839| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.05 r_work: 0.3044 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35637 Z= 0.150 Angle : 0.539 9.738 48252 Z= 0.282 Chirality : 0.042 0.192 4990 Planarity : 0.004 0.054 6238 Dihedral : 5.229 76.815 4713 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.31 % Allowed : 13.15 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.80 (0.13), residues: 4235 helix: 0.36 (0.13), residues: 1737 sheet: -0.15 (0.21), residues: 630 loop : -1.49 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 741 TYR 0.024 0.001 TYR D 72 PHE 0.018 0.001 PHE A 160 TRP 0.023 0.001 TRP D 734 HIS 0.003 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00359 (35634) covalent geometry : angle 0.53545 (48246) SS BOND : bond 0.00950 ( 3) SS BOND : angle 5.71900 ( 6) hydrogen bonds : bond 0.03805 ( 1410) hydrogen bonds : angle 4.83946 ( 3957) *********************** 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 412 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 327 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8135 (tt0) cc_final: 0.7880 (pt0) REVERT: A 325 TYR cc_start: 0.6384 (m-80) cc_final: 0.6061 (m-80) REVERT: A 355 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: A 751 ASP cc_start: 0.7291 (t0) cc_final: 0.6809 (t0) REVERT: A 763 LYS cc_start: 0.8763 (mppt) cc_final: 0.8138 (ttmm) REVERT: A 773 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7633 (mm-40) REVERT: A 792 ASP cc_start: 0.7545 (t0) cc_final: 0.7054 (OUTLIER) REVERT: A 804 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.5935 (tmm) REVERT: B 246 TRP cc_start: 0.6513 (t-100) cc_final: 0.6297 (t-100) REVERT: B 363 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6680 (mmm160) REVERT: B 502 MET cc_start: 0.9102 (mtp) cc_final: 0.8795 (mtm) REVERT: B 512 TYR cc_start: 0.8305 (p90) cc_final: 0.7598 (p90) REVERT: B 645 ASN cc_start: 0.9089 (t0) cc_final: 0.8695 (t0) REVERT: B 765 LYS cc_start: 0.7927 (mppt) cc_final: 0.7716 (mppt) REVERT: B 775 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4979 (pp) REVERT: D 1 MET cc_start: 0.5985 (tmm) cc_final: 0.5279 (tpt) REVERT: D 229 MET cc_start: 0.7257 (mtp) cc_final: 0.6891 (mtt) REVERT: D 247 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7709 (tp30) REVERT: D 249 ARG cc_start: 0.6869 (mmm-85) cc_final: 0.6475 (mmm160) REVERT: D 438 ASP cc_start: 0.8315 (t70) cc_final: 0.8104 (t70) REVERT: D 502 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8389 (mtp) REVERT: D 764 ILE cc_start: 0.7435 (mp) cc_final: 0.7203 (mt) REVERT: D 789 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.5982 (mp10) REVERT: E 249 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7789 (mmm160) REVERT: E 363 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6072 (ptm-80) REVERT: E 512 TYR cc_start: 0.8747 (p90) cc_final: 0.8455 (p90) REVERT: E 671 ASN cc_start: 0.8297 (t0) cc_final: 0.7910 (t0) REVERT: E 792 ASP cc_start: 0.7379 (t70) cc_final: 0.6868 (t0) REVERT: E 815 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6668 (tt0) REVERT: C 306 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6998 (mm) REVERT: C 392 PHE cc_start: 0.7416 (m-10) cc_final: 0.7210 (m-10) REVERT: C 643 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.4472 (t80) REVERT: C 698 MET cc_start: 0.8785 (tpp) cc_final: 0.8559 (tpt) REVERT: C 756 MET cc_start: 0.4174 (OUTLIER) cc_final: 0.3332 (ppp) REVERT: C 773 GLN cc_start: 0.5374 (tm-30) cc_final: 0.5143 (mm-40) outliers start: 85 outliers final: 41 residues processed: 382 average time/residue: 0.7504 time to fit residues: 340.9292 Evaluate side-chains 360 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 804 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 363 ARG Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 756 MET Chi-restraints excluded: chain C residue 796 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 