Starting phenix.real_space_refine on Sun Feb 18 04:02:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcu_31896/02_2024/7vcu_31896_updated.pdb" } resolution = 3.15 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 12 5.21 5 S 384 5.16 5 C 44940 2.51 5 N 12744 2.21 5 O 13812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 191": "NH1" <-> "NH2" Residue "K ARG 287": "NH1" <-> "NH2" Residue "K ARG 313": "NH1" <-> "NH2" Residue "K ARG 322": "NH1" <-> "NH2" Residue "K ARG 338": "NH1" <-> "NH2" Residue "K ARG 424": "NH1" <-> "NH2" Residue "K ARG 465": "NH1" <-> "NH2" Residue "K ARG 586": "NH1" <-> "NH2" Residue "K ARG 635": "NH1" <-> "NH2" Residue "K ARG 733": "NH1" <-> "NH2" Residue "K ARG 766": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 766": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D ARG 766": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 766": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L ARG 287": "NH1" <-> "NH2" Residue "L ARG 313": "NH1" <-> "NH2" Residue "L ARG 322": "NH1" <-> "NH2" Residue "L ARG 338": "NH1" <-> "NH2" Residue "L ARG 424": "NH1" <-> "NH2" Residue "L ARG 465": "NH1" <-> "NH2" Residue "L ARG 586": "NH1" <-> "NH2" Residue "L ARG 635": "NH1" <-> "NH2" Residue "L ARG 733": "NH1" <-> "NH2" Residue "L ARG 766": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 287": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 424": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 586": "NH1" <-> "NH2" Residue "G ARG 635": "NH1" <-> "NH2" Residue "G ARG 733": "NH1" <-> "NH2" Residue "G ARG 766": "NH1" <-> "NH2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 287": "NH1" <-> "NH2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H ARG 424": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 586": "NH1" <-> "NH2" Residue "H ARG 635": "NH1" <-> "NH2" Residue "H ARG 733": "NH1" <-> "NH2" Residue "H ARG 766": "NH1" <-> "NH2" Residue "I ARG 191": "NH1" <-> "NH2" Residue "I ARG 287": "NH1" <-> "NH2" Residue "I ARG 313": "NH1" <-> "NH2" Residue "I ARG 322": "NH1" <-> "NH2" Residue "I ARG 338": "NH1" <-> "NH2" Residue "I ARG 424": "NH1" <-> "NH2" Residue "I ARG 465": "NH1" <-> "NH2" Residue "I ARG 586": "NH1" <-> "NH2" Residue "I ARG 635": "NH1" <-> "NH2" Residue "I ARG 733": "NH1" <-> "NH2" Residue "I ARG 766": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ARG 287": "NH1" <-> "NH2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "J ARG 322": "NH1" <-> "NH2" Residue "J ARG 338": "NH1" <-> "NH2" Residue "J ARG 424": "NH1" <-> "NH2" Residue "J ARG 465": "NH1" <-> "NH2" Residue "J ARG 586": "NH1" <-> "NH2" Residue "J ARG 635": "NH1" <-> "NH2" Residue "J ARG 733": "NH1" <-> "NH2" Residue "J 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: 71952 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "B" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "C" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "D" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "E" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "F" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "A" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "L" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "G" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "H" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "I" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "J" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5937 Classifications: {'peptide': 757} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 714} Chain: "K" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 28.16, per 1000 atoms: 0.39 Number of scatterers: 71952 At special positions: 0 Unit cell: (179.28, 182.52, 189, 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 384 16.00 P 60 15.00 Mg 12 11.99 O 13812 8.00 N 12744 7.00 C 44940 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.47 Conformation dependent library (CDL) restraints added in 10.3 seconds 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 408 helices and 60 sheets defined 40.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.80 Creating SS restraints... Processing helix chain 'K' and resid 43 through 49 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 90 Processing helix chain 'K' and resid 120 through 122 No H-bonds generated for 'chain 'K' and resid 120 through 122' Processing helix chain 'K' and resid 135 through 138 No H-bonds generated for 'chain 'K' and resid 135 through 138' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 210 through 225 removed outlier: 4.824A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 309 No H-bonds generated for 'chain 'K' and resid 306 through 309' Processing helix chain 'K' and resid 320 through 334 Processing helix chain 'K' and resid 355 through 358 Processing helix chain 'K' and resid 374 through 384 Processing helix chain 'K' and resid 396 through 402 Processing helix chain 'K' and resid 408 through 425 Processing helix chain 'K' and resid 427 through 432 Processing helix chain 'K' and resid 439 through 443 Processing helix chain 'K' and resid 449 through 455 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: 4.236A 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 506 Processing helix chain 'K' and resid 524 through 534 Processing helix chain 'K' and resid 544 through 552 Processing helix chain 'K' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL K 559 " --> pdb=" O GLU K 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG K 560 " --> pdb=" O ALA K 557 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP K 564 " --> pdb=" O GLU K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 586 Processing helix chain 'K' and resid 599 through 610 Processing helix chain 'K' and resid 631 through 633 No H-bonds generated for 'chain 'K' and resid 631 through 633' Processing helix chain 'K' and resid 650 through 660 Processing helix chain 'K' and resid 672 through 