Starting phenix.real_space_refine on Wed Aug 27 00:04:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_30035.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_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 { model { file = "/net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_30035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_30035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_30035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m0s_30035/08_2025/6m0s_30035.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 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. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 2, 'TYR:plan': 1} 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: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} 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: 8.05, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.12 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: 10.60 Time building geometry restraints manager: 5.96 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: 0.00 - 1.34: 77556 1.34 - 2.69: 3760 2.69 - 4.03: 263 4.03 - 5.38: 66 5.38 - 6.72: 11 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: 19337 15.46 - 30.91: 1193 30.91 - 46.37: 281 46.37 - 61.83: 310 61.83 - 77.28: 14 Dihedral angle restraints: 21135 sinusoidal: 11282 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 21132 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 2.450 nonbonded pdb=" O SER A 797 " pdb=" HD1 HIS A 801 " model vdw 1.691 2.450 nonbonded pdb=" OE2 GLU B 14 " pdb=" HE ARG B 18 " model vdw 1.726 2.450 nonbonded pdb=" O ASP A 243 " pdb=" HZ2 LYS A 247 " model vdw 1.729 2.450 nonbonded pdb=" O SER A 11 " pdb="HH11 ARG A 403 " model vdw 1.731 2.450 ... (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 Time spend for trying shortcut: 0.00 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 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: 0.430 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: 0.300 Extract box with map and model: 0.730 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 41.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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= 0.176 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 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.019 0.002 TYR B 30 PHE 0.020 0.002 PHE C 80 TRP 0.028 0.002 TRP M 22 HIS 0.014 0.002 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00414 (22488) covalent geometry : angle 0.64572 (30538) hydrogen bonds : bond 0.31892 ( 1279) hydrogen bonds : angle 10.20032 ( 3762) *********************** 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 to be fit. rotamer outliers: 0 poor density : 654 time to evaluate : 1.216 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 revert: symmetry clash REVERT: A 53 ARG cc_start: 0.6209 (mtt180) cc_final: 0.5433 (mtm180) REVERT: A 73 TYR cc_start: 0.7346 (t80) cc_final: 0.7093 (t80) REVERT: A 116 TYR cc_start: 0.6781 (p90) cc_final: 0.6451 (p90) REVERT: A 200 GLU cc_start: 0.8001 (tt0) cc_final: 0.7761 (tt0) REVERT: A 379 THR cc_start: 0.8769 (m) cc_final: 0.8294 (p) REVERT: A 425 ASP cc_start: 0.7937 (t0) cc_final: 0.7494 (t70) REVERT: A 481 ASP cc_start: 0.6988 (t0) cc_final: 0.6663 (t0) REVERT: A 531 PHE cc_start: 0.8719 (t80) cc_final: 0.8508 (t80) REVERT: M 22 TRP cc_start: 0.7918 (t-100) cc_final: 0.7240 (t60) REVERT: O 72 GLN cc_start: 0.5536 (tt0) cc_final: 0.4963 (mp10) REVERT: B 40 GLU cc_start: 0.5608 (mp0) cc_final: 0.3665 (tt0) REVERT: B 249 TYR cc_start: 0.8194 (t80) cc_final: 0.7514 (t80) REVERT: C 174 ASP cc_start: 0.8040 (t0) cc_final: 0.7628 (t70) REVERT: C 213 GLN cc_start: 0.6229 (mp10) cc_final: 0.5816 (mt0) REVERT: F 34 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7769 (mmtt) REVERT: H 8 TYR cc_start: 0.7004 (p90) cc_final: 0.6749 (p90) REVERT: H 106 PHE cc_start: 0.6981 (m-10) cc_final: 0.6705 (t80) REVERT: J 2 THR cc_start: 0.7812 (m) cc_final: 0.7499 (m) REVERT: N 220 THR cc_start: 0.8485 (p) cc_final: 0.8216 (m) REVERT: N 255 GLU cc_start: 0.7062 (tt0) cc_final: 0.6810 (mm-30) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.4265 time to fit residues: 414.1681 Evaluate side-chains 353 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 E 121 GLN G 90 GLN I 156 GLN K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117729 restraints weight = 91069.