58 optimal weight: 1.9990 chunk 385 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 415 optimal weight: 0.2980 chunk 422 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 416 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 810 ASN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.148410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100695 restraints weight = 45387.278| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.11 r_work: 0.3047 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35637 Z= 0.135 Angle : 0.524 10.990 48252 Z= 0.274 Chirality : 0.042 0.211 4990 Planarity : 0.004 0.054 6238 Dihedral : 5.141 76.914 4713 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.66 % Allowed : 13.26 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.66 (0.13), residues: 4235 helix: 0.46 (0.13), residues: 1743 sheet: -0.03 (0.21), residues: 630 loop : -1.42 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 741 TYR 0.020 0.001 TYR B 696 PHE 0.032 0.001 PHE B 300 TRP 0.025 0.001 TRP D 734 HIS 0.003 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00321 (35634) covalent geometry : angle 0.52050 (48246) SS BOND : bond 0.00723 ( 3) SS BOND : angle 5.76168 ( 6) hydrogen bonds : bond 0.03623 ( 1410) hydrogen bonds : angle 4.77032 ( 3957) *********************** 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 427 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 329 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6419 (m-80) cc_final: 0.6099 (m-80) REVERT: A 335 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8488 (mtp) REVERT: A 668 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9223 (ttp) REVERT: A 751 ASP cc_start: 0.7299 (t0) cc_final: 0.6836 (t0) REVERT: A 763 LYS cc_start: 0.8747 (mppt) cc_final: 0.8259 (mmmt) REVERT: A 773 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7629 (mm-40) REVERT: A 792 ASP cc_start: 0.7549 (t0) cc_final: 0.7125 (OUTLIER) REVERT: B 246 TRP cc_start: 0.6640 (t-100) cc_final: 0.5739 (t-100) REVERT: B 363 ARG cc_start: 0.7021 (mmm-85) cc_final: 0.6634 (mmm160) REVERT: B 502 MET cc_start: 0.9111 (mtp) cc_final: 0.8821 (mtm) REVERT: B 512 TYR cc_start: 0.8270 (p90) cc_final: 0.7589 (p90) REVERT: B 645 ASN cc_start: 0.9095 (t0) cc_final: 0.8718 (t0) REVERT: B 775 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4906 (pp) REVERT: D 229 MET cc_start: 0.7237 (mtp) cc_final: 0.6863 (mtt) REVERT: D 247 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7745 (tp30) REVERT: D 249 ARG cc_start: 0.6898 (mmm-85) cc_final: 0.6499 (mmm160) REVERT: D 502 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8389 (mtp) REVERT: D 754 MET cc_start: 0.8284 (ttt) cc_final: 0.8000 (ttt) REVERT: D 764 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7131 (mt) REVERT: D 789 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6097 (mp10) REVERT: E 42 TYR cc_start: 0.8465 (p90) cc_final: 0.7916 (p90) REVERT: E 249 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7732 (mmm160) REVERT: E 352 MET cc_start: 0.8325 (mtm) cc_final: 0.8114 (mtp) REVERT: E 363 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.6016 (ptm-80) REVERT: E 512 TYR cc_start: 0.8760 (p90) cc_final: 0.8472 (p90) REVERT: E 521 ASP cc_start: 0.8622 (t0) cc_final: 0.8410 (t70) REVERT: E 668 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: E 671 ASN cc_start: 0.8306 (t0) cc_final: 0.7917 (t0) REVERT: E 792 ASP cc_start: 0.7419 (t70) cc_final: 0.7012 (t0) REVERT: E 815 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: C 74 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6242 (mmt180) REVERT: C 116 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8685 (mt-10) REVERT: C 253 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: C 306 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7002 (mm) REVERT: C 554 LEU cc_start: 0.8896 (tp) cc_final: 0.7989 (mp) REVERT: C 579 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: C 643 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.4384 (t80) REVERT: C 698 MET cc_start: 0.8778 (tpp) cc_final: 0.8551 (tpt) REVERT: C 756 MET cc_start: 0.4210 (pmm) cc_final: 0.3249 (ppp) outliers start: 98 outliers final: 50 residues processed: 390 average time/residue: 0.7403 time to fit residues: 345.7307 Evaluate side-chains 377 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 363 ARG Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 668 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 720 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 313 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 416 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 12 GLN C 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099262 restraints weight = 45530.755| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.10 r_work: 0.3026 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35637 Z= 0.175 Angle : 0.559 10.713 48252 Z= 0.291 Chirality : 0.043 0.203 4990 Planarity : 0.004 0.053 6238 Dihedral : 5.146 75.592 4713 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.93 % Allowed : 13.23 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.68 (0.13), residues: 4235 helix: 0.44 (0.13), residues: 1749 sheet: -0.04 (0.21), residues: 630 loop : -1.43 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 741 TYR 0.021 0.001 TYR B 696 PHE 0.020 0.001 PHE A 160 TRP 0.027 0.001 TRP D 734 HIS 0.004 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00422 (35634) covalent geometry : angle 0.55533 (48246) SS BOND : bond 0.01022 ( 3) SS BOND : angle 5.99269 ( 6) hydrogen bonds : bond 0.03878 ( 1410) hydrogen bonds : angle 4.81469 ( 3957) *********************** 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 431 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 323 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6456 (m-80) cc_final: 0.6128 (m-80) REVERT: A 335 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8537 (mtp) REVERT: A 668 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.9268 (ttp) REVERT: A 751 ASP cc_start: 0.7300 (t0) cc_final: 0.6818 (t0) REVERT: A 763 LYS cc_start: 0.8711 (mppt) cc_final: 0.8202 (tttt) REVERT: A 773 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7631 (mm-40) REVERT: A 792 ASP cc_start: 0.7624 (t0) cc_final: 0.7170 (OUTLIER) REVERT: B 1 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4389 (ttm) REVERT: B 246 TRP cc_start: 0.6769 (t-100) cc_final: 0.5934 (t-100) REVERT: B 363 ARG cc_start: 0.7038 (mmm-85) cc_final: 0.6463 (mmm160) REVERT: B 512 TYR cc_start: 0.8309 (p90) cc_final: 0.7665 (p90) REVERT: B 645 ASN cc_start: 0.9100 (t0) cc_final: 0.8720 (t0) REVERT: B 775 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4931 (pp) REVERT: D 1 MET cc_start: 0.5975 (tmm) cc_final: 0.5112 (tpt) REVERT: D 229 MET cc_start: 0.7272 (mtp) cc_final: 0.6918 (mtt) REVERT: D 247 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7757 (tp30) REVERT: D 502 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8443 (mtp) REVERT: D 764 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7062 (mt) REVERT: D 789 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6059 (mp10) REVERT: D 828 THR cc_start: 0.7903 (m) cc_final: 0.7670 (m) REVERT: E 249 ARG cc_start: 0.8067 (tpp80) cc_final: 0.7730 (mmm160) REVERT: E 352 MET cc_start: 0.8340 (mtm) cc_final: 0.8120 (mtp) REVERT: E 363 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5970 (ptm-80) REVERT: E 512 TYR cc_start: 0.8776 (p90) cc_final: 0.8495 (p90) REVERT: E 671 ASN cc_start: 0.8349 (t0) cc_final: 0.7961 (t0) REVERT: E 754 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.5499 (pmt) REVERT: E 792 ASP cc_start: 0.7371 (t70) cc_final: 0.7043 (t0) REVERT: E 815 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6710 (tt0) REVERT: C 74 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6239 (mmt180) REVERT: C 116 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8770 (mt-10) REVERT: C 276 CYS cc_start: 0.8347 (m) cc_final: 0.7846 (p) REVERT: C 300 PHE cc_start: 0.7689 (t80) cc_final: 0.7462 (t80) REVERT: C 306 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6985 (mm) REVERT: C 579 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: C 643 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.4388 (t80) REVERT: C 698 MET cc_start: 0.8796 (tpp) cc_final: 0.8574 (tpt) REVERT: C 742 TRP cc_start: 0.3748 (t-100) cc_final: 0.2600 (m100) REVERT: C 773 GLN cc_start: 0.5374 (tm-30) cc_final: 0.5114 (mm-40) outliers start: 108 outliers final: 54 residues processed: 387 average time/residue: 0.7346 time to fit residues: 340.9113 Evaluate side-chains 380 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 764 ILE Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 363 ARG Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 680 GLU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 796 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 148 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 421 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 249 optimal weight: 0.0470 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 12 GLN E 810 ASN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101062 restraints weight = 45507.175| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.06 r_work: 0.3054 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35637 Z= 0.131 Angle : 0.534 12.478 48252 Z= 0.277 Chirality : 0.042 0.203 4990 Planarity : 0.004 0.054 6238 Dihedral : 5.058 76.236 4713 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.28 % Allowed : 14.32 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.56 (0.13), residues: 1742 sheet: 0.04 (0.21), residues: 630 loop : -1.35 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 741 TYR 0.020 0.001 TYR B 696 PHE 0.016 0.001 PHE A 160 TRP 0.029 0.001 TRP D 734 HIS 0.003 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00310 (35634) covalent geometry : angle 0.52992 (48246) SS BOND : bond 0.00900 ( 3) SS BOND : angle 5.86601 ( 6) hydrogen bonds : bond 0.03593 ( 1410) hydrogen bonds : angle 4.73401 ( 3957) *********************** 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 413 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 329 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 325 TYR cc_start: 0.6391 (m-80) cc_final: 0.6084 (m-80) REVERT: A 335 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8499 (mtp) REVERT: A 668 MET cc_start: 0.9568 (OUTLIER) cc_final: 0.9175 (ttp) REVERT: A 751 ASP cc_start: 0.7279 (t0) cc_final: 0.6777 (t0) REVERT: A 763 LYS cc_start: 0.8690 (mppt) cc_final: 0.8182 (tttt) REVERT: A 765 LYS cc_start: 0.8250 (tmmt) cc_final: 0.8029 (tmmt) REVERT: A 773 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7587 (mm-40) REVERT: A 792 ASP cc_start: 0.7576 (t0) cc_final: 0.7121 (OUTLIER) REVERT: B 1 MET cc_start: 0.4906 (OUTLIER) cc_final: 0.4390 (ttm) REVERT: B 246 TRP cc_start: 0.6732 (t-100) cc_final: 0.5953 (t-100) REVERT: B 363 ARG cc_start: 0.7075 (mmm-85) cc_final: 0.6547 (mmm160) REVERT: B 512 TYR cc_start: 0.8290 (p90) cc_final: 0.7588 (p90) REVERT: B 645 ASN cc_start: 0.9076 (t0) cc_final: 0.8708 (t0) REVERT: B 775 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4855 (pp) REVERT: D 229 MET cc_start: 0.7287 (mtp) cc_final: 0.6856 (mtt) REVERT: D 247 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7786 (tp30) REVERT: D 502 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: D 754 MET cc_start: 0.8226 (ttt) cc_final: 0.7915 (ttt) REVERT: D 789 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: D 828 THR cc_start: 0.7889 (m) cc_final: 0.7679 (m) REVERT: E 42 TYR cc_start: 0.8419 (p90) cc_final: 0.7883 (p90) REVERT: E 