678 removed outlier: 3.656A pdb=" N LYS K 677 " --> pdb=" O GLU K 673 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET K 678 " --> pdb=" O PHE K 674 " (cutoff:3.500A) Processing helix chain 'K' and resid 684 through 711 removed outlier: 3.946A pdb=" N ARG K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG K 741 " --> pdb=" O GLU K 737 " (cutoff:3.500A) removed outlier: 4.671A 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 'B' and resid 43 through 49 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 90 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.824A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 455 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: 4.236A 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 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 564 " --> pdb=" O GLU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.709A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.671A 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 43 through 49 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 90 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.263A pdb=" N GLU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.644A pdb=" N VAL C 559 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 564 " --> pdb=" O GLU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 599 through 610 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.708A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.671A 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 43 through 49 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 90 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.263A pdb=" N GLU D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 455 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: 4.236A 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 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL D 559 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 564 " --> pdb=" O GLU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 599 through 610 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.709A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.671A 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 43 through 49 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 90 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.822A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 334 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 427 through 432 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.644A pdb=" N VAL E 559 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 564 " --> pdb=" O GLU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'E' and resid 599 through 610 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.656A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 711 removed outlier: 3.946A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.709A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.670A 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 43 through 49 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 90 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 4.824A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.644A pdb=" N VAL F 559 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP F 564 " --> pdb=" O GLU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 599 through 610 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.656A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.709A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.670A 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 'A' and resid 43 through 49 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 90 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.824A 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 279 through 295 removed outlier: 4.261A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 564 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 599 through 610 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 711 removed outlier: 3.946A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.670A 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 'L' and resid 43 through 49 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 90 Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'L' and resid 135 through 138 No H-bonds generated for 'chain 'L' and resid 135 through 138' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU L 283 " --> pdb=" O ALA L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 309 No H-bonds generated for 'chain 'L' and resid 306 through 309' Processing helix chain 'L' and resid 320 through 334 Processing helix chain 'L' and resid 355 through 358 Processing helix chain 'L' and resid 374 through 384 Processing helix chain 'L' and resid 396 through 402 Processing helix chain 'L' and resid 408 through 425 Processing helix chain 'L' and resid 427 through 432 Processing helix chain 'L' and resid 439 through 443 Processing helix chain 'L' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'L' and resid 524 through 534 Processing helix chain 'L' and resid 544 through 552 Processing helix chain 'L' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL L 559 " --> pdb=" O GLU L 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG L 560 " --> pdb=" O ALA L 557 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP L 564 " --> pdb=" O GLU L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 586 Processing helix chain 'L' and resid 599 through 610 Processing helix chain 'L' and resid 631 through 633 No H-bonds generated for 'chain 'L' and resid 631 through 633' Processing helix chain 'L' and resid 650 through 660 Processing helix chain 'L' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS L 677 " --> pdb=" O GLU L 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET L 678 " --> pdb=" O PHE L 674 " (cutoff:3.500A) Processing