Starting phenix.real_space_refine on Sun Feb 18 11:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcs_31894/02_2024/7vcs_31894_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 72 5.49 5 Mg 12 5.21 5 S 396 5.16 5 C 45480 2.51 5 N 12888 2.21 5 O 13980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 744": "NH1" <-> "NH2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 744": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ARG 662": "NH1" <-> "NH2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D ARG 744": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 560": "NH1" <-> "NH2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E ARG 662": "NH1" <-> "NH2" Residue "E ARG 711": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 744": "NH1" <-> "NH2" Residue "E ARG 745": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 560": "NH1" <-> "NH2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F ARG 711": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 744": "NH1" <-> "NH2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Residue "G ARG 239": "NH1" <-> "NH2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G ARG 453": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 560": "NH1" <-> "NH2" Residue "G ARG 625": "NH1" <-> "NH2" Residue "G ARG 635": "NH1" <-> "NH2" Residue "G ARG 662": "NH1" <-> "NH2" Residue "G ARG 711": "NH1" <-> "NH2" Residue "G ARG 713": "NH1" <-> "NH2" Residue "G ARG 732": "NH1" <-> "NH2" Residue "G ARG 733": "NH1" <-> "NH2" Residue "G ARG 744": "NH1" <-> "NH2" Residue "G ARG 745": "NH1" <-> "NH2" Residue "G ARG 753": "NH1" <-> "NH2" Residue "G ARG 766": "NH1" <-> "NH2" Residue "H ARG 239": "NH1" <-> "NH2" Residue "H ARG 359": "NH1" <-> "NH2" Residue "H ARG 453": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 560": "NH1" <-> "NH2" Residue "H ARG 625": "NH1" <-> "NH2" Residue "H ARG 635": "NH1" <-> "NH2" Residue "H ARG 662": "NH1" <-> "NH2" Residue "H ARG 711": "NH1" <-> "NH2" Residue "H ARG 713": "NH1" <-> "NH2" Residue "H ARG 732": "NH1" <-> "NH2" Residue "H ARG 733": "NH1" <-> "NH2" Residue "H ARG 744": "NH1" <-> "NH2" Residue "H ARG 745": "NH1" <-> "NH2" Residue "H ARG 753": "NH1" <-> "NH2" Residue "H ARG 766": "NH1" <-> "NH2" Residue "I ARG 239": "NH1" <-> "NH2" Residue "I ARG 359": "NH1" <-> "NH2" Residue "I ARG 453": "NH1" <-> "NH2" Residue "I ARG 465": "NH1" <-> "NH2" Residue "I ARG 560": "NH1" <-> "NH2" Residue "I ARG 625": "NH1" <-> "NH2" Residue "I ARG 635": "NH1" <-> "NH2" Residue "I ARG 662": "NH1" <-> "NH2" Residue "I ARG 711": "NH1" <-> "NH2" Residue "I ARG 713": "NH1" <-> "NH2" Residue "I ARG 732": "NH1" <-> "NH2" Residue "I ARG 733": "NH1" <-> "NH2" Residue "I ARG 744": "NH1" <-> "NH2" Residue "I ARG 745": "NH1" <-> "NH2" Residue "I ARG 753": "NH1" <-> "NH2" Residue "I ARG 766": "NH1" <-> "NH2" Residue "J ARG 239": "NH1" <-> "NH2" Residue "J ARG 359": "NH1" <-> "NH2" Residue "J ARG 453": "NH1" <-> "NH2" Residue "J ARG 465": "NH1" <-> "NH2" Residue "J ARG 560": "NH1" <-> "NH2" Residue "J ARG 625": "NH1" <-> "NH2" Residue "J ARG 635": "NH1" <-> "NH2" Residue "J ARG 662": "NH1" <-> "NH2" Residue "J ARG 711": "NH1" <-> "NH2" Residue "J ARG 713": "NH1" <-> "NH2" Residue "J ARG 732": "NH1" <-> "NH2" Residue "J ARG 733": "NH1" <-> "NH2" Residue "J ARG 744": "NH1" <-> "NH2" Residue "J ARG 745": "NH1" <-> "NH2" Residue "J ARG 753": "NH1" <-> "NH2" Residue "J ARG 766": "NH1" <-> "NH2" Residue "K ARG 239": "NH1" <-> "NH2" Residue "K ARG 359": "NH1" <-> "NH2" Residue "K ARG 453": "NH1" <-> "NH2" Residue "K ARG 465": "NH1" <-> "NH2" Residue "K ARG 560": "NH1" <-> "NH2" Residue "K ARG 625": "NH1" <-> "NH2" Residue "K ARG 635": "NH1" <-> "NH2" Residue "K ARG 662": "NH1" <-> "NH2" Residue "K ARG 711": "NH1" <-> "NH2" Residue "K ARG 713": "NH1" <-> "NH2" Residue "K ARG 732": "NH1" <-> "NH2" Residue "K ARG 733": "NH1" <-> "NH2" Residue "K ARG 744": "NH1" <-> "NH2" Residue "K ARG 745": "NH1" <-> "NH2" Residue "K ARG 753": "NH1" <-> "NH2" Residue "K ARG 766": "NH1" <-> "NH2" Residue "L ARG 239": "NH1" <-> "NH2" Residue "L ARG 359": "NH1" <-> "NH2" Residue "L ARG 453": "NH1" <-> "NH2" Residue "L ARG 465": "NH1" <-> "NH2" Residue "L ARG 560": "NH1" <-> "NH2" Residue "L ARG 625": "NH1" <-> "NH2" Residue "L ARG 635": "NH1" <-> "NH2" Residue "L ARG 662": "NH1" <-> "NH2" Residue "L ARG 711": "NH1" <-> "NH2" Residue "L ARG 713": "NH1" <-> "NH2" Residue "L ARG 732": "NH1" <-> "NH2" Residue "L ARG 733": "NH1" <-> "NH2" Residue "L ARG 744": "NH1" <-> "NH2" Residue "L ARG 745": "NH1" <-> "NH2" Residue "L ARG 753": "NH1" <-> "NH2" Residue "L ARG 766": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72828 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "B" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "C" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "D" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "E" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "F" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "G" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "H" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "I" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "J" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "K" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "L" Number of atoms: 6006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6006 Classifications: {'peptide': 766} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 723} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 27.54, per 1000 atoms: 0.38 Number of scatterers: 72828 At special positions: 0 Unit cell: (176.04, 171.72, 219.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 396 16.00 P 72 15.00 Mg 12 11.99 O 13980 8.00 N 12888 7.00 C 45480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.69 Conformation dependent library (CDL) restraints added in 9.9 seconds 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 396 helices and 72 sheets defined 41.0% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.80 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.826A pdb=" N ASN A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.233A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 4.139A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.689A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 553 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.831A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'C' and resid 45 through 48 No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.826A pdb=" N ASN C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.353A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS C 386 " --> pdb=" O GLN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 4.139A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 458 removed outlier: 3.591A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 553 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.831A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 553 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.233A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 Processing helix chain 'E' and resid 45 through 48 No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.826A pdb=" N ASN E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.353A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 553 Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 Processing helix chain 'F' and resid 45 through 48 No H-bonds generated for 'chain 'F' and resid 45 through 48' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.353A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 4.139A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.589A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 4.691A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 553 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.328A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 761 Processing helix chain 'G' and resid 45 through 48 No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 136 through 139 No H-bonds generated for 'chain 'G' and resid 136 through 139' Processing helix chain 'G' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 251 through 262 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 282 through 295 Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 320 through 333 Processing helix chain 'G' and resid 355 through 358 Processing helix chain 'G' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS G 386 " --> pdb=" O GLN G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 402 Processing helix chain 'G' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER G 457 " --> pdb=" O ARG G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 478 No H-bonds generated for 'chain 'G' and resid 476 through 478' Processing helix chain 'G' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Proline residue: G 496 - end of helix Processing helix chain 'G' and resid 500 through 505 Processing helix chain 'G' and resid 524 through 534 Processing helix chain 'G' and resid 544 through 553 Processing helix chain 'G' and resid 557 through 568 Processing helix chain 'G' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 650 through 661 removed outlier: 3.831A pdb=" N LEU G 661 " --> pdb=" O LEU G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 672 through 678 Processing helix chain 'G' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG G 708 " --> pdb=" O GLU G 704 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG G 741 " --> pdb=" O GLU G 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE G 742 " --> pdb=" O GLU G 738 " (cutoff:3.500A) Processing helix chain 'G' and resid 749 through 761 Processing helix chain 'H' and resid 45 through 48 No H-bonds generated for 'chain 'H' and resid 45 through 48' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 86 through 91 Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 136 through 139 No H-bonds generated for 'chain 