Starting phenix.real_space_refine (version: dev) on Sat Apr 9 11:13:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m0s_30035/04_2022/6m0s_30035.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 44660 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 12033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 12033 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 21, 'TRANS': 722} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1159 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1044 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "B" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5490 Classifications: {'peptide': 345} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 335, 'PCIS': 2} Chain: "C" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3012 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "D" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2340 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 830 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 20.97, per 1000 atoms: 0.47 Number of scatterers: 44660 At special positions: 0 Unit cell: (135, 118.8, 126.36, 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 135 16.00 O 3929 8.00 N 3531 7.00 C 14447 6.00 H 22618 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 34.30 Conformation dependent library (CDL) restraints added in 3.7 seconds 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 4 sheets defined 76.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.803A pdb=" N ALA A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.827A pdb=" N LYS A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.840A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 64 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.622A pdb=" N TYR A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.667A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 4.116A pdb=" N ALA A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.543A pdb=" N LYS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 307 removed outlier: 3.587A pdb=" N GLN A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 removed outlier: 4.458A pdb=" N GLN A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.757A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 4.591A pdb=" N GLY A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.761A pdb=" N LEU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.826A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.655A pdb=" N MET A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 removed outlier: 3.818A pdb=" N LEU A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 563 removed outlier: 4.083A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS A 547 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 549 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.855A pdb=" N GLY A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 595 removed outlier: 3.514A pdb=" N ILE A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.783A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 659 removed outlier: 3.554A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 4.134A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix removed outlier: 3.564A pdb=" N PHE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 726 removed outlier: 3.623A pdb=" N THR A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 724 " --> pdb=" O ILE A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 733 removed outlier: 3.565A pdb=" N SER A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 753 removed outlier: 3.644A pdb=" N ALA A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 749 " --> pdb=" O GLN A 745 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 removed outlier: 4.291A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 759' Processing helix chain 'A' and resid 762 through 785 removed outlier: 3.569A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 803 removed outlier: 3.524A pdb=" N SER A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 25 removed outlier: 3.996A pdb=" N VAL M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP M 22 " --> pdb=" O SER M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 54 removed outlier: 3.798A pdb=" N ILE M 38 " --> pdb=" O ARG M 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA M 42 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET M 47 " --> pdb=" O MET M 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP M 48 " --> pdb=" O MET M 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR M 51 " --> pdb=" O MET M 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS M 54 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 33 removed outlier: 3.508A pdb=" N CYS O 12 " --> pdb=" O GLY O 8 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 40 Processing helix chain 'O' and resid 48 through 75 removed outlier: 4.349A pdb=" N THR O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR O 62 " --> pdb=" O ALA O 58 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN O 72 " --> pdb=" O PHE O 68 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.613A pdb=" N VAL B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.725A pdb=" N ASN B 32 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.540A pdb=" N LEU B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 47 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.631A pdb=" N ILE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.762A pdb=" N ILE B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.872A pdb=" N GLN B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.579A pdb=" N LEU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.717A pdb=" N PHE B 162 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.916A pdb=" N ILE B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.766A pdb=" N ALA B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.644A pdb=" N THR B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 230 removed outlier: 3.685A pdb=" N ASN B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.571A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.530A pdb=" N VAL B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 7.091A pdb=" N GLU B 274 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 