helix chain 'L' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG L 708 " --> pdb=" O GLU L 704 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 742 removed outlier: 4.709A pdb=" N ARG L 741 " --> pdb=" O GLU L 737 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE L 742 " --> pdb=" O GLU L 738 " (cutoff:3.500A) Processing helix chain 'L' and resid 749 through 761 Processing helix chain 'G' and resid 43 through 49 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 90 Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 135 through 138 No H-bonds generated for 'chain 'G' and resid 135 through 138' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.261A pdb=" N GLU G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 309 No H-bonds generated for 'chain 'G' and resid 306 through 309' Processing helix chain 'G' and resid 320 through 334 Processing helix chain 'G' and resid 355 through 358 Processing helix chain 'G' and resid 374 through 384 Processing helix chain 'G' and resid 396 through 402 Processing helix chain 'G' and resid 408 through 425 Processing helix chain 'G' and resid 427 through 432 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'G' and resid 524 through 534 Processing helix chain 'G' and resid 544 through 552 Processing helix chain 'G' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL G 559 " --> pdb=" O GLU G 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG G 560 " --> pdb=" O ALA G 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP G 564 " --> pdb=" O GLU G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 586 Processing helix chain 'G' and resid 599 through 610 Processing helix chain 'G' and resid 631 through 633 No H-bonds generated for 'chain 'G' and resid 631 through 633' Processing helix chain 'G' and resid 650 through 660 Processing helix chain 'G' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS G 677 " --> pdb=" O GLU G 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET G 678 " --> pdb=" O PHE G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG G 708 " --> pdb=" O GLU G 704 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG G 741 " --> pdb=" O GLU G 737 " (cutoff:3.500A) removed outlier: 4.670A 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 43 through 49 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 90 Processing helix chain 'H' and resid 120 through 122 No H-bonds generated for 'chain 'H' and resid 120 through 122' Processing helix chain 'H' and resid 135 through 138 No H-bonds generated for 'chain 'H' and resid 135 through 138' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 309 No H-bonds generated for 'chain 'H' and resid 306 through 309' Processing helix chain 'H' and resid 320 through 334 Processing helix chain 'H' and resid 355 through 358 Processing helix chain 'H' and resid 374 through 384 Processing helix chain 'H' and resid 396 through 402 Processing helix chain 'H' and resid 408 through 425 Processing helix chain 'H' and resid 427 through 432 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'H' and resid 524 through 534 Processing helix chain 'H' and resid 544 through 552 Processing helix chain 'H' and resid 556 through 568 removed outlier: 3.644A pdb=" N VAL H 559 " --> pdb=" O GLU H 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG H 560 " --> pdb=" O ALA H 557 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP H 564 " --> pdb=" O GLU H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 586 Processing helix chain 'H' and resid 599 through 610 Processing helix chain 'H' and resid 631 through 633 No H-bonds generated for 'chain 'H' and resid 631 through 633' Processing helix chain 'H' and resid 650 through 660 Processing helix chain 'H' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS H 677 " --> pdb=" O GLU H 673 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET H 678 " --> pdb=" O PHE H 674 " (cutoff:3.500A) Processing helix chain 'H' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG H 708 " --> pdb=" O GLU H 704 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG H 741 " --> pdb=" O GLU H 737 " (cutoff:3.500A) removed outlier: 4.670A 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 43 through 49 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 90 Processing helix chain 'I' and resid 120 through 122 No H-bonds generated for 'chain 'I' and resid 120 through 122' Processing helix chain 'I' and resid 135 through 138 No H-bonds generated for 'chain 'I' and resid 135 through 138' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 309 No H-bonds generated for 'chain 'I' and resid 306 through 309' Processing helix chain 'I' and resid 320 through 334 Processing helix chain 'I' and resid 355 through 358 Processing helix chain 'I' and resid 374 through 384 Processing helix chain 'I' and resid 396 through 402 Processing helix chain 'I' and resid 408 through 425 Processing helix chain 'I' and resid 427 through 432 Processing helix chain 'I' and resid 439 through 443 Processing helix chain 'I' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'I' and resid 524 through 534 Processing helix chain 'I' and resid 544 through 552 Processing helix chain 'I' and resid 556 through 568 removed outlier: 3.645A pdb=" N VAL I 559 " --> pdb=" O GLU I 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG I 560 " --> pdb=" O ALA I 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP I 564 " --> pdb=" O GLU I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 586 Processing helix chain 'I' and resid 599 through 610 Processing helix chain 'I' and resid 631 through 633 No H-bonds generated for 'chain 'I' and resid 631 through 633' Processing helix chain 'I' and resid 650 through 660 Processing helix chain 'I' and resid 672 through 678 removed outlier: 3.656A pdb=" N LYS I 677 " --> pdb=" O GLU I 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET I 678 " --> pdb=" O PHE