'H' and resid 136 through 139' Processing helix chain 'H' and resid 191 through 199 removed outlier: 3.826A pdb=" N ASN H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 227 through 233 Processing helix chain 'H' and resid 251 through 262 Processing helix chain 'H' and resid 271 through 275 Processing helix chain 'H' and resid 282 through 295 Processing helix chain 'H' and resid 306 through 308 No H-bonds generated for 'chain 'H' and resid 306 through 308' Processing helix chain 'H' and resid 320 through 333 Processing helix chain 'H' and resid 355 through 358 Processing helix chain 'H' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS H 386 " --> pdb=" O GLN H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 402 Processing helix chain 'H' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER H 457 " --> pdb=" O ARG H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 478 No H-bonds generated for 'chain 'H' and resid 476 through 478' Processing helix chain 'H' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR H 495 " --> pdb=" O GLU H 491 " (cutoff:3.500A) Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 500 through 505 Processing helix chain 'H' and resid 524 through 534 Processing helix chain 'H' and resid 544 through 553 Processing helix chain 'H' and resid 557 through 568 Processing helix chain 'H' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE H 582 " --> pdb=" O LEU H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 609 Processing helix chain 'H' and resid 626 through 628 No H-bonds generated for 'chain 'H' and resid 626 through 628' Processing helix chain 'H' and resid 650 through 661 removed outlier: 3.831A pdb=" N LEU H 661 " --> pdb=" O LEU H 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 678 Processing helix chain 'H' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG H 708 " --> pdb=" O GLU H 704 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG H 741 " --> pdb=" O GLU H 737 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE H 742 " --> pdb=" O GLU H 738 " (cutoff:3.500A) Processing helix chain 'H' and resid 749 through 761 Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 86 through 91 Processing helix chain 'I' and resid 130 through 134 Processing helix chain 'I' and resid 136 through 139 No H-bonds generated for 'chain 'I' and resid 136 through 139' Processing helix chain 'I' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 227 through 233 Processing helix chain 'I' and resid 251 through 262 Processing helix chain 'I' and resid 271 through 275 Processing helix chain 'I' and resid 282 through 295 Processing helix chain 'I' and resid 306 through 308 No H-bonds generated for 'chain 'I' and resid 306 through 308' Processing helix chain 'I' and resid 320 through 333 Processing helix chain 'I' and resid 355 through 358 Processing helix chain 'I' and resid 374 through 386 removed outlier: 3.928A pdb=" N LYS I 386 " --> pdb=" O GLN I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 402 Processing helix chain 'I' and resid 408 through 426 removed outlier: 4.139A pdb=" N LYS I 426 " --> pdb=" O ALA I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 443 Processing helix chain 'I' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER I 457 " --> pdb=" O ARG I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 478 No H-bonds generated for 'chain 'I' and resid 476 through 478' Processing helix chain 'I' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR I 495 " --> pdb=" O GLU I 491 " (cutoff:3.500A) Proline residue: I 496 - end of helix Processing helix chain 'I' and resid 500 through 505 Processing helix chain 'I' and resid 524 through 534 Processing helix chain 'I' and resid 544 through 553 Processing helix chain 'I' and resid 557 through 568 Processing helix chain 'I' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE I 582 " --> pdb=" O LEU I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 626 through 628 No H-bonds generated for 'chain 'I' and resid 626 through 628' Processing helix chain 'I' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU I 661 " --> pdb=" O LEU I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 672 through 678 Processing helix chain 'I' and resid 684 through 715 removed outlier: 3.794A pdb=" N ARG I 708 " --> pdb=" O GLU I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 742 removed outlier: 4.328A pdb=" N ARG I 741 " --> pdb=" O GLU I 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE I 742 " --> pdb=" O GLU I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 749 through 761 Processing helix chain 'J' and resid 45 through 48 No H-bonds generated for 'chain 'J' and resid 45 through 48' Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 86 through 91 Processing helix chain 'J' and resid 130 through 134 Processing helix chain 'J' and resid 136 through 139 No H-bonds generated for 'chain 'J' and resid 136 through 139' Processing helix chain 'J' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 225 removed outlier: 4.353A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 227 through 233 Processing helix chain 'J' and resid 251 through 262 Processing helix chain 'J' and resid 271 through 275 Processing helix chain 'J' and resid 282 through 295 Processing helix chain 'J' and resid 306 through 308 No H-bonds generated for 'chain 'J' and resid 306 through 308' Processing helix chain 'J' and resid 320 through 333 Processing helix chain 'J' and resid 355 through 358 Processing helix chain 'J' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS J 386 " --> pdb=" O GLN J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 402 Processing helix chain 'J' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS J 426 " --> pdb=" O ALA J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 443 Processing helix chain 'J' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER J 457 " --> pdb=" O ARG J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 478 No H-bonds generated for 'chain 'J' and resid 476 through 478' Processing helix chain 'J' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR J 495 " --> pdb=" O GLU J 491 " (cutoff:3.500A) Proline residue: J 496 - end of helix Processing helix chain 'J' and resid 500 through 505 Processing helix chain 'J' and resid 524 through 534 Processing helix chain 'J' and resid 544 through 553 Processing helix chain 'J' and resid 557 through 568 Processing helix chain 'J' and resid 579 through 586 removed outlier: 4.233A pdb=" N ILE J 582 " --> pdb=" O LEU J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 609 Processing helix chain 'J' and resid 626 through 628 No H-bonds generated for 'chain 'J' and resid 626 through 628' Processing helix chain 'J' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU J 661 " --> pdb=" O LEU J 657 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 678 Processing helix chain 'J' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG J 708 " --> pdb=" O GLU J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG J 741 " --> pdb=" O GLU J 737 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 749 through 761 Processing helix chain 'K' and resid 45 through 48 No H-bonds generated for 'chain 'K' and resid 45 through 48' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 136 through 139 No H-bonds generated for 'chain 'K' and resid 136 through 139' Processing helix chain 'K' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 227 through 233 Processing helix chain 'K' and resid 251 through 262 Processing helix chain 'K' and resid 271 through 275 Processing helix chain 'K' and resid 282 through 295 Processing helix chain 'K' and resid 306 through 308 No H-bonds generated for 'chain 'K' and resid 306 through 308' Processing helix chain 'K' and resid 320 through 333 Processing helix chain 'K' and resid 355 through 358 Processing helix chain 'K' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS K 386 " --> pdb=" O GLN K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 402 Processing helix chain 'K' and resid 408 through 426 removed outlier: 4.138A pdb=" N LYS K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 443 Processing helix chain 'K' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER K 457 " --> pdb=" O ARG K 453 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 478 No H-bonds generated for 'chain 'K' and resid 476 through 478' Processing helix chain 'K' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR K 495 " --> pdb=" O GLU K 491 " (cutoff:3.500A) Proline residue: K 496 - end of helix Processing helix chain 'K' and resid 500 through 505 Processing helix chain 'K' and resid 524 through 534 Processing helix chain 'K' and resid 544 through 553 Processing helix chain 'K' and resid 557 through 568 Processing helix chain 'K' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE K 582 " --> pdb=" O LEU K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 626 through 628 No H-bonds generated for 'chain 'K' and resid 626 through 628' Processing helix chain 'K' and resid 650 through 661 removed outlier: 3.830A pdb=" N LEU K 661 " --> pdb=" O LEU K 657 " (cutoff:3.500A) Processing helix chain 'K' and resid 672 through 678 Processing helix chain 'K' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 742 removed outlier: 4.327A pdb=" N ARG K 741 " --> pdb=" O GLU K 737 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE K 742 " --> pdb=" O GLU K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 749 through 761 Processing helix chain 'L' and resid 45 through 48 No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 130 through 134 Processing helix chain 'L' and resid 136 through 139 No H-bonds generated for 'chain 'L' and resid 136 through 139' Processing helix chain 'L' and resid 191 through 199 removed outlier: 3.825A pdb=" N ASN L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 225 removed outlier: 