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121487 restraints weight = 39413.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122426 restraints weight = 23885.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122756 restraints weight = 19539.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123000 restraints weight = 18115.056| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 22488 Z= 0.266 Angle : 0.747 9.605 30538 Z= 0.415 Chirality : 0.043 0.198 3639 Planarity : 0.005 0.055 3786 Dihedral : 4.735 21.745 3101 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.58 % Allowed : 7.37 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.13), residues: 2873 helix: -1.85 (0.10), residues: 2060 sheet: -1.63 (0.76), residues: 38 loop : -2.20 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 68 TYR 0.026 0.002 TYR A 116 PHE 0.032 0.002 PHE A 419 TRP 0.017 0.002 TRP M 22 HIS 0.009 0.002 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00525 (22488) covalent geometry : angle 0.74702 (30538) hydrogen bonds : bond 0.07944 ( 1279) hydrogen bonds : angle 5.55628 ( 3762) *********************** 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 458 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 421 time to evaluate : 1.124 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: A 217 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6438 (mm-30) REVERT: A 379 THR cc_start: 0.8710 (m) cc_final: 0.8429 (p) REVERT: A 425 ASP cc_start: 0.7562 (t0) cc_final: 0.7129 (t70) REVERT: M 22 TRP cc_start: 0.7831 (t-100) cc_final: 0.7329 (t60) REVERT: C 174 ASP cc_start: 0.8162 (t0) cc_final: 0.7794 (t70) REVERT: C 190 PHE cc_start: 0.6913 (m-10) cc_final: 0.6705 (m-80) REVERT: D 27 MET cc_start: 0.7070 (mmm) cc_final: 0.6845 (mmm) REVERT: E 106 PHE cc_start: 0.7850 (m-80) cc_final: 0.7466 (m-80) REVERT: H 8 TYR cc_start: 0.6697 (p90) cc_final: 0.6340 (p90) REVERT: J 59 MET cc_start: 0.6255 (mtp) cc_final: 0.6045 (mtp) outliers start: 37 outliers final: 26 residues processed: 441 average time/residue: 0.3657 time to fit residues: 251.0416 Evaluate side-chains 354 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 328 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain M residue 57 HIS Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 17 CYS Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 238 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 257 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 264 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 182 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 580 GLN B 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111988 restraints weight = 92342.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115392 restraints weight = 39329.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116103 restraints weight = 26058.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116606 restraints weight = 21418.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116732 restraints weight = 19581.477| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22488 Z= 0.220 Angle : 0.620 6.915 30538 Z= 0.340 Chirality : 0.040 0.153 3639 Planarity : 0.004 0.052 3786 Dihedral : 4.432 20.989 3101 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.01 % Allowed : 8.99 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.14), residues: 2873 helix: -1.18 (0.10), residues: 2118 sheet: -1.15 (0.86), residues: 34 loop : -2.07 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 117 TYR 0.019 0.002 TYR A 552 PHE 0.031 0.002 PHE C 80 TRP 0.022 0.002 TRP C 77 HIS 0.006 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00489 (22488) covalent geometry : angle 0.61968 (30538) hydrogen bonds : bond 0.08240 ( 1279) hydrogen bonds : angle 5.18146 ( 3762) *********************** 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 425 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 1.186 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: A 320 PHE cc_start: 0.7630 (m-80) cc_final: 0.7411 (m-10) REVERT: A 379 THR cc_start: 0.8850 (m) cc_final: 0.8479 (p) REVERT: A 425 ASP cc_start: 0.7443 (t0) cc_final: 0.6992 (t0) REVERT: A 481 ASP cc_start: 0.7446 (t0) cc_final: 0.6049 (t0) REVERT: A 640 MET cc_start: 0.7230 (tpp) cc_final: 0.6959 (tpp) REVERT: B 40 GLU cc_start: 0.4012 (mp0) cc_final: 0.2910 (tt0) REVERT: B 294 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7541 (mm-30) REVERT: E 59 MET cc_start: 