I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 684 through 711 removed outlier: 3.945A pdb=" N ARG I 708 " --> pdb=" O GLU I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG I 741 " --> pdb=" O GLU I 737 " (cutoff:3.500A) removed outlier: 4.670A 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 43 through 49 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 90 Processing helix chain 'J' and resid 120 through 122 No H-bonds generated for 'chain 'J' and resid 120 through 122' Processing helix chain 'J' and resid 135 through 138 No H-bonds generated for 'chain 'J' and resid 135 through 138' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 210 through 225 removed outlier: 4.823A 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 279 through 295 removed outlier: 4.262A pdb=" N GLU J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 309 No H-bonds generated for 'chain 'J' and resid 306 through 309' Processing helix chain 'J' and resid 320 through 334 Processing helix chain 'J' and resid 355 through 358 Processing helix chain 'J' and resid 374 through 384 Processing helix chain 'J' and resid 396 through 402 Processing helix chain 'J' and resid 408 through 425 Processing helix chain 'J' and resid 427 through 432 Processing helix chain 'J' and resid 439 through 443 Processing helix chain 'J' and resid 449 through 455 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: 4.235A 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 506 Processing helix chain 'J' and resid 524 through 534 Processing helix chain 'J' and resid 544 through 552 Processing helix chain 'J' and resid 556 through 568 removed outlier: 3.644A pdb=" N VAL J 559 " --> pdb=" O GLU J 556 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG J 560 " --> pdb=" O ALA J 557 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP J 564 " --> pdb=" O GLU J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 586 Processing helix chain 'J' and resid 599 through 610 Processing helix chain 'J' and resid 631 through 633 No H-bonds generated for 'chain 'J' and resid 631 through 633' Processing helix chain 'J' and resid 650 through 660 Processing helix chain 'J' and resid 672 through 678 removed outlier: 3.655A pdb=" N LYS J 677 " --> pdb=" O GLU J 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET J 678 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 684 through 711 removed outlier: 3.946A pdb=" N ARG J 708 " --> pdb=" O GLU J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.710A pdb=" N ARG J 741 " --> pdb=" O GLU J 737 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 749 through 761 Processing sheet with id= A, first strand: chain 'K' and resid 27 through 30 Processing sheet with id= B, first strand: chain 'K' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL K 39 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE K 70 " --> pdb=" O VAL K 39 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU K 41 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU K 72 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER K 101 " --> pdb=" O LYS K 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU K 117 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL K 165 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE K 241 " --> pdb=" O VAL K 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL K 343 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU K 243 " --> pdb=" O VAL K 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA K 345 " --> pdb=" O LEU K 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY K 245 " --> pdb=" O ALA K 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR K 347 " --> pdb=" O GLY K 245 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA K 299 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET K 344 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE K 301 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA K 346 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE K 303 " --> pdb=" O ALA K 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP K 304 " --> pdb=" O PHE K 267 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE K 269 " --> pdb=" O ASP K 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY K 518 " --> pdb=" O THR K 623 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP K 640 " --> pdb=" O GLY K 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU K 515 " --> pdb=" O ASP K 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU K 642 " --> pdb=" O LEU K 515 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR K 517 " --> pdb=" O LEU K 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR K 644 " --> pdb=" O TYR K 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.924A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 640 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= L, first strand: chain 'C' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.924A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY C 245 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR C 347 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 640 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 515 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU C 642 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR C 517 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR C 644 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= Q, first strand: chain 'D' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 369 removed outlier: 8.724A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 27 through 30 Processing sheet with id= V, first strand: chain 'E' and resid 38 through 42 removed outlier: 7.667A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.926A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLY E 245 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR E 347 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 640 