4.354A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 227 through 233 Processing helix chain 'L' and resid 251 through 262 Processing helix chain 'L' and resid 271 through 275 Processing helix chain 'L' and resid 282 through 295 Processing helix chain 'L' and resid 306 through 308 No H-bonds generated for 'chain 'L' and resid 306 through 308' Processing helix chain 'L' and resid 320 through 333 Processing helix chain 'L' and resid 355 through 358 Processing helix chain 'L' and resid 374 through 386 removed outlier: 3.927A pdb=" N LYS L 386 " --> pdb=" O GLN L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 402 Processing helix chain 'L' and resid 408 through 426 removed outlier: 4.139A pdb=" N LYS L 426 " --> pdb=" O ALA L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 Processing helix chain 'L' and resid 449 through 458 removed outlier: 3.590A pdb=" N SER L 457 " --> pdb=" O ARG L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 478 No H-bonds generated for 'chain 'L' and resid 476 through 478' Processing helix chain 'L' and resid 483 through 498 removed outlier: 4.690A pdb=" N TYR L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) Proline residue: L 496 - end of helix Processing helix chain 'L' and resid 500 through 505 Processing helix chain 'L' and resid 524 through 534 Processing helix chain 'L' and resid 544 through 553 Processing helix chain 'L' and resid 557 through 568 Processing helix chain 'L' and resid 579 through 586 removed outlier: 4.234A pdb=" N ILE L 582 " --> pdb=" O LEU L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 626 through 628 No H-bonds generated for 'chain 'L' and resid 626 through 628' Processing helix chain 'L' and resid 650 through 661 removed outlier: 3.831A pdb=" N LEU L 661 " --> pdb=" O LEU L 657 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 678 Processing helix chain 'L' and resid 684 through 715 removed outlier: 3.793A pdb=" N ARG L 708 " --> pdb=" O GLU L 704 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 742 removed outlier: 4.328A pdb=" N ARG L 741 " --> pdb=" O GLU L 737 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE L 742 " --> pdb=" O GLU L 738 " (cutoff:3.500A) Processing helix chain 'L' and resid 749 through 761 Processing sheet with id= A, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 163 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.872A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 640 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A 515 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 642 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 517 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR A 644 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 41 removed outlier: 8.059A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B 163 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.702A pdb=" N ASP B 640 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE C 163 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 150 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 640 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU C 515 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 642 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 517 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR C 644 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= T, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE D 163 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= W, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.702A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= Z, first strand: chain 'E' and resid 38 through 41 removed outlier: 8.059A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE E 163 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 150 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 640 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU E 515 " --> pdb=" O ASP E 640 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU E 642 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR E 517 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR E 644 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= AF, first strand: chain 'F' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE F 163 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP F 150 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AI, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 99 through 101 Processing sheet with id= AL, first strand: chain 'G' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL G 39 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE G 70 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU G 41 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU G 72 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS G 69 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU G 117 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 165 " --> pdb=" O LEU G 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE G 163 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE G 152 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP G 150 " --> pdb=" O VAL G 165 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 145 through 147 Processing sheet with id= AO, first strand: chain 'G' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE G 241 " --> pdb=" O VAL G 341 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL G 343 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU G 243 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA G 345 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA G 346 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE G 303 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP G 304 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE G 269 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY G 518 " --> pdb=" O THR G 623 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP G 640 " --> pdb=" O GLY G 513 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU G 515 " --> pdb=" O ASP G 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU G 642 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR G 517 " --> pdb=" O LEU G 642 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR G 644 " --> pdb=" O TYR G 517 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 99 through 101 Processing sheet with id= AR, first strand: chain 'H' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL H 39 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE H 70 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU H 41 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU H 72 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS H 69 " --> pdb=" O VAL H 57 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU H 117 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL H 165 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 163 " --> pdb=" O PHE H 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE H 152 " --> pdb=" O PHE H 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 150 " --> pdb=" O VAL H 165 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 145 through 147 Processing sheet with id= AU, first strand: chain 'H' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE H 241 " --> pdb=" O VAL H 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL H 343 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU H 243 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA H 345 " --> pdb=" O LEU H 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA H 346 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE H 303 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP H 304 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE H 269 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY H 518 " --> pdb=" O THR H 623 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP H 640 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU H 515 " --> pdb=" O ASP H 640 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU H 642 " --> pdb=" O LEU H 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR H 517 " --> pdb=" O LEU H 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR H 644 " --> pdb=" O TYR H 517 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 99 through 101 Processing sheet with id= AX, first strand: chain 'I' and resid 38 through 41 removed outlier: 8.059A pdb=" N VAL I 39 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE I 70 " --> pdb=" O VAL I 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU I 41 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU I 72 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS I 69 " --> pdb=" O VAL I 57 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU I 117 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL I 165 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE I 163 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE I 152 " --> pdb=" O PHE I 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP I 150 " --> pdb=" O VAL I 165 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'I' and resid 145 through 147 Processing sheet with id= BA, first strand: chain 'I' and resid 365 through 368 removed outlier: 8.872A pdb=" N ILE I 241 " --> pdb=" O VAL I 341 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL I 343 " --> pdb=" O ILE I 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU I 243 " --> pdb=" O VAL I 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA I 345 " --> pdb=" O LEU I 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA I 346 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE I 303 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP I 304 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE I 269 " --> pdb=" O ASP I 304 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 538 through 542 removed outlier: 3.703A pdb=" N ASP I 640 " --> pdb=" O GLY I 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU I 515 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU I 642 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR I 517 " --> pdb=" O LEU I 642 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR I 644 " --> pdb=" O TYR I 517 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'J' and resid 99 through 101 Processing sheet with id= BD, first strand: chain 'J' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL J 39 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE J 70 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU J 41 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU J 72 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS J 69 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'J' and resid 181 through 183 removed outlier: 6.483A pdb=" N LEU J 117 " --> pdb=" O VAL J 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL J 165 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE J 163 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE J 152 " --> pdb=" O PHE J 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP J 150 " --> pdb=" O VAL J 165 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 145 through 147 Processing sheet with id= BG, first strand: chain 'J' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE J 241 " --> pdb=" O VAL J 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL J 343 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU J 243 " --> pdb=" O VAL J 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA J 345 " --> pdb=" O LEU J 243 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA J 346 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE J 303 " --> pdb=" O ALA J 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP J 304 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE J 269 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 538 through 542 removed outlier: 3.500A pdb=" N GLY J 518 " --> pdb=" O THR J 623 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP J 640 " --> pdb=" O GLY J 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU J 515 " --> pdb=" O ASP J 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU J 642 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR J 517 " --> pdb=" O LEU J 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR J 644 " --> pdb=" O TYR J 517 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'K' and resid 99 through 101 Processing sheet with id= BJ, first strand: chain 'K' and resid 38 through 41 removed outlier: 8.060A pdb=" N VAL K 39 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE K 70 " --> pdb=" O VAL K 39 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU K 41 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU K 72 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS K 69 " --> pdb=" O VAL K 57 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'K' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU K 117 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL K 165 " --> pdb=" O LEU K 117 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE K 163 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE K 152 " --> pdb=" O PHE K 163 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP K 150 " --> pdb=" O VAL K 165 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'K' and resid 145 through 147 Processing sheet with id= BM, first strand: chain 'K' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE K 241 " --> pdb=" O VAL K 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL K 343 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU K 243 " --> pdb=" O VAL K 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA K 345 " --> pdb=" O LEU K 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA K 346 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE K 303 " --> pdb=" O ALA K 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP K 304 " --> pdb=" O PHE K 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE K 269 " --> pdb=" O ASP K 304 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'K' and resid 538 through 542 removed outlier: 3.703A pdb=" N ASP K 640 " --> pdb=" O GLY K 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU K 515 " --> pdb=" O ASP K 640 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU K 642 " --> pdb=" O LEU K 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR K 517 " --> pdb=" O LEU K 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR K 644 " --> pdb=" O TYR K 517 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'L' and resid 99 through 101 Processing sheet with id= BP, first strand: chain 'L' and resid 38 through 41 removed outlier: 8.059A pdb=" N VAL L 39 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE L 70 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU L 41 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU L 72 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS L 69 " --> pdb=" O VAL L 57 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'L' and resid 181 through 183 removed outlier: 6.484A pdb=" N LEU L 117 " --> pdb=" O VAL L 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL L 165 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE L 163 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE L 152 " --> pdb=" O PHE L 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP L 150 " --> pdb=" O VAL L 165 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'L' and resid 145 through 147 Processing sheet with id= BS, first strand: chain 'L' and resid 365 through 368 removed outlier: 8.871A pdb=" N ILE L 241 " --> pdb=" O VAL L 341 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL L 343 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU L 243 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA L 345 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA L 346 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE L 303 " --> pdb=" O ALA L 346 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP L 304 " --> pdb=" O PHE L 267 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE L 269 " --> pdb=" O ASP L 304 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'L' and resid 538 through 542 removed outlier: 3.501A pdb=" N GLY L 518 " --> pdb=" O THR L 623 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 640 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU L 515 " --> pdb=" O ASP L 640 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU L 642 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR L 517 " --> pdb=" O LEU L 642 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR L 644 " --> pdb=" O TYR L 517 " (cutoff:3.500A) 2452 hydrogen bonds defined for protein. 7140 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: 28.49 Time building geometry restraints manager: 22.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 25267 1.36 - 1.51: 22321 1.51 - 1.66: 25840 1.66 - 1.80: 523 1.80 - 1.95: 101 Bond restraints: 74052 Sorted by residual: bond pdb=" N MET A 757 " pdb=" CA MET A 757 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.75e+00 bond pdb=" C SER G 171 " pdb=" N PRO G 172 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.40e+00 bond pdb=" N ARG H 753 " pdb=" CA ARG H 753 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.31e+00 bond pdb=" C SER F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.29e+00 bond pdb=" C SER L 171 " pdb=" N PRO L 172 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.28e+00 ... (remaining 74047 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 2241 105.99 - 113.00: 40212 113.00 - 120.01: 25714 120.01 - 127.02: 31221 127.02 - 134.02: 764 Bond angle restraints: 100152 Sorted by residual: angle pdb=" C ALA L 297 " pdb=" N PRO L 298 " pdb=" CA PRO L 298 " ideal model delta sigma weight residual 119.84 114.91 4.93 1.25e+00 6.40e-01 1.56e+01 angle pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta sigma weight residual 119.84 114.92 4.92 1.25e+00 6.40e-01 1.55e+01 angle pdb=" C ALA K 297 " pdb=" N PRO K 298 " pdb=" CA PRO K 298 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.55e+01 angle pdb=" C ALA G 297 " pdb=" N PRO G 298 " pdb=" CA PRO G 298 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.54e+01 angle pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta sigma weight residual 119.84 114.93 4.91 1.25e+00 6.40e-01 1.54e+01 ... (remaining 100147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 44235 16.06 - 32.13: 1317 32.13 - 48.19: 408 48.19 - 64.26: 72 64.26 - 80.32: 60 Dihedral angle restraints: 46092 sinusoidal: 19620 harmonic: 26472 Sorted by residual: dihedral pdb=" CA VAL L 728 " pdb=" C VAL L 728 " pdb=" N PRO L 729 " pdb=" CA PRO L 729 " ideal model delta harmonic sigma weight residual 180.00 152.30 27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL I 728 " pdb=" C VAL I 728 " pdb=" N PRO I 729 " pdb=" CA PRO I 729 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA VAL J 728 " pdb=" C VAL J 728 " pdb=" N PRO J 729 " pdb=" CA PRO J 729 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 46089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 7877 0.050 - 0.100: 2640 0.100 - 0.150: 585 0.150 - 0.200: 118 0.200 - 0.250: 12 Chirality restraints: 11232 Sorted by residual: chirality pdb=" CB ILE F 126 " pdb=" CA ILE F 126 " pdb=" CG1 ILE F 126 " pdb=" CG2 ILE F 126 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE B 126 " pdb=" CA ILE B 126 " pdb=" CG1 ILE B 126 " pdb=" CG2 ILE B 126 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE H 126 " pdb=" CA ILE H 126 " pdb=" CG1 ILE H 126 " pdb=" CG2 ILE H 126 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 11229 not shown) Planarity restraints: 13188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 169 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO G 170 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 170 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 170 