0.7156 (mmm) cc_final: 0.6510 (mtt) REVERT: F 95 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8231 (mm) REVERT: G 66 TYR cc_start: 0.7591 (m-10) cc_final: 0.7342 (m-10) REVERT: G 152 SER cc_start: 0.8232 (m) cc_final: 0.8004 (t) REVERT: H 137 GLU cc_start: 0.7678 (tp30) cc_final: 0.7448 (tp30) REVERT: I 43 CYS cc_start: 0.7249 (m) cc_final: 0.6929 (m) REVERT: J 30 TYR cc_start: 0.8828 (t80) cc_final: 0.8426 (t80) outliers start: 47 outliers final: 35 residues processed: 412 average time/residue: 0.3516 time to fit residues: 227.2331 Evaluate side-chains 342 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 535 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain N residue 238 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 29 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 0.0870 chunk 193 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111306 restraints weight = 92422.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115282 restraints weight = 39538.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115890 restraints weight = 24355.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116126 restraints weight = 19817.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116395 restraints weight = 19051.583| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22488 Z= 0.159 Angle : 0.540 7.328 30538 Z= 0.294 Chirality : 0.037 0.156 3639 Planarity : 0.003 0.062 3786 Dihedral : 4.244 21.626 3101 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 10.49 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 2873 helix: -0.65 (0.11), residues: 2103 sheet: -1.04 (0.88), residues: 34 loop : -1.81 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 297 TYR 0.013 0.001 TYR E 85 PHE 0.019 0.001 PHE C 80 TRP 0.011 0.001 TRP A 309 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00346 (22488) covalent geometry : angle 0.54048 (30538) hydrogen bonds : bond 0.06024 ( 1279) hydrogen bonds : angle 4.62322 ( 3762) *********************** 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 388 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 1.321 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: A 110 TYR cc_start: 0.7954 (m-10) cc_final: 0.7681 (m-80) REVERT: A 320 PHE cc_start: 0.7598 (m-80) cc_final: 0.7334 (m-10) REVERT: A 481 ASP cc_start: 0.7592 (t0) cc_final: 0.7385 (t0) REVERT: A 712 MET cc_start: 0.6303 (tpt) cc_final: 0.6102 (tpt) REVERT: B 174 ASP cc_start: 0.5551 (OUTLIER) cc_final: 0.5257 (t0) REVERT: B 190 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: C 213 GLN cc_start: 0.6064 (mp10) cc_final: 0.5733 (mp10) REVERT: D 152 MET cc_start: 0.7380 (ptm) cc_final: 0.7096 (ptt) REVERT: J 30 TYR cc_start: 0.8700 (t80) cc_final: 0.8373 (t80) REVERT: L 137 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7912 (tt0) outliers start: 48 outliers final: 37 residues processed: 369 average time/residue: 0.3589 time to fit residues: 211.4388 Evaluate side-chains 342 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain N residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 47 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 D 130 GLN G 122 GLN I 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106623 restraints weight = 93978.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110231 restraints weight = 41110.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112484 restraints weight = 25433.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113718 restraints weight = 19023.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114464 restraints weight = 16065.418| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22488 Z= 0.199 Angle : 0.567 8.879 30538 Z= 0.310 Chirality : 0.038 0.146 3639 Planarity : 0.004 0.051 3786 Dihedral : 4.271 21.100 3101 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.48 % Allowed : 10.88 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.15), residues: 2873 helix: -0.51 (0.11), residues: 2114 sheet: -1.31 (0.81), residues: 35 loop : -1.99 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.014 0.001 TYR D 90 PHE 0.039 0.002 PHE G 88 TRP 0.016 0.001 TRP C 77 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00445 (22488) covalent geometry : angle 0.56669 (30538) hydrogen bonds : bond 0.06487 ( 1279) hydrogen bonds : angle 4.71263 ( 3762) *********************** 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 394 