275 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 276 " --> pdb=" O TYR B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 276' Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.627A pdb=" N HIS B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 332 removed outlier: 3.919A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 removed outlier: 4.226A pdb=" N TYR C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR C 23 " --> pdb=" O HIS C 19 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 26 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 46 through 53 removed outlier: 3.607A pdb=" N PHE C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 4.165A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 63 " --> pdb=" O TRP C 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 92 No H-bonds generated for 'chain 'C' and resid 91 through 92' Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.708A pdb=" N ILE C 96 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 98 " --> pdb=" O ARG C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 93 through 98' Processing helix chain 'C' and resid 99 through 100 No H-bonds generated for 'chain 'C' and resid 99 through 100' Processing helix chain 'C' and resid 101 through 123 removed outlier: 3.589A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 117 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 177 removed outlier: 3.797A pdb=" N THR C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 151 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 206 removed outlier: 3.596A pdb=" N ILE C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 206 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 49 removed outlier: 3.868A pdb=" N ALA D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY D 22 " --> pdb=" O PHE D 18 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 27 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 37 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 removed outlier: 3.590A pdb=" N LEU D 55 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 56 " --> pdb=" O PRO D 53 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET D 57 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS D 58 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 82 removed outlier: 4.001A pdb=" N VAL D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 126 removed outlier: 3.616A pdb=" N GLY D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 164 removed outlier: 3.771A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.918A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 15 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA E 20 " --> pdb=" O GLY E 16 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS E 40 " --> pdb=" O GLY E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 76 removed outlier: 3.777A pdb=" N ILE E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 120 removed outlier: 3.920A pdb=" N GLN E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 125 through 154 removed outlier: 3.848A pdb=" N ILE E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 43 removed outlier: 3.920A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 45 No H-bonds generated for 'chain 'F' and resid 44 through 45' Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.670A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 73 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 120 removed outlier: 3.707A pdb=" N ILE F 89 " --> pdb=" O TYR F 85 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY F 98 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE F 110 " --> pdb=" O PHE F 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 152 removed outlier: 4.342A pdb=" N GLY F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU F 149 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 43 removed outlier: 3.840A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA G 20 " --> pdb=" O GLY G 16 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.886A pdb=" N LEU G 50 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 76 removed outlier: 3.619A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL G 70 " --> pdb=" O TYR G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 118 removed outlier: 3.845A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 124 No H-bonds generated for 'chain 'G' and resid 122 through 124' Processing helix chain 'G' and resid 125 through 156 removed outlier: 3.734A pdb=" N ILE G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA G 147 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 43 removed outlier: 4.020A pdb=" N GLY H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 29 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.893A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 76 removed outlier: 3.614A pdb=" N ILE H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 120 removed outlier: 3.567A pdb=" N GLN H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL H 116 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 124 No H-bonds generated for 'chain 'H' and resid 122 through 124' Processing helix chain 'H' and resid 125 through 153 removed outlier: 3.987A pdb=" N PHE H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA H 136 " --> pdb=" O ILE H 132 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 148 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 3.663A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE I 15 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY I 16 " --> pdb=" O PHE I 12 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY I 31 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS I 40 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 53 removed outlier: 4.490A pdb=" N PHE I 51 " --> pdb=" O ASP I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.948A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.847A pdb=" N ILE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 151 removed outlier: 3.918A pdb=" N ILE I 130 " --> pdb=" O PHE I 126 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU I 131 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA I 136 " --> pdb=" O ILE I 132 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL I 146 