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 169 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO H 170 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO H 170 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 170 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 169 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO E 170 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 170 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 170 " -0.035 5.00e-02 4.00e+02 ... (remaining 13185 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 729 2.64 - 3.21: 62462 3.21 - 3.77: 105972 3.77 - 4.34: 143942 4.34 - 4.90: 236732 Nonbonded interactions: 549837 Sorted by model distance: nonbonded pdb=" O2G AGS H 901 " pdb="MG MG H 902 " model vdw 2.076 2.170 nonbonded pdb=" O2G AGS G 901 " pdb="MG MG G 902 " model vdw 2.076 2.170 nonbonded pdb=" O2G AGS K 901 " pdb="MG MG K 902 " model vdw 2.076 2.170 nonbonded pdb=" O2G AGS A 901 " pdb="MG MG A 902 " model vdw 2.076 2.170 nonbonded pdb=" O2G AGS C 901 " pdb="MG MG C 902 " model vdw 2.077 2.170 ... (remaining 549832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.050 Extract box with map and model: 7.880 Check model and map are aligned: 0.820 Set scattering table: 0.500 Process input model: 147.910 Find NCS groups from input model: 3.910 Set up NCS constraints: 0.530 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:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.007 0.061 74052 Z= 0.465 Angle : 0.887 8.802 100152 Z= 0.518 Chirality : 0.052 0.250 11232 Planarity : 0.008 0.062 13188 Dihedral : 10.131 80.320 28932 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.07), residues: 9168 helix: -2.12 (0.06), residues: 3816 sheet: -0.92 (0.14), residues: 1200 loop : -1.60 (0.09), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 454 HIS 0.010 0.002 HIS K 404 PHE 0.028 0.003 PHE F 682 TYR 0.029 0.003 TYR A 495 ARG 0.017 0.001 ARG K 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 7.065 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: B 46 MET cc_start: 0.2530 (mtp) cc_final: 0.2301 (mtp) REVERT: B 115 HIS cc_start: 0.5734 (t70) cc_final: 0.5494 (t70) REVERT: B 199 ASN cc_start: 0.7799 (m-40) cc_final: 0.7568 (p0) REVERT: B 219 MET cc_start: 0.8710 (mtt) cc_final: 0.8398 (mtt) REVERT: B 427 MET cc_start: 0.8852 (tpp) cc_final: 0.8565 (tpt) REVERT: C 115 HIS cc_start: 0.5770 (t70) cc_final: 0.5296 (t70) REVERT: C 181 VAL cc_start: 0.7652 (t) cc_final: 0.7375 (p) REVERT: C 304 ASP cc_start: 0.7597 (t0) cc_final: 0.7393 (p0) REVERT: D 115 HIS cc_start: 0.5257 (t70) cc_final: 0.4813 (t70) REVERT: D 176 VAL cc_start: 0.5796 (t) cc_final: 0.5471 (m) REVERT: D 199 ASN cc_start: 0.8231 (m-40) cc_final: 0.7967 (p0) REVERT: D 720 MET cc_start: 0.4723 (ttt) cc_final: 0.4172 (mmp) REVERT: G 199 ASN cc_start: 0.7109 (m-40) cc_final: 0.6864 (p0) REVERT: G 213 LEU cc_start: 0.8640 (mt) cc_final: 0.8398 (tp) REVERT: H 115 HIS cc_start: 0.5440 (t70) cc_final: 0.5115 (t70) REVERT: H 219 MET cc_start: 0.9024 (mtt) cc_final: 0.8674 (mtt) REVERT: I 115 HIS cc_start: 0.5228 (t70) cc_final: 0.4782 (t70) REVERT: I 199 ASN cc_start: 0.8127 (m-40) cc_final: 0.7913 (p0) REVERT: I 550 MET cc_start: 0.8873 (mtm) cc_final: 0.8664 (mtm) REVERT: I 720 MET cc_start: 0.4712 (ttt) cc_final: 0.4389 (mmt) REVERT: K 449 MET cc_start: 0.8801 (tpt) cc_final: 0.8368 (tpp) REVERT: L 115 HIS cc_start: 0.5362 (t70) cc_final: 0.4971 (t70) outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 0.7877 time to fit residues: 969.6809 Evaluate side-chains 362 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 6.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 9.9990 chunk 691 optimal weight: 0.9980 chunk 383 optimal weight: 7.9990 chunk 236 optimal weight: 40.0000 chunk 466 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 714 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 434 optimal weight: 2.9990 chunk 532 optimal weight: 50.0000 chunk 828 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 ASN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 558 ASN ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 558 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN C 558 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 337 GLN E 558 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 199 ASN F 337 GLN F 340 HIS F 558 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 337 GLN H 558 ASN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 GLN J 36 ASN J 337 GLN J 558 ASN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 199 ASN K 337 GLN K 558 ASN ** L 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 337 GLN L 558 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 74052 Z= 0.292 Angle : 0.590 6.847 100152 Z= 0.308 Chirality : 0.044 0.160 11232 Planarity : 0.005 0.057 13188 Dihedral : 8.236 59.963 10488 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.71 % Allowed : 4.03 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.08), residues: 9168 helix: -0.25 (0.08), residues: 3792 sheet: -0.55 (0.14), residues: 1164 loop : -1.07 (0.09), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.005 0.001 HIS H 406 PHE 0.018 0.002 PHE C 163 TYR 0.015 0.002 TYR D 203 ARG 0.015 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 381 time to evaluate : 6.658 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: B 46 MET cc_start: 0.2585 (mtp) cc_final: 0.2333 (mtp) REVERT: B 199 ASN cc_start: 0.7749 (m-40) cc_final: 0.7528 (p0) REVERT: B 219 MET cc_start: 0.8493 (mtt) cc_final: 0.8269 (mtt) REVERT: B 561 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: C 115 HIS cc_start: 0.5472 (t70) cc_final: 0.5169 (t70) REVERT: C 163 PHE cc_start: 0.6601 (m-80) cc_final: 0.6238 (t80) REVERT: C 427 MET cc_start: 0.8902 (mmm) cc_final: 0.8697 (mmm) REVERT: C 550 MET cc_start: 0.8824 (mtm) cc_final: 0.8528 (mtm) REVERT: C 720 MET cc_start: 0.3601 (mmp) cc_final: 0.2577 (tpp) REVERT: D 115 HIS cc_start: 0.5064 (t70) cc_final: 0.4789 (t70) REVERT: D 158 MET cc_start: 0.5247 (pmm) cc_final: 0.4999 (pmm) REVERT: D 163 PHE cc_start: 0.7614 (m-80) cc_final: 0.7183 (t80) REVERT: D 199 ASN cc_start: 0.8233 (m-40) cc_final: 0.8010 (p0) REVERT: D 720 MET cc_start: 0.4791 (ttt) cc_final: 0.4150 (mmp) REVERT: E 193 ASP cc_start: 0.8180 (m-30) cc_final: 0.7959 (p0) REVERT: E 449 MET cc_start: 0.8812 (tpp) cc_final: 0.8598 (tpp) REVERT: E 678 MET cc_start: 0.8656 (tpp) cc_final: 0.8453 (tpp) REVERT: G 163 PHE cc_start: 0.6853 (m-80) cc_final: 0.6536 (t80) REVERT: G 199 ASN cc_start: 0.7045 (m-40) cc_final: 0.6811 (p0) REVERT: H 115 HIS cc_start: 0.5523 (t70) cc_final: 0.5253 (t70) REVERT: H 219 MET cc_start: 0.8959 (mtt) cc_final: 0.8744 (mtt) REVERT: H 561 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: I 84 MET cc_start: 0.5271 (ptt) cc_final: 0.5050 (ptt) REVERT: I 115 HIS cc_start: 0.4962 (t70) cc_final: 0.4562 (t70) REVERT: I 158 MET cc_start: 0.5578 (pmm) cc_final: 0.5290 (pmm) REVERT: I 163 PHE cc_start: 0.7443 (m-80) cc_final: 0.7019 (t80) REVERT: I 199 ASN cc_start: 0.8090 (m-40) cc_final: 0.7887 (p0) REVERT: I 720 MET cc_start: 0.4883 (ttt) cc_final: 0.4481 (mmp) REVERT: I 740 MET cc_start: 0.9130 (mmm) cc_final: 0.8791 (mmm) REVERT: J 84 MET cc_start: 0.6134 (ptt) cc_final: 0.5913 (ptt) REVERT: K 84 MET cc_start: 0.5973 (ptt) cc_final: 0.5747 (ptt) REVERT: K 449 MET cc_start: 0.8784 (tpt) cc_final: 0.8513 (tpt) REVERT: K 550 MET cc_start: 0.8848 (mtm) cc_final: 0.8589 (mtm) REVERT: L 115 HIS cc_start: 0.5337 (t70) cc_final: 0.5089 (t70) REVERT: L 158 MET cc_start: 0.6362 (pmm) cc_final: 0.5960 (pmm) REVERT: L 402 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7668 (mt-10) outliers start: 56 outliers final: 19 residues processed: 415 average time/residue: 0.6964 time to fit residues: 491.8072 Evaluate side-chains 346 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 324 time to evaluate : 6.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 633 ILE Chi-restraints excluded: chain H residue 561 GLU Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 689 optimal weight: 30.0000 chunk 563 optimal weight: 9.9990 chunk 228 optimal weight: 50.0000 chunk 829 optimal weight: 7.9990 chunk 896 optimal weight: 6.9990 chunk 738 optimal weight: 5.9990 chunk 822 optimal weight: 0.4980 chunk 282 optimal weight: 6.9990 chunk 665 optimal weight: 9.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 558 ASN D 33 ASN D 384 HIS ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 384 HIS G 558 ASN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 384 HIS I 558 ASN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN L 33 ASN L 558 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 74052 Z= 0.209 Angle : 0.512 7.708 100152 Z= 0.263 Chirality : 0.043 0.140 11232 Planarity : 0.005 0.054 13188 Dihedral : 7.660 59.778 10488 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.60 % Allowed : 5.05 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.09), residues: 9168 helix: 0.55 (0.08), residues: 3780 sheet: -0.49 (0.14), residues: 1236 loop : -0.78 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 454 HIS 0.004 0.001 HIS B 406 PHE 0.019 0.001 PHE F 163 TYR 0.014 0.001 TYR H 495 ARG 0.007 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 6.551 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: B 46 MET cc_start: 0.2520 (mtp) cc_final: 0.2272 (mtp) REVERT: B 199 ASN cc_start: 0.7731 (m-40) cc_final: 0.7516 (p0) REVERT: C 115 HIS cc_start: 0.5480 (t70) cc_final: 0.5256 (t70) REVERT: C 163 PHE cc_start: 0.6582 (m-80) cc_final: 0.6232 (t80) REVERT: C 427 MET cc_start: 0.8914 (mmm) cc_final: 0.8702 (mmm) REVERT: C 720 MET cc_start: 0.3964 (mmp) cc_final: 0.3110 (mmt) REVERT: D 163 PHE cc_start: 0.7597 (m-80) cc_final: 0.7181 (t80) REVERT: D 720 MET cc_start: 0.4727 (ttt) cc_final: 0.4139 (mmp) REVERT: E 84 MET cc_start: 0.6526 (ptt) cc_final: 0.6323 (ptt) REVERT: E 193 ASP cc_start: 0.8166 (m-30) cc_final: 0.7955 (p0) REVERT: E 550 MET cc_start: 0.9052 (mtm) cc_final: 0.8647 (mtm) REVERT: G 720 MET cc_start: 0.3918 (mmp) cc_final: 0.3134 (mmt) REVERT: H 219 MET cc_start: 0.8904 (mtt) cc_final: 0.8653 (mtt) REVERT: H 561 GLU cc_start: 0.7599 (pt0) cc_final: 0.7387 (pt0) REVERT: I 84 MET cc_start: 0.5180 (ptt) cc_final: 0.4924 (ptt) REVERT: I 115 HIS cc_start: 0.5025 (t70) cc_final: 0.4796 (t70) REVERT: I 163 PHE cc_start: 0.7410 (m-80) cc_final: 0.6965 (t80) REVERT: I 442 MET cc_start: 0.8575 (ppp) cc_final: 0.8191 (ppp) REVERT: I 720 MET cc_start: 0.4537 (ttt) cc_final: 0.4266 (mmt) REVERT: J 84 MET cc_start: 0.6038 (ptt) cc_final: 0.5798 (ptt) REVERT: J 720 MET cc_start: 0.5126 (tpt) cc_final: 0.4365 (tpp) REVERT: K 84 MET cc_start: 0.5694 (ptt) cc_final: 0.5437 (ptt) REVERT: K 550 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8566 (mtm) REVERT: K 720 MET cc_start: 0.4838 (tpt) cc_final: 0.4223 (tpp) REVERT: L 163 PHE cc_start: 0.6957 (m-80) cc_final: 0.6615 (t80) outliers start: 47 outliers final: 23 residues processed: 381 average time/residue: 0.7011 time to fit residues: 455.2922 Evaluate side-chains 326 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 302 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 561 GLU Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 5.9990 chunk 623 optimal weight: 8.9990 chunk 430 optimal weight: 0.0670 chunk 91 optimal weight: 50.0000 chunk 395 optimal weight: 0.9980 chunk 557 optimal weight: 5.9990 chunk 832 optimal weight: 0.9990 chunk 881 optimal weight: 5.9990 chunk 435 optimal weight: 7.9990 chunk 789 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN D 558 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 558 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 74052 Z= 0.175 Angle : 0.486 7.789 100152 Z= 0.247 Chirality : 0.042 0.137 11232 Planarity : 0.004 0.052 13188 Dihedral : 7.367 59.501 10488 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.83 % Allowed : 5.30 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 9168 helix: 1.04 (0.09), residues: 3780 sheet: -0.32 (0.14), residues: 1236 loop : -0.59 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP I 454 HIS 0.003 0.001 HIS E 406 PHE 0.016 0.001 PHE H 163 TYR 0.013 0.001 TYR E 495 ARG 0.010 0.000 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 326 time to evaluate : 6.609 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: B 46 MET cc_start: 0.2531 (mtp) cc_final: 0.2275 (mtp) REVERT: C 163 PHE cc_start: 0.6543 (m-80) cc_final: 0.6184 (t80) REVERT: C 427 MET cc_start: 0.8923 (mmm) cc_final: 0.8690 (mmm) REVERT: C 720 MET cc_start: 0.3641 (mmp) cc_final: 0.2950 (mmt) REVERT: D 163 PHE cc_start: 0.7550 (m-80) cc_final: 0.7135 (t80) REVERT: D 720 MET cc_start: 0.4806 (ttt) cc_final: 0.4188 (mmp) REVERT: E 46 MET cc_start: 0.3117 (tpp) cc_final: 0.2643 (tpp) REVERT: E 84 MET cc_start: 0.6623 (ptt) cc_final: 0.6383 (ptt) REVERT: E 193 ASP cc_start: 0.8180 (m-30) cc_final: 0.7945 (p0) REVERT: E 720 MET cc_start: 0.4708 (tpt) cc_final: 0.3972 (tpp) REVERT: F 550 MET cc_start: 0.8837 (mtm) cc_final: 0.8610 (mtm) REVERT: F 720 MET cc_start: 0.4095 (OUTLIER) cc_final: 0.3608 (mmm) REVERT: G 84 MET cc_start: 0.4152 (tmm) cc_final: 0.3910 (tmm) REVERT: G 163 PHE cc_start: 0.6831 (m-80) cc_final: 0.6583 (t80) REVERT: G 720 MET cc_start: 0.4365 (mmp) cc_final: 0.3593 (mmt) REVERT: H 219 MET cc_start: 0.8868 (mtt) cc_final: 0.8621 (mtt) REVERT: I 84 MET cc_start: 0.5228 (ptt) cc_final: 0.5019 (ptt) REVERT: I 163 PHE cc_start: 0.7409 (m-80) cc_final: 0.7059 (t80) REVERT: I 442 MET cc_start: 0.8590 (ppp) cc_final: 0.8323 (ppp) REVERT: I 720 MET cc_start: 0.4482 (ttt) cc_final: 0.4183 (mmt) REVERT: J 84 MET cc_start: 0.6040 (ptt) cc_final: 0.5721 (ptt) REVERT: J 546 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7316 (tm-30) REVERT: J 720 MET cc_start: 0.5139 (tpt) cc_final: 0.4435 (tpp) REVERT: K 84 MET cc_start: 0.5947 (ptt) cc_final: 0.5697 (ptt) REVERT: K 550 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: K 720 MET cc_start: 0.5076 (tpt) cc_final: 0.4595 (tpp) REVERT: L 163 PHE cc_start: 0.6834 (m-80) cc_final: 0.6519 (t80) REVERT: L 402 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7703 (mt-10) outliers start: 65 outliers final: 39 residues processed: 368 average time/residue: 0.6810 time to fit residues: 439.7276 Evaluate side-chains 338 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 296 time to evaluate : 6.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 720 MET Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain K residue 332 MET Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain K residue 731 ILE Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 734 optimal weight: 8.9990 chunk 500 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 656 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 752 optimal weight: 7.9990 chunk 609 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 450 optimal weight: 5.9990 chunk 791 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 199 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 74052 Z= 0.216 Angle : 0.490 7.869 100152 Z= 0.249 Chirality : 0.042 0.137 11232 Planarity : 0.004 0.053 13188 Dihedral : 7.258 59.507 10488 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.94 % Allowed : 5.62 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 9168 helix: 1.24 (0.09), residues: 3792 sheet: -0.27 (0.14), residues: 1236 loop : -0.51 (0.10), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 454 HIS 0.004 0.001 HIS D 735 PHE 0.012 0.001 PHE D 758 TYR 0.013 0.001 TYR J 495 ARG 0.008 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 6.652 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 402 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 550 MET cc_start: 0.8860 (mtm) cc_final: 0.8570 (mtm) REVERT: B 46 MET cc_start: 0.2555 (mtp) cc_final: 0.2291 (mtp) REVERT: C 163 PHE cc_start: 0.6527 (m-80) cc_final: 0.6156 (t80) REVERT: C 427 MET cc_start: 0.8967 (mmm) cc_final: 0.8711 (mmm) REVERT: C 720 MET cc_start: 0.3750 (mmp) cc_final: 0.2923 (mmt) REVERT: D 163 PHE cc_start: 0.7476 (m-80) cc_final: 0.7084 (t80) REVERT: D 720 MET cc_start: 0.4752 (ttt) cc_final: 0.4163 (mmp) REVERT: E 46 MET cc_start: 0.2879 (tpp) cc_final: 0.2414 (tpp) REVERT: E 84 MET cc_start: 0.6608 (ptt) cc_final: 0.6319 (ptt) REVERT: E 193 ASP cc_start: 0.8178 (m-30) cc_final: 0.7946 (p0) REVERT: E 720 MET cc_start: 0.4696 (tpt) cc_final: 0.3925 (tpp) REVERT: F 84 MET cc_start: 0.6181 (ptt) cc_final: 0.5925 (ttp) REVERT: F 550 MET cc_start: 0.8835 (mtm) cc_final: 0.8576 (mtm) REVERT: G 163 PHE cc_start: 0.6787 (m-80) cc_final: 0.6537 (t80) REVERT: G 332 MET cc_start: 0.8886 (tpp) cc_final: 0.8437 (ttt) REVERT: G 720 MET cc_start: 0.4334 (mmp) cc_final: 0.3578 (mmt) REVERT: H 84 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.4427 (tmm) REVERT: I 84 MET cc_start: 0.5198 (ptt) cc_final: 0.4971 (ptt) REVERT: I 163 PHE cc_start: 0.7387 (m-80) cc_final: 0.7031 (t80) REVERT: I 442 MET cc_start: 0.8628 (ppp) cc_final: 0.8422 (ppp) REVERT: J 84 MET cc_start: 0.6109 (ptt) cc_final: 0.5627 (ptt) REVERT: J 720 MET cc_start: 0.5074 (tpt) cc_final: 0.4387 (tpp) REVERT: K 84 MET cc_start: 0.5907 (ptt) cc_final: 0.5646 (ptt) REVERT: K 550 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8601 (mtm) REVERT: K 720 MET cc_start: 0.5212 (tpt) cc_final: 0.4321 (tpp) REVERT: L 163 PHE cc_start: 0.6754 (m-80) cc_final: 0.6440 (t80) REVERT: L 402 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: L 720 MET cc_start: 0.4307 (mmp) cc_final: 0.1966 (mtm) outliers start: 74 outliers final: 47 residues processed: 356 average time/residue: 0.6598 time to fit residues: 410.5172 Evaluate side-chains 347 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 6.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 754 LYS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 332 MET Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain K residue 731 ILE Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 296 optimal weight: 9.9990 chunk 793 optimal weight: 3.9990 chunk 174 optimal weight: 0.0010 chunk 517 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 882 optimal weight: 0.8980 chunk 732 optimal weight: 0.6980 chunk 408 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 463 optimal weight: 20.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN G 340 HIS ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN L 33 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 74052 Z= 0.128 Angle : 0.465 8.951 100152 Z= 0.234 Chirality : 0.042 0.139 11232 Planarity : 0.004 0.051 13188 Dihedral : 7.097 59.956 10488 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.00 % Allowed : 5.79 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 9168 helix: 1.53 (0.09), residues: 3792 sheet: 0.01 (0.14), residues: 1212 loop : -0.43 (0.10), residues: 4164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP I 454 HIS 0.003 0.000 HIS G 340 PHE 0.017 0.001 PHE B 363 TYR 0.010 0.001 TYR J 495 ARG 0.003 0.000 ARG I 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 323 time to evaluate : 6.