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU E 515 " --> pdb=" O ASP E 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU E 642 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR E 517 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR E 644 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 27 through 30 Processing sheet with id= AA, first strand: chain 'F' and resid 38 through 42 removed outlier: 7.665A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY F 245 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR F 347 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.730A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 27 through 30 Processing sheet with id= AF, first strand: chain 'A' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.924A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 365 through 369 removed outlier: 8.724A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 640 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 515 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 642 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR A 517 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR A 644 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 27 through 30 Processing sheet with id= AK, first strand: chain 'L' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL L 39 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE L 70 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU L 41 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU L 72 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER L 101 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU L 117 " --> pdb=" O VAL L 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL L 165 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 365 through 369 removed outlier: 8.726A pdb=" N ILE L 241 " --> pdb=" O VAL L 341 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL L 343 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU L 243 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA L 345 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY L 245 " --> pdb=" O ALA L 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR L 347 " --> pdb=" O GLY L 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA L 299 " --> pdb=" O ILE L 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET L 344 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE L 301 " --> pdb=" O MET L 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA L 346 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE L 303 " --> pdb=" O ALA L 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP L 304 " --> pdb=" O PHE L 267 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE L 269 " --> pdb=" O ASP L 304 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY L 518 " --> pdb=" O THR L 623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP L 640 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU L 515 " --> pdb=" O ASP L 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU L 642 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR L 517 " --> pdb=" O LEU L 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR L 644 " --> pdb=" O TYR L 517 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 27 through 30 Processing sheet with id= AP, first strand: chain 'G' and resid 38 through 42 removed outlier: 7.667A pdb=" N VAL G 39 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE G 70 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU G 41 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU G 72 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER G 101 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 181 through 183 removed outlier: 6.926A pdb=" N LEU G 117 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL G 165 " --> pdb=" O LEU G 117 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE G 241 " --> pdb=" O VAL G 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL G 343 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU G 243 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA G 345 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLY G 245 " --> pdb=" O ALA G 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR G 347 " --> pdb=" O GLY G 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA G 299 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET G 344 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE G 301 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA G 346 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE G 303 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP G 304 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE G 269 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY G 518 " --> pdb=" O THR G 623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP G 640 " --> pdb=" O GLY G 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU G 515 " --> pdb=" O ASP G 640 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU G 642 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR G 517 " --> pdb=" O LEU G 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR G 644 " --> pdb=" O TYR G 517 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 27 through 30 Processing sheet with id= AU, first strand: chain 'H' and resid 38 through 42 removed outlier: 7.667A pdb=" N VAL H 39 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE H 70 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU H 41 " --> pdb=" O ILE H 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU H 72 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER H 101 " --> pdb=" O LYS H 60 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 181 through 183 removed outlier: 6.926A pdb=" N LEU H 117 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL H 165 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE H 241 " --> pdb=" O VAL H 341 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 