249 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7700 (mmm160) REVERT: E 352 MET cc_start: 0.8309 (mtm) cc_final: 0.8089 (mtp) REVERT: E 363 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6119 (ptm-80) REVERT: E 512 TYR cc_start: 0.8747 (p90) cc_final: 0.8470 (p90) REVERT: E 521 ASP cc_start: 0.8641 (t0) cc_final: 0.8432 (t70) REVERT: E 671 ASN cc_start: 0.8291 (t0) cc_final: 0.7904 (t0) REVERT: E 792 ASP cc_start: 0.7323 (t70) cc_final: 0.6893 (t0) REVERT: E 815 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: C 74 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6211 (mmt180) REVERT: C 116 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: C 276 CYS cc_start: 0.8308 (m) cc_final: 0.7840 (p) REVERT: C 300 PHE cc_start: 0.7675 (t80) cc_final: 0.7436 (t80) REVERT: C 306 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6878 (mm) REVERT: C 328 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6812 (pm20) REVERT: C 560 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 579 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8136 (mtm) REVERT: C 643 TYR cc_start: 0.5348 (OUTLIER) cc_final: 0.4344 (t80) REVERT: C 742 TRP cc_start: 0.3705 (t-100) cc_final: 0.2597 (m100) REVERT: C 756 MET cc_start: 0.3285 (pmt) cc_final: 0.2088 (tmm) REVERT: C 773 GLN cc_start: 0.5334 (tm-30) cc_final: 0.5126 (mm-40) outliers start: 84 outliers final: 49 residues processed: 379 average time/residue: 0.7506 time to fit residues: 339.6704 Evaluate side-chains 374 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 363 ARG Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 643 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 201 optimal weight: 0.0670 chunk 390 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 417 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN D 545 HIS E 12 GLN C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100031 restraints weight = 45258.503| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.07 r_work: 0.3049 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35637 Z= 0.167 Angle : 0.561 15.229 48252 Z= 0.291 Chirality : 0.043 0.216 4990 Planarity : 0.004 0.059 6238 Dihedral : 5.075 75.140 4713 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.28 % Allowed : 14.81 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.58 (0.13), residues: 4235 helix: 0.52 (0.13), residues: 1749 sheet: -0.02 (0.21), residues: 634 loop : -1.37 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 741 TYR 0.021 0.001 TYR B 696 PHE 0.019 0.001 PHE A 160 TRP 0.033 0.001 TRP D 734 HIS 0.003 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00404 (35634) covalent geometry : angle 0.55724 (48246) SS BOND : bond 0.00961 ( 3) SS BOND : angle 5.69943 ( 6) hydrogen bonds : bond 0.03850 ( 1410) hydrogen bonds : angle 4.76718 ( 3957) *********************** 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 404 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 320 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6459 (m-80) cc_final: 0.6131 (m-80) REVERT: A 335 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (mtp) REVERT: A 668 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.9249 (ttp) REVERT: A 751 ASP cc_start: 0.7311 (t0) cc_final: 0.6832 (t0) REVERT: A 763 LYS cc_start: 0.8728 (mppt) cc_final: 0.8267 (mmmt) REVERT: A 765 LYS cc_start: 0.8278 (tmmt) cc_final: 0.8070 (tmmt) REVERT: A 773 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7647 (mm-40) REVERT: A 792 ASP cc_start: 0.7714 (t0) cc_final: 0.7252 (OUTLIER) REVERT: B 246 TRP cc_start: 0.6763 (t-100) cc_final: 0.5998 (t-100) REVERT: B 363 ARG cc_start: 0.7149 (mmm-85) cc_final: 0.6647 (mmm160) REVERT: B 512 TYR cc_start: 0.8323 (p90) cc_final: 0.7657 (p90) REVERT: B 645 ASN cc_start: 0.9125 (t0) cc_final: 0.8776 (t0) REVERT: B 765 LYS cc_start: 0.7890 (mppt) cc_final: 0.7482 (mptp) REVERT: B 775 LEU cc_start: 