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 1.278 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: A 481 ASP cc_start: 0.7663 (t0) cc_final: 0.7394 (t0) REVERT: A 712 MET cc_start: 0.6738 (tpt) cc_final: 0.6436 (tpt) REVERT: B 44 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6479 (mp) REVERT: B 190 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: B 226 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7443 (t0) REVERT: C 213 GLN cc_start: 0.6394 (mp10) cc_final: 0.5980 (mt0) REVERT: D 90 TYR cc_start: 0.8706 (t80) cc_final: 0.8451 (t80) REVERT: D 152 MET cc_start: 0.7465 (ptm) cc_final: 0.7188 (ptt) REVERT: E 59 MET cc_start: 0.7081 (mmm) cc_final: 0.6800 (mtt) REVERT: F 95 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8306 (mm) REVERT: G 59 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7774 (mtt) REVERT: H 45 LEU cc_start: 0.7572 (mm) cc_final: 0.7060 (mt) REVERT: I 43 CYS cc_start: 0.6795 (m) cc_final: 0.6503 (m) REVERT: J 30 TYR cc_start: 0.8778 (t80) cc_final: 0.8433 (t80) REVERT: K 77 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8100 (t) REVERT: K 141 LEU cc_start: 0.8520 (tp) cc_final: 0.8272 (tt) REVERT: L 5 CYS cc_start: 0.7436 (m) cc_final: 0.7171 (p) outliers start: 58 outliers final: 43 residues processed: 372 average time/residue: 0.3672 time to fit residues: 217.0633 Evaluate side-chains 358 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 309 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain I residue 151 ASN Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 88 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 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 339 ASN C 61 ASN I 151 ASN K 121 GLN K 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106386 restraints weight = 94921.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108788 restraints weight = 42551.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109328 restraints weight = 28793.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110264 restraints weight = 26456.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110314 restraints weight = 23205.299| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22488 Z= 0.218 Angle : 0.566 6.978 30538 Z= 0.311 Chirality : 0.038 0.142 3639 Planarity : 0.004 0.051 3786 Dihedral : 4.318 29.369 3101 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.31 % Allowed : 12.55 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.15), residues: 2873 helix: -0.46 (0.11), residues: 2107 sheet: -1.71 (0.78), residues: 37 loop : -1.91 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 297 TYR 0.014 0.001 TYR E 85 PHE 0.027 0.002 PHE C 80 TRP 0.014 0.001 TRP A 309 HIS 0.005 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00496 (22488) covalent geometry : angle 0.56597 (30538) hydrogen bonds : bond 0.06302 ( 1279) hydrogen bonds : angle 4.71519 ( 3762) *********************** 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 371 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 1.313 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: A 110 TYR cc_start: 0.8018 (m-10) cc_final: 0.7785 (m-80) REVERT: A 712 MET cc_start: 0.7011 (tpt) cc_final: 0.6326 (tpt) REVERT: A 713 ILE cc_start: 0.8014 (mm) cc_final: 0.7723 (mt) REVERT: B 44 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 190 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: B 226 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 213 GLN cc_start: 0.6721 (mp10) cc_final: 0.6243 (mt0) REVERT: D 90 TYR cc_start: 0.8768 (t80) cc_final: 0.8550 (t80) REVERT: D 152 MET cc_start: 0.7450 (ptm) cc_final: 0.7125 (ptt) REVERT: F 42 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7802 (t) REVERT: F 95 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8356 (mm) REVERT: G 59 MET cc_start: 0.8506 (mpp) cc_final: 0.8082 (mtt) REVERT: H 45 LEU cc_start: 0.7902 (mm) cc_final: 0.7647 (mt) REVERT: I 43 CYS cc_start: 0.6853 (m) cc_final: 0.6548 (m) REVERT: J 30 TYR cc_start: 0.8766 (t80) cc_final: 0.8476 (t80) REVERT: K 77 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8096 (t) REVERT: L 137 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7879 (tt0) outliers start: 54 outliers final: 40 residues processed: 352 average time/residue: 0.3691 time to fit residues: 203.1682 Evaluate side-chains 348 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 43 MET Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 276 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS E 80 GLN K 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104671 restraints weight = 95012.