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA I 147 " --> pdb=" O GLY I 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 41 removed outlier: 3.798A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR J 32 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 54 through 67 removed outlier: 4.167A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 76 removed outlier: 3.812A pdb=" N SER J 71 " --> pdb=" O GLY J 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 120 removed outlier: 3.605A pdb=" N ILE J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY J 94 " --> pdb=" O GLN J 90 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY J 109 " --> pdb=" O GLY J 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 124 No H-bonds generated for 'chain 'J' and resid 122 through 124' Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.700A pdb=" N LEU J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 153 removed outlier: 3.846A pdb=" N GLY J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL J 146 " --> pdb=" O TYR J 142 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN J 151 " --> pdb=" O ALA J 147 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 43 removed outlier: 4.018A pdb=" N GLY K 16 " --> pdb=" O PHE K 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS K 40 " --> pdb=" O GLY K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.901A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 122 removed outlier: 3.520A pdb=" N GLY K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 97 " --> pdb=" O ALA K 93 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN K 121 " --> pdb=" O ARG K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 153 removed outlier: 3.557A pdb=" N ILE K 130 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 43 removed outlier: 3.662A pdb=" N ALA L 20 " --> pdb=" O GLY L 16 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 45 No H-bonds generated for 'chain 'L' and resid 44 through 45' Processing helix chain 'L' and resid 46 through 50 removed outlier: 3.763A pdb=" N LEU L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 62 removed outlier: 3.650A pdb=" N ALA L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 74 removed outlier: 3.508A pdb=" N GLY L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL L 69 " --> pdb=" O ILE L 65 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL L 70 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 78 removed outlier: 3.593A pdb=" N LEU L 78 " --> pdb=" O CYS L 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 75 through 78' Processing helix chain 'L' and resid 83 through 120 removed outlier: 3.560A pdb=" N PHE L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER L 96 " --> pdb=" O GLY L 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L 102 " --> pdb=" O GLY L 98 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA L 103 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY L 109 " --> pdb=" O GLY L 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 124 No H-bonds generated for 'chain 'L' and resid 122 through 124' Processing helix chain 'L' and resid 125 through 138 removed outlier: 3.513A pdb=" N MET L 129 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA L 136 " --> pdb=" O ILE L 132 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 137 " --> pdb=" O LEU L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 153 removed outlier: 4.210A pdb=" N GLY L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL L 146 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU L 148 " --> pdb=" O LEU L 144 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 225 Processing helix chain 'N' and resid 227 through 246 removed outlier: 3.977A pdb=" N LEU N 237 " --> pdb=" O LEU N 233 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER N 242 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.540A pdb=" N ALA A 337 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 341 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 15 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 371 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 369 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.861A pdb=" N GLY A 189 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 236 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 237 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 214 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 212 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 507 1281 hydrogen bonds defined for protein. 3762 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: 15.41 Time building geometry restraints manager: 35.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22552 1.03 - 1.23: 67 1.23 - 1.42: 9280 1.42 - 1.62: 13003 1.62 - 1.81: 204 Bond restraints: 45106 Sorted by residual: bond pdb=" C LEU B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.331 1.353 -0.021 1.21e-02 6.83e+03 3.08e+00 bond pdb=" C THR B 156 " pdb=" N PRO B 157 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.67e+00 bond pdb=" CB PRO A 574 " pdb=" CG PRO A 574 " ideal model delta sigma weight residual 1.492 1.429 0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" CB TRP A 737 " pdb=" CG TRP A 737 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.10e+00 bond pdb=" CA VAL K 55 " pdb=" CB VAL K 55 " ideal model delta sigma weight residual 1.534 1.541 -0.007 6.80e-03 2.16e+04 1.06e+00 ... (remaining 45101 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 430 105.83 - 112.88: 53165 112.88 - 119.94: 12481 119.94 - 126.99: 15394 126.99 - 134.05: 186 Bond angle restraints: 81656 Sorted by residual: angle pdb=" C PHE A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.24 123.53 -3.29 6.30e-01 2.52e+00 2.72e+01 angle pdb=" N ILE F 54 " pdb=" CA ILE F 54 " pdb=" C ILE F 54 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.85e+01 angle pdb=" CA GLY F 79 " pdb=" C GLY F 79 " pdb=" N GLN F 80 " ideal model delta sigma weight residual 114.58 117.48 -2.90 8.60e-01 1.35e+00 1.13e+01 angle pdb=" C SER G 35 " pdb=" N GLY G 36 " pdb=" CA GLY G 36 " ideal model delta sigma weight residual 120.03 123.78 -3.75 1.12e+00 7.97e-01 1.12e+01 angle pdb=" C ILE A 573 " pdb=" CA ILE A 573 " pdb=" CB ILE A 573 " ideal model delta sigma