0.5134 (OUTLIER) cc_final: 0.4757 (pp) REVERT: D 1 MET cc_start: 0.6174 (tmm) cc_final: 0.5250 (tmm) REVERT: D 229 MET cc_start: 0.7232 (mtp) cc_final: 0.6853 (mtt) REVERT: D 247 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7794 (tp30) REVERT: D 502 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8418 (mtp) REVERT: D 754 MET cc_start: 0.8256 (ttt) cc_final: 0.7857 (ttt) REVERT: D 764 ILE cc_start: 0.7096 (mt) cc_final: 0.6789 (mp) REVERT: D 789 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: D 828 THR cc_start: 0.7901 (m) cc_final: 0.7674 (m) REVERT: E 42 TYR cc_start: 0.8456 (p90) cc_final: 0.7926 (p90) REVERT: E 249 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7708 (mmm160) REVERT: E 352 MET cc_start: 0.8374 (mtm) cc_final: 0.8152 (mtp) REVERT: E 512 TYR cc_start: 0.8817 (p90) cc_final: 0.8549 (p90) REVERT: E 521 ASP cc_start: 0.8663 (t0) cc_final: 0.8462 (t70) REVERT: E 671 ASN cc_start: 0.8350 (t0) cc_final: 0.7967 (t0) REVERT: E 792 ASP cc_start: 0.7347 (t70) cc_final: 0.6949 (t0) REVERT: E 815 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6725 (tt0) REVERT: C 116 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8753 (mt-10) REVERT: C 276 CYS cc_start: 0.8369 (m) cc_final: 0.7924 (p) REVERT: C 300 PHE cc_start: 0.7734 (t80) cc_final: 0.7485 (t80) REVERT: C 306 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6968 (mm) REVERT: C 328 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6806 (pm20) REVERT: C 579 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8241 (mtm) REVERT: C 643 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.4461 (t80) REVERT: C 742 TRP cc_start: 0.3694 (t-100) cc_final: 0.2481 (m100) REVERT: C 756 MET cc_start: 0.3240 (pmt) cc_final: 0.2006 (tmm) outliers start: 84 outliers final: 54 residues processed: 371 average time/residue: 0.7367 time to fit residues: 328.1741 Evaluate side-chains 375 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 360 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 307 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 381 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 12 GLN C 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099928 restraints weight = 45503.258| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.07 r_work: 0.3046 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35637 Z= 0.169 Angle : 0.563 14.875 48252 Z= 0.292 Chirality : 0.043 0.219 4990 Planarity : 0.004 0.058 6238 Dihedral : 5.089 74.585 4713 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.88 % Allowed : 15.22 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.57 (0.13), residues: 4235 helix: 0.53 (0.13), residues: 1749 sheet: -0.03 (0.21), residues: 634 loop : -1.36 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 741 TYR 0.027 0.001 TYR D 72 PHE 0.019 0.001 PHE A 160 TRP 0.037 0.001 TRP D 734 HIS 0.004 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00408 (35634) covalent geometry : angle 0.55936 (48246) SS BOND : bond 0.00947 ( 3) SS BOND : angle 5.61141 ( 6) hydrogen bonds : bond 0.03855 ( 1410) hydrogen bonds : angle 4.78803 ( 3957) ********************** 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 386 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 317 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6463 (m-80) cc_final: 0.6141 (m-80) REVERT: A 335 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (mtp) REVERT: A 668 MET cc_start: 0.9607 (OUTLIER) cc_final: 0.9252 (ttp) REVERT: A 751 ASP cc_start: 0.7312 (t0) cc_final: 0.6829 (t0) REVERT: A 763 LYS cc_start: 0.8726 (mppt) cc_final: 0.8262 (mmmt) REVERT: A 765 LYS cc_start: 0.8269 (tmmt) cc_final: 0.8061 (tmmt) REVERT: A 792 ASP cc_start: 0.7720 (t0) cc_final: 0.7303 (OUTLIER) REVERT: B 246 TRP cc_start: 0.6727 (t-100) cc_final: 0.5990 (t-100) REVERT: B 363 ARG cc_start: 0.7153 (mmm-85) cc_final: 0.6677 (mmm160) REVERT: B 512 