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108205 restraints weight = 42135.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110357 restraints weight = 26145.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111656 restraints weight = 19695.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112307 restraints weight = 16585.800| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22488 Z= 0.209 Angle : 0.560 6.116 30538 Z= 0.307 Chirality : 0.038 0.147 3639 Planarity : 0.004 0.066 3786 Dihedral : 4.299 21.829 3101 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.61 % Allowed : 12.93 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.15), residues: 2873 helix: -0.41 (0.11), residues: 2100 sheet: -1.74 (0.76), residues: 37 loop : -1.93 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 352 TYR 0.014 0.001 TYR F 66 PHE 0.026 0.002 PHE C 80 TRP 0.012 0.001 TRP A 309 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00476 (22488) covalent geometry : angle 0.55972 (30538) hydrogen bonds : bond 0.06308 ( 1279) hydrogen bonds : angle 4.69008 ( 3762) *********************** 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 380 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8070 (m-10) cc_final: 0.7850 (m-80) REVERT: A 712 MET cc_start: 0.7213 (tpt) cc_final: 0.6620 (tpt) REVERT: A 713 ILE cc_start: 0.8160 (mm) cc_final: 0.7898 (mt) REVERT: B 190 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: B 226 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7697 (t0) REVERT: D 90 TYR cc_start: 0.8812 (t80) cc_final: 0.8555 (t80) REVERT: D 152 MET cc_start: 0.7357 (ptm) cc_final: 0.7054 (ptt) REVERT: F 42 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7827 (t) REVERT: F 95 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8270 (mm) REVERT: G 50 LEU cc_start: 0.7985 (tp) cc_final: 0.7564 (mt) REVERT: G 59 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: H 45 LEU cc_start: 0.7868 (mm) cc_final: 0.7582 (mt) REVERT: H 110 ILE cc_start: 0.9034 (mm) cc_final: 0.8615 (mt) REVERT: I 43 CYS cc_start: 0.6954 (m) cc_final: 0.6686 (m) REVERT: J 30 TYR cc_start: 0.8777 (t80) cc_final: 0.8478 (t80) REVERT: J 135 PHE cc_start: 0.8207 (m-80) cc_final: 0.7963 (m-10) REVERT: K 77 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8091 (t) REVERT: L 51 PHE cc_start: 0.8161 (m-80) cc_final: 0.7949 (m-80) outliers start: 61 outliers final: 46 residues processed: 360 average time/residue: 0.3776 time to fit residues: 214.7619 Evaluate side-chains 360 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 123 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS B 7 ASN C 61 ASN I 151 ASN K 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101480 restraints weight = 96891.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104372 restraints weight = 46363.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105273 restraints weight = 29698.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105787 restraints weight = 24877.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105954 restraints weight = 22736.608| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.8736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 22488 Z= 0.294 Angle : 0.654 5.802 30538 Z= 0.362 Chirality : 0.042 0.171 3639 Planarity : 0.004 0.042 3786 Dihedral : 4.638 21.736 3101 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.91 % Allowed : 13.45 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.15), residues: 2873 helix: -0.70 (0.11), residues: 2101 sheet: -2.01 (0.72), residues: 37 loop : -2.14 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 46 TYR 0.017 0.002 TYR E 85 PHE 0.036 0.002 PHE C 80 TRP 0.016 0.002 TRP N 243 HIS 0.007 0.002 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00683 (22488) covalent geometry : angle 0.65375 (30538) hydrogen bonds : bond 0.07091 ( 1279) hydrogen bonds : angle 5.08167 ( 3762) *********************** 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 397 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 329 time to evaluate : 1.316 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: A 566 ILE cc_start: 0.8342 (pt) cc_final: 0.7892 (mm) REVERT: A 712 MET cc_start: 0.7443 (tpt) cc_final: 0.6947 (tpt) REVERT: A 713 ILE cc_start: 0.8186 (mm) cc_final: 0.7958 (mt) REVERT: A 750 LEU cc_start: 0.8598 (tp) cc_final: 0.8319 (mt) REVERT: B 164 ASN cc_start: 0.7238 (t0) cc_final: 0.6160 (p0) REVERT: B 186 LYS cc_start: 0.7753 (tttp) cc_final: 0.5825 (ttpp) REVERT: B 189 LEU cc_start: 0.9417 (mt) cc_final: 0.9132 (mt) REVERT: B 190 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: B 274 GLU cc_start: 0.7690 (mp0) cc_final: 0.7314 (mt-10) REVERT: B 275 TYR cc_start: 0.7134 (m-80) cc_final: 0.6536 (m-80) REVERT: C 61 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8365 (m110) REVERT: D 152 MET cc_start: 0.7428 (ptm) cc_final: 0.7082 (ptt) REVERT: E 149 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8647 (mm) REVERT: F 42 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8046 (t) REVERT: F 95 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8310 (mm) REVERT: G 50 LEU cc_start: 0.8194 (tp) cc_final: 0.7754 (mt) REVERT: H 45 LEU cc_start: 0.8032 (mm) cc_final: 0.7807 (mt) REVERT: H 110 ILE cc_start: 0.9042 (mm) cc_final: 0.8666 (mt) REVERT: I 129 MET cc_start: 0.8254 (ttp) cc_final: 0.7816 (ttm) REVERT: J 30 TYR cc_start: 0.8802 (t80) cc_final: 0.8570 (t80) REVERT: K 77 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8101 (t) outliers start: 68 outliers final: 47 residues processed: 376 average time/residue: 0.3834 time to fit residues: 227.7960 Evaluate side-chains 350 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 17 CYS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 101 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 29 ASN B 255 HIS C 61 ASN K 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103051 restraints weight = 95905.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105883 restraints weight = 45261.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106570 restraints weight = 28680.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107556 restraints weight = 24843.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107654 restraints weight = 21927.716| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.8851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22488 Z= 0.201 Angle : 0.577 6.293 30538 Z= 0.317 Chirality : 0.038 0.153 3639 Planarity : 0.004 0.053 3786 Dihedral : 4.487 21.689 3101 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.57 % Allowed : 14.35 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 2873 helix: -0.57 (0.11), residues: 2110 sheet: -2.11 (0.71), residues: 37 loop : -2.03 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 352 TYR 0.028 0.001 TYR A 110 PHE 0.028 0.002 PHE C 80 TRP 0.016 0.001 TRP A 309 HIS 0.004 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00454 (22488) covalent geometry : angle 0.57706 (30538) hydrogen bonds : bond 0.06633 ( 1279) hydrogen bonds : angle 4.79879 ( 3762) *********************** 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 373 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.261 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: A 712 MET cc_start: 0.7436 (tpt) cc_final: 0.6948 (tpt) REVERT: A 713 ILE cc_start: 0.8159 (mm) cc_final: 0.7940 (mt) REVERT: A 750 LEU cc_start: 0.8561 (tp) cc_final: 0.8265 (mt) REVERT: B 186 LYS cc_start: 0.7567 (tttp) cc_final: 0.5559 (ttpp) REVERT: B 189 LEU cc_start: 0.9405 (mt) cc_final: 0.9114 (mt) REVERT: B 190 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 274 GLU cc_start: 0.7655 (mp0) cc_final: 0.7251 (mt-10) REVERT: B 275 TYR cc_start: 0.7111 (m-80) cc_final: 0.6509 (m-80) REVERT: D 65 MET cc_start: 0.7972 (mtt) cc_final: 0.7739 (mtp) REVERT: D 152 MET cc_start: 0.7384 (ptm) cc_final: 0.7049 (ptt) REVERT: E 149 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8627 (mm) REVERT: F 42 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7979 (t) REVERT: F 95 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8353 (mm) REVERT: G 50 LEU cc_start: 0.8119 (tp) cc_final: 0.7656 (mt) REVERT: H 45 LEU cc_start: 0.8070 (mm) cc_final: 0.7814 (mt) REVERT: H 59 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6770 (mpp) REVERT: H 110 ILE cc_start: 0.9027 (mm) cc_final: 0.8657 (mt) REVERT: J 30 TYR cc_start: 0.8786 (t80) cc_final: 0.8548 (t80) REVERT: K 77 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8088 (t) outliers start: 60 outliers final: 50 residues processed: 354 average time/residue: 0.3909 time to fit residues: 216.7849 Evaluate side-chains 354 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 265 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 HIS A 634 GLN C 61 ASN K 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105138 restraints weight = 95269.