343 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU H 243 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA H 345 " --> pdb=" O LEU H 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY H 245 " --> pdb=" O ALA H 345 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR H 347 " --> pdb=" O GLY H 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA H 299 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET H 344 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE H 301 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA H 346 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE H 303 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP H 304 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE H 269 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 538 through 542 removed outlier: 3.729A pdb=" N GLY H 518 " --> pdb=" O THR H 623 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP H 640 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU H 515 " --> pdb=" O ASP H 640 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU H 642 " --> pdb=" O LEU H 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR H 517 " --> pdb=" O LEU H 642 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR H 644 " --> pdb=" O TYR H 517 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 27 through 30 Processing sheet with id= AZ, first strand: chain 'I' and resid 38 through 42 removed outlier: 7.667A pdb=" N VAL I 39 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE I 70 " --> pdb=" O VAL I 39 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU I 41 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU I 72 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 101 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'I' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU I 117 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL I 165 " --> pdb=" O LEU I 117 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE I 241 " --> pdb=" O VAL I 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 343 " --> pdb=" O ILE I 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU I 243 " --> pdb=" O VAL I 343 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA I 345 " --> pdb=" O LEU I 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY I 245 " --> pdb=" O ALA I 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR I 347 " --> pdb=" O GLY I 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA I 299 " --> pdb=" O ILE I 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET I 344 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE I 301 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA I 346 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE I 303 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP I 304 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE I 269 " --> pdb=" O ASP I 304 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 538 through 542 removed outlier: 3.730A pdb=" N GLY I 518 " --> pdb=" O THR I 623 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP I 640 " --> pdb=" O GLY I 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU I 515 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU I 642 " --> pdb=" O LEU I 515 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR I 517 " --> pdb=" O LEU I 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR I 644 " --> pdb=" O TYR I 517 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 27 through 30 Processing sheet with id= BE, first strand: chain 'J' and resid 38 through 42 removed outlier: 7.666A pdb=" N VAL J 39 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE J 70 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU J 41 " --> pdb=" O ILE J 70 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU J 72 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER J 101 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 181 through 183 removed outlier: 6.925A pdb=" N LEU J 117 " --> pdb=" O VAL J 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL J 165 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'J' and resid 365 through 369 removed outlier: 8.725A pdb=" N ILE J 241 " --> pdb=" O VAL J 341 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL J 343 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU J 243 " --> pdb=" O VAL J 343 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA J 345 " --> pdb=" O LEU J 243 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY J 245 " --> pdb=" O ALA J 345 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR J 347 " --> pdb=" O GLY J 245 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA J 299 " --> pdb=" O ILE J 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET J 344 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE J 301 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA J 346 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE J 303 " --> pdb=" O ALA J 346 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP J 304 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 6.987A 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: 3.730A pdb=" N GLY J 518 " --> pdb=" O THR J 623 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP J 640 " --> pdb=" O GLY J 513 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU J 515 " --> pdb=" O ASP J 640 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU J 642 " --> pdb=" O LEU J 515 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR J 517 " --> pdb=" O LEU J 642 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR J 644 " --> pdb=" O TYR J 517 " (cutoff:3.500A) 2400 hydrogen bonds defined for protein. 