weight residual 114.35 110.98 3.37 1.06e+00 8.90e-01 1.01e+01 ... (remaining 81651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 16782 15.46 - 30.91: 1013 30.91 - 46.37: 61 46.37 - 61.83: 2 61.83 - 77.28: 14 Dihedral angle restraints: 17872 sinusoidal: 8019 harmonic: 9853 Sorted by residual: dihedral pdb=" CA VAL B 152 " pdb=" C VAL B 152 " pdb=" N LEU B 153 " pdb=" CA LEU B 153 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE A 423 " pdb=" C PHE A 423 " pdb=" N GLY A 424 " pdb=" CA GLY A 424 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP B 132 " pdb=" C TRP B 132 " pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 17869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2186 0.029 - 0.059: 974 0.059 - 0.088: 358 0.088 - 0.118: 103 0.118 - 0.147: 18 Chirality restraints: 3639 Sorted by residual: chirality pdb=" CA VAL A 100 " pdb=" N VAL A 100 " pdb=" C VAL A 100 " pdb=" CB VAL A 100 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE B 200 " pdb=" N ILE B 200 " pdb=" C ILE B 200 " pdb=" CB ILE B 200 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL A 190 " pdb=" N VAL A 190 " pdb=" C VAL A 190 " pdb=" CB VAL A 190 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 3636 not shown) Planarity restraints: 6592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 21 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 22 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 5 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO H 6 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 6 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 6 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 22 " -0.013 2.00e-02 2.50e+03 8.24e-03 2.72e+00 pdb=" CG TRP M 22 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP M 22 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP M 22 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 22 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 22 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP M 22 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 22 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 22 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP M 22 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP M 22 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP M 22 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP M 22 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 22 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 22 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP M 22 " 0.001 2.00e-02 2.50e+03 ... (remaining 6589 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3116 2.23 - 2.82: 99244 2.82 - 3.42: 110422 3.42 - 4.01: 151814 4.01 - 4.60: 241875 Nonbonded interactions: 606471 Sorted by model distance: nonbonded pdb=" OE1 GLN B 86 " pdb="HH11 ARG L 117 " model vdw 1.640 1.850 nonbonded pdb=" O SER A 797 " pdb=" HD1 HIS A 801 " model vdw 1.691 1.850 nonbonded pdb=" OE2 GLU B 14 " pdb=" HE ARG B 18 " model vdw 1.726 1.850 nonbonded pdb=" O ASP A 243 " pdb=" HZ2 LYS A 247 " model vdw 1.729 1.850 nonbonded pdb=" O SER A 11 " pdb="HH11 ARG A 403 " model vdw 1.731 1.850 ... (remaining 606466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 14447 2.51 5 N 3531 2.21 5 O 3929 1.98 5 H 22618 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.680 Extract box with map and model: 6.200 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.390 Process input model: 125.720 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.004 0.063 22488 Z= 0.268 Angle : 0.646 6.725 30538 Z= 0.356 Chirality : 0.039 0.147 3639 Planarity : 0.004 0.044 3786 Dihedral : 8.185 77.284 7827 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.12), residues: 2873 helix: -3.47 (0.07), residues: 2016 sheet: -2.11 (0.71), residues: 37 loop : -2.08 (0.21), residues: 820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 654 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.8116 time to fit residues: 796.1312 Evaluate side-chains 350 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 3.756 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 559 HIS A 580 GLN B 81 ASN C 41 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN I 156 GLN K 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.287 22488 Z= 0.370 Angle : 0.780 21.534 30538 Z= 0.431 Chirality : 0.044 0.329 3639 Planarity : 0.005 0.054 3786 Dihedral : 4.778 21.776 3101 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.13), residues: 2873 helix: -1.98 (0.09), residues: 2065 sheet: -1.75 (0.77), residues: 40 loop : -2.26 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 413 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 38 residues processed: 440 average time/residue: 0.7481 time to fit residues: 513.9967 Evaluate side-chains 361 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 323 time to evaluate : 3.726 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5260 time to fit residues: 40.7257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 10 ASN B 244 ASN B 302 GLN F 90 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.236 22488 Z= 0.339 Angle : 0.619 22.664 30538 Z= 0.337 Chirality : 0.039 0.180 3639 Planarity : 0.004 0.060 3786 Dihedral : 4.527 21.252 3101 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 2873 helix: -1.30 (0.10), residues: 2136 sheet: -1.01 (0.90), residues: 34 loop : -2.21 (0.22), residues: 703 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 382 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 399 average time/residue: 0.7186 time to fit residues: 451.8055 Evaluate side-chains 331 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 3.694 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4667 time to fit residues: 18.4418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 146 GLN A 499 HIS B 7 ASN B 10 ASN B 339 ASN D 130 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.107 22488 Z= 0.367 Angle : 0.669 16.869 30538 Z= 0.364 Chirality : 0.041 0.233 3639 Planarity : 0.005 0.092 3786 Dihedral : 4.685 21.656 3101 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2873 helix: -1.03 (0.11), residues: 2133 sheet: -1.32 (0.86), residues: 36 loop : -2.27 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 354 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 