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108130 restraints weight = 42082.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109145 restraints weight = 28003.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109339 restraints weight = 23209.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109482 restraints weight = 21615.521| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.8920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22488 Z= 0.144 Angle : 0.529 6.782 30538 Z= 0.287 Chirality : 0.037 0.163 3639 Planarity : 0.003 0.046 3786 Dihedral : 4.274 21.277 3101 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 14.95 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 2873 helix: -0.30 (0.11), residues: 2100 sheet: -2.03 (0.73), residues: 37 loop : -1.91 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.031 0.001 TYR A 110 PHE 0.019 0.001 PHE C 80 TRP 0.016 0.001 TRP A 309 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00313 (22488) covalent geometry : angle 0.52925 (30538) hydrogen bonds : bond 0.06101 ( 1279) hydrogen bonds : angle 4.49959 ( 3762) ********************** 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 370 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 1.188 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: A 712 MET cc_start: 0.7396 (tpt) cc_final: 0.6887 (tpt) REVERT: A 713 ILE cc_start: 0.8101 (mm) cc_final: 0.7887 (mt) REVERT: B 164 ASN cc_start: 0.6905 (t0) cc_final: 0.5765 (p0) REVERT: B 189 LEU cc_start: 0.9389 (mt) cc_final: 0.9088 (mt) REVERT: B 190 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: B 274 GLU cc_start: 0.7631 (mp0) cc_final: 0.7207 (mt-10) REVERT: B 275 TYR cc_start: 0.7098 (m-80) cc_final: 0.6470 (m-80) REVERT: D 65 MET cc_start: 0.7965 (mtt) cc_final: 0.7734 (mtp) REVERT: D 152 MET cc_start: 0.7368 (ptm) cc_final: 0.7003 (ptt) REVERT: F 42 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7912 (t) REVERT: F 95 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8283 (mm) REVERT: G 50 LEU cc_start: 0.8016 (tp) cc_final: 0.7551 (mt) REVERT: H 45 LEU cc_start: 0.8050 (mm) cc_final: 0.7816 (mt) REVERT: H 110 ILE cc_start: 0.9027 (mm) cc_final: 0.8687 (mt) REVERT: J 30 TYR cc_start: 0.8763 (t80) cc_final: 0.8513 (t80) REVERT: K 77 SER cc_start: 0.8260 (p) cc_final: 0.8041 (t) outliers start: 55 outliers final: 47 residues processed: 352 average time/residue: 0.3815 time to fit residues: 210.5802 Evaluate side-chains 353 residues out of total 2349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 134 ILE Chi-restraints excluded: chain J residue 17 CYS Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain N residue 242 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 249 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 201 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 241 HIS A 480 ASN A 499 HIS I 151 ASN K 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103156 restraints weight = 96861.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106276 restraints weight = 45966.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107105 restraints weight = 29112.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107306 restraints weight = 24206.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107425 restraints weight = 22936.668| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.9055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22488 Z= 0.213 Angle : 0.573 7.726 30538 Z= 0.313 Chirality : 0.038 0.139 3639 Planarity : 0.004 0.044 3786 Dihedral : 4.348 21.057 3101 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.48 % Allowed : 15.12 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.15), residues: 2873 helix: -0.26 (0.11), residues: 2042 sheet: -2.17 (0.73), residues: 37 loop : -1.85 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 153 TYR 0.026 0.001 TYR A 110 PHE 0.026 0.002 PHE C 80 TRP 0.012 0.001 TRP A 309 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00487 (22488) covalent geometry : angle 0.57292 (30538) hydrogen bonds : bond 0.06344 ( 1279) hydrogen bonds : angle 4.65649 ( 3762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6898.57 seconds wall clock time: 118 minutes 27.02 seconds (7107.02 seconds total)