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: B 46 MET cc_start: 0.2538 (mtp) cc_final: 0.2264 (mtp) REVERT: B 84 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.4286 (tmm) REVERT: B 720 MET cc_start: 0.3814 (mmp) cc_final: 0.2963 (mmm) REVERT: B 766 ARG cc_start: 0.7171 (mpt180) cc_final: 0.6899 (mpt90) REVERT: C 163 PHE cc_start: 0.6614 (m-80) cc_final: 0.6229 (t80) REVERT: C 427 MET cc_start: 0.8979 (mmm) cc_final: 0.8723 (mmm) REVERT: C 442 MET cc_start: 0.8238 (ppp) cc_final: 0.7792 (pmm) REVERT: C 550 MET cc_start: 0.8822 (mtm) cc_final: 0.8553 (mtm) REVERT: C 720 MET cc_start: 0.3877 (mmp) cc_final: 0.3078 (mmt) REVERT: D 163 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7083 (t80) REVERT: D 442 MET cc_start: 0.8515 (ppp) cc_final: 0.8295 (ppp) REVERT: D 720 MET cc_start: 0.4748 (ttt) cc_final: 0.4121 (mmp) REVERT: E 46 MET cc_start: 0.3167 (tpp) cc_final: 0.2721 (tpp) REVERT: E 84 MET cc_start: 0.6590 (ptt) cc_final: 0.6297 (ptt) REVERT: E 193 ASP cc_start: 0.8184 (m-30) cc_final: 0.7945 (p0) REVERT: E 720 MET cc_start: 0.4762 (tpt) cc_final: 0.4006 (tpp) REVERT: F 84 MET cc_start: 0.6353 (ptt) cc_final: 0.6098 (ttp) REVERT: F 720 MET cc_start: 0.4284 (mmt) cc_final: 0.4003 (mmm) REVERT: G 84 MET cc_start: 0.4512 (tmm) cc_final: 0.4183 (tmm) REVERT: G 126 ILE cc_start: 0.0867 (OUTLIER) cc_final: 0.0558 (tp) REVERT: G 163 PHE cc_start: 0.6810 (m-80) cc_final: 0.6537 (t80) REVERT: G 720 MET cc_start: 0.4324 (mmp) cc_final: 0.3515 (mmt) REVERT: H 84 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.4326 (tmm) REVERT: I 84 MET cc_start: 0.5166 (ptt) cc_final: 0.4915 (ptt) REVERT: I 138 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: I 163 PHE cc_start: 0.7366 (m-80) cc_final: 0.6981 (t80) REVERT: I 720 MET cc_start: 0.3921 (mmt) cc_final: 0.2858 (mmt) REVERT: J 46 MET cc_start: 0.2084 (tpp) cc_final: 0.1164 (tpp) REVERT: J 84 MET cc_start: 0.6075 (ptt) cc_final: 0.5582 (ptt) REVERT: J 546 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7170 (tm-30) REVERT: J 720 MET cc_start: 0.5122 (tpt) cc_final: 0.4780 (tpp) REVERT: K 84 MET cc_start: 0.5945 (ptt) cc_final: 0.5667 (ptt) REVERT: K 550 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: K 720 MET cc_start: 0.5245 (tpt) cc_final: 0.4753 (tpp) REVERT: L 163 PHE cc_start: 0.6657 (m-80) cc_final: 0.6277 (t80) REVERT: L 402 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: L 445 LEU cc_start: 0.8185 (mm) cc_final: 0.7861 (mm) REVERT: L 720 MET cc_start: 0.3991 (mmp) cc_final: 0.1856 (mtm) outliers start: 78 outliers final: 38 residues processed: 378 average time/residue: 0.6466 time to fit residues: 431.0635 Evaluate side-chains 338 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 292 time to evaluate : 6.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 332 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain K residue 731 ILE Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 850 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 502 optimal weight: 0.0370 chunk 644 optimal weight: 1.9990 chunk 499 optimal weight: 7.9990 chunk 742 optimal weight: 8.9990 chunk 492 optimal weight: 3.9990 chunk 879 optimal weight: 30.0000 chunk 550 optimal weight: 6.9990 chunk 535 optimal weight: 8.9990 chunk 405 optimal weight: 10.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 GLN ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN J 296 ASN K 750 ASN L 33 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 74052 Z= 0.236 Angle : 0.506 9.428 100152 Z= 0.254 Chirality : 0.043 0.189 11232 Planarity : 0.004 0.053 13188 Dihedral : 7.090 59.475 10488 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.14 % Allowed : 6.06 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 9168 helix: 1.59 (0.09), residues: 3804 sheet: -0.01 (0.14), residues: 1224 loop : -0.47 (0.10), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 551 HIS 0.004 0.001 HIS J 735 PHE 0.015 0.001 PHE L 758 TYR 0.013 0.001 TYR K 495 ARG 0.009 0.000 ARG I 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 301 time to evaluate : 6.608 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 402 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 46 MET cc_start: 0.2587 (mtp) cc_final: 0.2308 (mtp) REVERT: B 84 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.4188 (tmm) REVERT: B 126 ILE cc_start: 0.2458 (OUTLIER) cc_final: 0.2106 (tp) REVERT: B 720 MET cc_start: 0.3995 (mmp) cc_final: 0.3118 (mmm) REVERT: C 163 PHE cc_start: 0.6703 (m-80) cc_final: 0.6319 (t80) REVERT: C 442 MET cc_start: 0.8254 (ppp) cc_final: 0.7838 (pmm) REVERT: C 720 MET cc_start: 0.3897 (mmp) cc_final: 0.3128 (mmt) REVERT: D 163 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7063 (t80) REVERT: D 720 MET cc_start: 0.4718 (ttt) cc_final: 0.4136 (mmp) REVERT: E 84 MET cc_start: 0.6604 (ptt) cc_final: 0.6292 (ptt) REVERT: F 720 MET cc_start: 0.4130 (mmt) cc_final: 0.3645 (mmm) REVERT: G 84 MET cc_start: 0.4586 (tmm) cc_final: 0.4235 (tmm) REVERT: G 126 ILE cc_start: 0.0684 (OUTLIER) cc_final: 0.0365 (tp) REVERT: G 163 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6553 (t80) REVERT: G 720 MET cc_start: 0.4343 (mmp) cc_final: 0.3559 (mmt) REVERT: H 84 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.4263 (tmm) REVERT: I 84 MET cc_start: 0.5015 (ptt) cc_final: 0.4708 (ptt) REVERT: I 138 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5633 (m-10) REVERT: I 163 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6931 (t80) REVERT: I 442 MET cc_start: 0.8419 (ppp) cc_final: 0.7692 (pmm) REVERT: I 720 MET cc_start: 0.4028 (mmt) cc_final: 0.3252 (mmt) REVERT: J 46 MET cc_start: 0.1974 (tpp) cc_final: 0.1109 (tpp) REVERT: J 84 MET cc_start: 0.6047 (ptt) cc_final: 0.5549 (ptt) REVERT: J 720 MET cc_start: 0.4977 (tpt) cc_final: 0.4420 (tpp) REVERT: K 84 MET cc_start: 0.5979 (ptt) cc_final: 0.5690 (ptt) REVERT: K 550 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: K 720 MET cc_start: 0.5181 (tpt) cc_final: 0.4206 (tpp) REVERT: L 163 PHE cc_start: 0.6641 (m-80) cc_final: 0.6355 (t80) REVERT: L 402 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: L 445 LEU cc_start: 0.8157 (mm) cc_final: 0.7814 (mm) outliers start: 89 outliers final: 46 residues processed: 360 average time/residue: 0.6615 time to fit residues: 417.7131 Evaluate side-chains 347 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 6.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 163 PHE Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 313 ARG Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain J residue 731 ILE Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 0.0270 chunk 351 optimal weight: 7.9990 chunk 524 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 558 optimal weight: 7.9990 chunk 598 optimal weight: 1.9990 chunk 434 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 690 optimal weight: 20.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN L 33 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 74052 Z= 0.186 Angle : 0.492 10.209 100152 Z= 0.245 Chirality : 0.042 0.193 11232 Planarity : 0.004 0.053 13188 Dihedral : 7.004 59.714 10488 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.96 % Allowed : 6.30 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 9168 helix: 1.69 (0.09), residues: 3792 sheet: 0.07 (0.14), residues: 1224 loop : -0.39 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 551 HIS 0.003 0.001 HIS C 406 PHE 0.015 0.001 PHE H 363 TYR 0.015 0.001 TYR I 173 ARG 0.007 0.000 ARG I 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 309 time to evaluate : 8.246 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 402 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: B 46 MET cc_start: 0.2537 (mtp) cc_final: 0.2258 (mtp) REVERT: B 84 MET cc_start: 0.4446 (OUTLIER) cc_final: 0.4166 (tmm) REVERT: B 126 ILE cc_start: 0.2482 (OUTLIER) cc_final: 0.2068 (tp) REVERT: B 720 MET cc_start: 0.4038 (mmp) cc_final: 0.3161 (mmm) REVERT: C 163 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6261 (t80) REVERT: C 442 MET cc_start: 0.8280 (ppp) cc_final: 0.7848 (pmm) REVERT: C 720 MET cc_start: 0.3957 (mmp) cc_final: 0.2747 (mmt) REVERT: D 163 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7000 (t80) REVERT: D 720 MET cc_start: 0.4720 (ttt) cc_final: 0.4145 (mmp) REVERT: E 46 MET cc_start: 0.2881 (tpp) cc_final: 0.2544 (tpt) REVERT: E 84 MET cc_start: 0.6588 (ptt) cc_final: 0.6282 (ptt) REVERT: E 720 MET cc_start: 0.4362 (mmt) cc_final: 0.4107 (mmm) REVERT: F 550 MET cc_start: 0.8857 (mtm) cc_final: 0.8581 (mtm) REVERT: F 720 MET cc_start: 0.4210 (mmt) cc_final: 0.3798 (mmm) REVERT: G 84 MET cc_start: 0.4741 (tmm) cc_final: 0.4367 (tmm) REVERT: G 126 ILE cc_start: 0.0737 (OUTLIER) cc_final: 0.0448 (tp) REVERT: G 163 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6538 (t80) REVERT: G 720 MET cc_start: 0.4126 (mmp) cc_final: 0.3402 (mmt) REVERT: H 84 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.4204 (tmm) REVERT: H 126 ILE cc_start: 0.2984 (OUTLIER) cc_final: 0.2660 (tp) REVERT: I 84 MET cc_start: 0.5027 (ptt) cc_final: 0.4738 (ptt) REVERT: I 163 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6985 (t80) REVERT: I 442 MET cc_start: 0.8394 (ppp) cc_final: 0.7176 (pmm) REVERT: I 720 MET cc_start: 0.4178 (mmt) cc_final: 0.3282 (mmt) REVERT: J 46 MET cc_start: 0.1848 (tpp) cc_final: 0.1501 (tpt) REVERT: J 84 MET cc_start: 0.6062 (ptt) cc_final: 0.5546 (ptt) REVERT: J 720 MET cc_start: 0.4941 (tpt) cc_final: 0.4394 (tpp) REVERT: K 84 MET cc_start: 0.5982 (ptt) cc_final: 0.5689 (ptt) REVERT: K 550 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: K 720 MET cc_start: 0.5174 (tpt) cc_final: 0.4197 (tpp) REVERT: L 163 PHE cc_start: 0.6626 (m-80) cc_final: 0.6362 (t80) REVERT: L 402 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: L 445 LEU cc_start: 0.8113 (mm) cc_final: 0.7736 (mm) REVERT: L 720 MET cc_start: 0.4077 (mmp) cc_final: 0.1799 (mtm) outliers start: 75 outliers final: 47 residues processed: 354 average time/residue: 0.6622 time to fit residues: 412.5980 Evaluate side-chains 345 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 286 time to evaluate : 6.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 163 PHE Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 313 ARG Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 761 THR Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain J residue 731 ILE Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 332 MET Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 20.0000 chunk 842 optimal weight: 0.9980 chunk 768 optimal weight: 0.9990 chunk 819 optimal weight: 5.9990 chunk 841 optimal weight: 9.9990 chunk 493 optimal weight: 0.9980 chunk 356 optimal weight: 9.9990 chunk 643 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 740 optimal weight: 3.9990 chunk 774 optimal weight: 50.