TYR cc_start: 0.8330 (p90) cc_final: 0.7671 (p90) REVERT: B 645 ASN cc_start: 0.9120 (t0) cc_final: 0.8780 (t0) REVERT: B 765 LYS cc_start: 0.7948 (mppt) cc_final: 0.7469 (mptp) REVERT: B 776 ASN cc_start: 0.6788 (t0) cc_final: 0.6256 (m110) REVERT: D 1 MET cc_start: 0.6304 (tmm) cc_final: 0.5229 (tmm) REVERT: D 229 MET cc_start: 0.7263 (mtp) cc_final: 0.6804 (mtt) REVERT: D 247 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7784 (tp30) REVERT: D 502 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8419 (mtp) REVERT: D 754 MET cc_start: 0.8261 (ttt) cc_final: 0.7851 (ttt) REVERT: D 764 ILE cc_start: 0.7121 (mt) cc_final: 0.6810 (mp) REVERT: D 789 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6111 (mp10) REVERT: D 828 THR cc_start: 0.7904 (m) cc_final: 0.7676 (m) REVERT: E 42 TYR cc_start: 0.8469 (p90) cc_final: 0.7942 (p90) REVERT: E 249 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7727 (mmm160) REVERT: E 352 MET cc_start: 0.8385 (mtm) cc_final: 0.8169 (mtp) REVERT: E 512 TYR cc_start: 0.8826 (p90) cc_final: 0.8557 (p90) REVERT: E 521 ASP cc_start: 0.8668 (t0) cc_final: 0.8464 (t70) REVERT: E 671 ASN cc_start: 0.8355 (t0) cc_final: 0.7981 (t0) REVERT: E 792 ASP cc_start: 0.7313 (t70) cc_final: 0.6928 (t70) REVERT: E 815 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6761 (tt0) REVERT: C 116 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8761 (mt-10) REVERT: C 276 CYS cc_start: 0.8476 (m) cc_final: 0.7939 (p) REVERT: C 300 PHE cc_start: 0.7729 (t80) cc_final: 0.7500 (t80) REVERT: C 328 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6801 (pm20) REVERT: C 579 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: C 612 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7326 (mtm) REVERT: C 643 TYR cc_start: 0.5483 (OUTLIER) cc_final: 0.4451 (t80) REVERT: C 742 TRP cc_start: 0.3628 (t-100) cc_final: 0.2432 (m100) REVERT: C 756 MET cc_start: 0.3189 (pmt) cc_final: 0.1924 (tmm) outliers start: 69 outliers final: 54 residues processed: 363 average time/residue: 0.7206 time to fit residues: 313.6200 Evaluate side-chains 372 residues out of total 3680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 789 GLN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 292 TYR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 779 VAL Chi-restraints excluded: chain E residue 815 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 292 TYR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 643 TYR Chi-restraints excluded: chain C residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 287 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 292 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 263 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 HIS E 12 GLN C 280 HIS C 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102184 restraints weight = 45372.894| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.05 r_work: 0.3072 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35637 Z= 0.118 Angle : 0.522 9.970 48252 Z= 0.272 Chirality : 0.041 0.202 4990 Planarity : 0.004 0.059 6238 Dihedral : 4.945 76.078 4713 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.93 % Allowed : 15.30 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.34 (0.13), residues: 4235 helix: 0.70 (0.13), residues: 1744 sheet: 0.14 (0.21), residues: 644 loop : -1.24 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 741 TYR 0.019 0.001 TYR B 174 PHE 0.019 0.001 PHE D 677 TRP 0.034 0.001 TRP D 734 HIS 0.002 0.001 HIS E 534 Details of bonding type rmsd covalent geometry : bond 0.00276 (35634) covalent geometry : angle 0.51906 (48246) SS BOND : bond 0.00719 ( 3) SS BOND : angle 5.15596 ( 6) hydrogen bonds : bond 0.03438 ( 1410) hydrogen bonds : angle 4.63602 ( 3957) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13396.17 seconds wall clock time: 228 minutes 45.95 seconds (13725.95 seconds total)