379 average time/residue: 0.7637 time to fit residues: 456.1461 Evaluate side-chains 325 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 301 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4817 time to fit residues: 25.3214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS ** A 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN C 61 ASN D 130 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN K 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 22488 Z= 0.276 Angle : 0.563 17.461 30538 Z= 0.305 Chirality : 0.038 0.145 3639 Planarity : 0.003 0.042 3786 Dihedral : 4.420 21.807 3101 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 2873 helix: -0.74 (0.11), residues: 2127 sheet: -1.36 (0.85), residues: 36 loop : -2.03 (0.22), residues: 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 327 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 343 average time/residue: 0.7672 time to fit residues: 410.3468 Evaluate side-chains 319 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 306 time to evaluate : 3.929 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4867 time to fit residues: 16.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS B 10 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.115 22488 Z= 0.330 Angle : 0.595 16.526 30538 Z= 0.324 Chirality : 0.039 0.150 3639 Planarity : 0.003 0.040 3786 Dihedral : 4.444 21.580 3101 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2873 helix: -0.59 (0.11), residues: 2108 sheet: -1.42 (0.81), residues: 37 loop : -2.08 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 326 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 345 average time/residue: 0.7574 time to fit residues: 411.4511 Evaluate side-chains 317 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 302 time to evaluate : 3.616 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5052 time to fit residues: 18.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS A 580 GLN A 630 GLN B 255 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.8528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 22488 Z= 0.262 Angle : 0.547 16.527 30538 Z= 0.294 Chirality : 0.037 0.145 3639 Planarity : 0.003 0.039 3786 Dihedral : 4.277 21.535 3101 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2873 helix: -0.40 (0.11), residues: 2101 sheet: -1.45 (0.80), residues: 37 loop : -1.98 (0.22), residues: 735 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 324 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 341 average time/residue: 0.7638 time to fit residues: 407.5126 Evaluate side-chains 312 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 300 time to evaluate : 3.954 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4744 time to fit residues: 15.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.0770 chunk 171 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.8743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 22488 Z= 0.283 Angle : 0.556 16.343 30538 Z= 0.300 Chirality : 0.037 0.140 3639 Planarity : 0.003 0.036 3786 Dihedral : 4.270 21.298 3101 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 2873 helix: -0.33 (0.11), residues: 2098 sheet: -1.52 (0.81), residues: 37 loop : -1.98 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 320 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 326 average time/residue: 0.7735 time to fit residues: 393.9105 Evaluate side-chains 309 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 302 time to evaluate : 3.524 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5561 time to fit residues: 11.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 chunk 197 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 237 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN I 90 GLN K 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.8855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 22488 Z= 0.160 Angle : 0.499 16.402 30538 Z= 0.264 Chirality : 0.036 0.152 3639 Planarity : 0.003 0.039 3786 Dihedral : 3.987 20.705 3101 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2873 helix: 0.04 (0.11), residues: 2095 sheet: -1.36 (0.82), residues: 37 loop : -1.76 (0.22), residues: 741 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 334 average time/residue: 0.7778 time to fit residues: 410.6106 Evaluate side-chains 303 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 301 time to evaluate : 3.578 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9352 time to fit residues: 7.0526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.8929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 22488 Z= 0.187 Angle : 0.506 16.278 30538 Z= 0.268 Chirality : 0.036 0.146 3639 Planarity : 0.003 0.037 3786 Dihedral : 3.940 20.442 3101 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2873 helix: 0.14 (0.11), residues: 2097 sheet: -1.29 (0.83), residues: 37 loop : -1.77 (0.22), residues: 739 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 230 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 313 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 318 average time/residue: 0.7904 time to fit residues: 391.7211 Evaluate side-chains 307 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 302 time to evaluate : 3.879 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4674 time to fit residues: 8.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS A 558 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110425 restraints weight = 94213.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113902 restraints weight = 42866.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116061 restraints weight = 26765.033| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.9025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.129 22488 Z= 0.146 Angle : 0.485 16.577 30538 Z= 0.253 Chirality : 0.035 0.150 3639 Planarity : 0.003 0.055 3786 Dihedral : 3.736 19.747 3101 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2873 helix: 0.60 (0.12), residues: 2051 sheet: -1.03 (0.84), residues: 37 loop : -1.57 (0.22), residues: 785 =============================================================================== Job complete usr+sys time: 8686.15 seconds wall clock time: 154 minutes 39.09 seconds (9279.09 seconds total)