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 74052 Z= 0.137 Angle : 0.475 10.659 100152 Z= 0.236 Chirality : 0.041 0.162 11232 Planarity : 0.004 0.051 13188 Dihedral : 6.864 59.996 10488 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.91 % Allowed : 6.43 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 9168 helix: 1.84 (0.09), residues: 3792 sheet: 0.14 (0.14), residues: 1224 loop : -0.32 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 551 HIS 0.002 0.000 HIS G 115 PHE 0.015 0.001 PHE E 674 TYR 0.011 0.001 TYR I 173 ARG 0.006 0.000 ARG I 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 313 time to evaluate : 6.832 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 402 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 46 MET cc_start: 0.2525 (mtp) cc_final: 0.2246 (mtp) REVERT: B 84 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.4234 (tmm) REVERT: B 126 ILE cc_start: 0.2480 (OUTLIER) cc_final: 0.2218 (tp) REVERT: B 720 MET cc_start: 0.4038 (mmp) cc_final: 0.3194 (mmm) REVERT: C 163 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6428 (t80) REVERT: C 442 MET cc_start: 0.8270 (ppp) cc_final: 0.7828 (pmm) REVERT: C 720 MET cc_start: 0.3935 (mmp) cc_final: 0.3104 (mmt) REVERT: D 163 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6932 (t80) REVERT: D 720 MET cc_start: 0.4638 (ttt) cc_final: 0.4085 (mmp) REVERT: E 46 MET cc_start: 0.2800 (tpp) cc_final: 0.2486 (tpt) REVERT: E 84 MET cc_start: 0.6568 (ptt) cc_final: 0.6263 (ptt) REVERT: F 550 MET cc_start: 0.8842 (mtm) cc_final: 0.8639 (mtm) REVERT: F 720 MET cc_start: 0.4196 (mmt) cc_final: 0.3804 (mmm) REVERT: G 84 MET cc_start: 0.4893 (tmm) cc_final: 0.4522 (tmm) REVERT: G 126 ILE cc_start: 0.0630 (OUTLIER) cc_final: 0.0286 (tp) REVERT: G 163 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6478 (t80) REVERT: G 720 MET cc_start: 0.3941 (mmp) cc_final: 0.3282 (mmt) REVERT: H 84 MET cc_start: 0.4306 (OUTLIER) cc_final: 0.4106 (tmm) REVERT: H 126 ILE cc_start: 0.2853 (OUTLIER) cc_final: 0.2533 (tp) REVERT: I 84 MET cc_start: 0.4910 (ptt) cc_final: 0.4628 (ptt) REVERT: I 138 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5805 (m-10) REVERT: I 163 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6936 (t80) REVERT: I 442 MET cc_start: 0.8351 (ppp) cc_final: 0.7652 (pmm) REVERT: I 720 MET cc_start: 0.4190 (mmp) cc_final: 0.3449 (mmt) REVERT: J 46 MET cc_start: 0.1784 (tpp) cc_final: 0.1450 (tpt) REVERT: J 84 MET cc_start: 0.6040 (ptt) cc_final: 0.5520 (ptt) REVERT: J 720 MET cc_start: 0.5008 (tpt) cc_final: 0.4455 (tpp) REVERT: K 84 MET cc_start: 0.6064 (ptt) cc_final: 0.5756 (ptt) REVERT: K 550 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: K 720 MET cc_start: 0.5205 (tpt) cc_final: 0.4246 (tpp) REVERT: L 163 PHE cc_start: 0.6624 (OUTLIER) cc_final: 0.6386 (t80) REVERT: L 402 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: L 445 LEU cc_start: 0.8066 (mm) cc_final: 0.7703 (mm) REVERT: L 720 MET cc_start: 0.4201 (mmp) cc_final: 0.1885 (mtm) outliers start: 71 outliers final: 44 residues processed: 358 average time/residue: 0.6557 time to fit residues: 411.9217 Evaluate side-chains 349 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 291 time to evaluate : 6.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 731 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain G residue 731 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 163 PHE Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 313 ARG Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain I residue 761 THR Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain J residue 731 ILE Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 332 MET Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 373 ASP Chi-restraints excluded: chain K residue 550 MET Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Chi-restraints excluded: chain L residue 731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 2.9990 chunk 537 optimal weight: 50.0000 chunk 866 optimal weight: 9.9990 chunk 528 optimal weight: 9.9990 chunk 410 optimal weight: 0.4980 chunk 602 optimal weight: 7.9990 chunk 908 optimal weight: 9.9990 chunk 836 optimal weight: 30.0000 chunk 723 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 558 optimal weight: 9.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 36 ASN ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 750 ASN J 443 ASN L 33 ASN ** L 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 74052 Z= 0.330 Angle : 0.567 11.331 100152 Z= 0.283 Chirality : 0.044 0.164 11232 Planarity : 0.005 0.056 13188 Dihedral : 7.015 57.240 10488 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.79 % Allowed : 6.73 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 9168 helix: 1.63 (0.09), residues: 3804 sheet: 0.00 (0.14), residues: 1224 loop : -0.37 (0.10), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.008 0.001 HIS E 115 PHE 0.018 0.001 PHE L 758 TYR 0.014 0.001 TYR E 495 ARG 0.031 0.001 ARG L 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18336 Ramachandran restraints generated. 9168 Oldfield, 0 Emsley, 9168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 289 time to evaluate : 6.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: B 84 MET cc_start: 0.4623 (OUTLIER) cc_final: 0.4267 (ttp) REVERT: B 126 ILE cc_start: 0.2558 (OUTLIER) cc_final: 0.2223 (tp) REVERT: B 720 MET cc_start: 0.4087 (mmp) cc_final: 0.3276 (mmm) REVERT: C 163 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6415 (t80) REVERT: C 442 MET cc_start: 0.8273 (ppp) cc_final: 0.7818 (pmm) REVERT: C 720 MET cc_start: 0.4154 (mmp) cc_final: 0.3323 (mmt) REVERT: D 163 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7007 (t80) REVERT: D 720 MET cc_start: 0.4648 (ttt) cc_final: 0.4389 (mmp) REVERT: E 46 MET cc_start: 0.2680 (tpp) cc_final: 0.2365 (tpt) REVERT: E 84 MET cc_start: 0.6609 (ptt) cc_final: 0.6291 (ptt) REVERT: F 720 MET cc_start: 0.4303 (mmt) cc_final: 0.3812 (mmm) REVERT: G 84 MET cc_start: 0.4818 (tmm) cc_final: 0.4503 (tmm) REVERT: G 126 ILE cc_start: 0.0811 (OUTLIER) cc_final: 0.0504 (tp) REVERT: G 163 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6595 (t80) REVERT: G 442 MET cc_start: 0.8623 (ppp) cc_final: 0.7998 (pmm) REVERT: G 550 MET cc_start: 0.8901 (mtm) cc_final: 0.8674 (mtm) REVERT: G 720 MET cc_start: 0.4039 (mmp) cc_final: 0.3373 (mmt) REVERT: I 84 MET cc_start: 0.4972 (ptt) cc_final: 0.4668 (ptt) REVERT: I 163 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6948 (t80) REVERT: I 442 MET cc_start: 0.8357 (ppp) cc_final: 0.7678 (pmm) REVERT: I 720 MET cc_start: 0.4100 (mmp) cc_final: 0.3317 (mmt) REVERT: J 46 MET cc_start: 0.1777 (tpp) cc_final: 0.1446 (tpt) REVERT: J 84 MET cc_start: 0.6041 (ptt) cc_final: 0.5527 (ptt) REVERT: J 720 MET cc_start: 0.4901 (tpt) cc_final: 0.4314 (tpp) REVERT: K 84 MET cc_start: 0.6012 (ptt) cc_final: 0.5720 (ptt) REVERT: K 720 MET cc_start: 0.5140 (tpt) cc_final: 0.4714 (tpp) REVERT: L 163 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6397 (t80) REVERT: L 402 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: L 442 MET cc_start: 0.8542 (ppp) cc_final: 0.7797 (pmm) REVERT: L 445 LEU cc_start: 0.8102 (mm) cc_final: 0.7705 (mm) REVERT: L 720 MET cc_start: 0.4311 (mmp) cc_final: 0.4096 (mmp) outliers start: 62 outliers final: 39 residues processed: 324 average time/residue: 0.6603 time to fit residues: 376.8938 Evaluate side-chains 333 residues out of total 7836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 6.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 PHE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 611 MET Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain H residue 442 MET Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain I residue 163 PHE Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 224 LEU Chi-restraints excluded: chain I residue 313 ARG Chi-restraints excluded: chain I residue 761 THR Chi-restraints excluded: chain J residue 204 ASP Chi-restraints excluded: chain J residue 205 ASP Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 332 MET Chi-restraints excluded: chain K residue 205 ASP Chi-restraints excluded: chain K residue 344 MET Chi-restraints excluded: chain K residue 442 MET Chi-restraints excluded: chain L residue 138 TYR Chi-restraints excluded: chain L residue 163 PHE Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 402 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 0.7980 chunk 574 optimal weight: 0.0670 chunk 770 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 667 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 201 optimal weight: 1.9990 chunk 724 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 744 optimal weight: 2.9990 chunk 91 optimal weight: 50.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 750 ASN L 33 ASN L 183 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.109302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.073880 restraints weight = 193557.844| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.62 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 74052 Z= 0.127 Angle : 0.488 11.141 100152 Z= 0.242 Chirality : 0.042 0.168 11232 Planarity : 0.004 0.051 13188 Dihedral : 6.756 56.835 10488 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.68 % Allowed : 6.80 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 9168 helix: 1.87 (0.09), residues: 3792 sheet: 0.20 (0.14), residues: 1224 loop : -0.24 (0.10), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP L 551 HIS 0.005 0.001 HIS E 115 PHE 0.012 0.001 PHE L 674 TYR 0.011 0.001 TYR J 495 ARG 0.006 0.000 ARG I 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10803.11 seconds wall clock time: 193 minutes 37.40 seconds (11617.40 seconds total)