6876 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: 28.62 Time building geometry restraints manager: 23.70 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: 25051 1.36 - 1.51: 20782 1.51 - 1.65: 26731 1.65 - 1.80: 429 1.80 - 1.95: 183 Bond restraints: 73176 Sorted by residual: bond pdb=" C ASP I 169 " pdb=" N PRO I 170 " ideal model delta sigma weight residual 1.334 1.383 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C ASP G 169 " pdb=" N PRO G 170 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 bond pdb=" C ASP L 169 " pdb=" N PRO L 170 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.40e+00 bond pdb=" C ASP K 169 " pdb=" N PRO K 170 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.39e+00 bond pdb=" C ASP H 169 " pdb=" N PRO H 170 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.37e+00 ... (remaining 73171 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.63: 2607 106.63 - 114.01: 41905 114.01 - 121.38: 36485 121.38 - 128.76: 17585 128.76 - 136.14: 382 Bond angle restraints: 98964 Sorted by residual: angle pdb=" C GLY J 588 " pdb=" N ASN J 589 " pdb=" CA ASN J 589 " ideal model delta sigma weight residual 122.40 129.24 -6.84 1.45e+00 4.76e-01 2.22e+01 angle pdb=" C GLY A 588 " pdb=" N ASN A 589 " pdb=" CA ASN A 589 " ideal model delta sigma weight residual 122.40 129.20 -6.80 1.45e+00 4.76e-01 2.20e+01 angle pdb=" C GLY E 588 " pdb=" N ASN E 589 " pdb=" CA ASN E 589 " ideal model delta sigma weight residual 122.40 129.20 -6.80 1.45e+00 4.76e-01 2.20e+01 angle pdb=" C GLY H 588 " pdb=" N ASN H 589 " pdb=" CA ASN H 589 " ideal model delta sigma weight residual 122.40 129.20 -6.80 1.45e+00 4.76e-01 2.20e+01 angle pdb=" C GLY G 588 " pdb=" N ASN G 589 " pdb=" CA ASN G 589 " ideal model delta sigma weight residual 122.40 129.19 -6.79 1.45e+00 4.76e-01 2.19e+01 ... (remaining 98959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 44923 30.20 - 60.41: 436 60.41 - 90.61: 60 90.61 - 120.81: 3 120.81 - 151.01: 10 Dihedral angle restraints: 45432 sinusoidal: 19284 harmonic: 26148 Sorted by residual: dihedral pdb=" O2A ADP G 903 " pdb=" O3A ADP G 903 " pdb=" PA ADP G 903 " pdb=" PB ADP G 903 " ideal model delta sinusoidal sigma weight residual -60.00 91.01 -151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C5' ADP L 903 " pdb=" O5' ADP L 903 " pdb=" PA ADP L 903 " pdb=" O2A ADP L 903 " ideal model delta sinusoidal sigma weight residual -60.00 89.30 -149.30 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP H 903 " pdb=" O5' ADP H 903 " pdb=" PA ADP H 903 " pdb=" O2A ADP H 903 " ideal model delta sinusoidal sigma weight residual -60.00 88.63 -148.63 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 45429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 7016 0.042 - 0.084: 2708 0.084 - 0.125: 1088 0.125 - 0.167: 216 0.167 - 0.209: 24 Chirality restraints: 11052 Sorted by residual: chirality pdb=" CB THR F 316 " pdb=" CA THR F 316 " pdb=" OG1 THR F 316 " pdb=" CG2 THR F 316 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR D 316 " pdb=" CA THR D 316 " pdb=" OG1 THR D 316 " pdb=" CG2 THR D 316 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR H 316 " pdb=" CA THR H 316 " pdb=" OG1 THR H 316 " pdb=" CG2 THR H 316 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 11049 not shown) Planarity restraints: 13068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 544 " 0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO K 545 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 545 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 545 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 544 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO A 545 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " -0.041 5.00e-02 4.00e+02 6.07e-02 5.90e+00 pdb=" N PRO B 545 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " -0.034 5.00e-02 4.00e+02 ... (remaining 13065 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 133 2.42 - 3.04: 38309 3.04 - 3.66: 102500 3.66 - 4.28: 149480 4.28 - 4.90: 247667 Nonbonded interactions: 538089 Sorted by model distance: nonbonded pdb=" OD2 ASP G 304 " pdb="MG MG G 902 " model vdw 1.802 2.170 nonbonded pdb=" OE2 GLU L 218 " pdb=" NH2 ARG G 424 " model vdw 1.900 2.520 nonbonded pdb=" OD2 ASP F 304 " pdb="MG MG F 902 " model vdw 1.997 2.170 nonbonded pdb=" OD2 ASP A 304 " pdb="MG MG A 902 " model vdw 2.054 2.170 nonbonded pdb=" O2G AGS J 901 " pdb="MG MG J 902 " model vdw 2.098 2.170 ... (remaining 538084 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: 1.180 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: 0.040 Extract box with map and model: 8.670 Check model and map are aligned: 0.830 Set scattering table: 0.490 Process input model: 157.870 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.570 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 73176 Z= 0.378 Angle : 0.845 7.760 98964 Z= 0.482 Chirality : 0.052 0.209 11052 Planarity : 0.007 0.061 13068 Dihedral : 9.754 151.013 28488 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.77 (0.07), residues: 9060 helix: -2.08 (0.07), residues: 3756 sheet: -0.79 (0.13), residues: 1344 loop : -1.82 (0.09), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 454 HIS 0.013 0.002 HIS L 406 PHE 0.035 0.003 PHE C 516 TYR 0.016 0.003 TYR C 517 ARG 0.009 0.001 ARG K 733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 728 time to evaluate : 6.465 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: K 155 ARG cc_start: 0.6725 (mtt90) cc_final: 0.6252 (ttm110) REVERT: K 420 LEU cc_start: 0.8302 (mt) cc_final: 0.7945 (tt) REVERT: K 449 MET cc_start: 0.8259 (tpt) cc_final: 0.7479 (tpp) REVERT: B 173 TYR cc_start: 0.5644 (p90) cc_final: 0.5354 (p90) REVERT: B 199 ASN cc_start: 0.6460 (t0) cc_final: 0.5970 (p0) REVERT: B 449 MET cc_start: 0.8297 (tpt) cc_final: 0.8038 (tpt) REVERT: B 690 ILE cc_start: 0.8848 (tt) cc_final: 0.8555 (pt) REVERT: C 84 MET cc_start: 0.6147 (ptp) cc_final: 0.5806 (ptp) REVERT: D 84 MET cc_start: 0.6425 (ptp) cc_final: 0.6148 (ptp) REVERT: D 199 ASN cc_start: 0.6040 (t0) cc_final: 0.5636 (p0) REVERT: E 39 VAL cc_start: 0.6663 (m) cc_final: 0.6139 (p) REVERT: E 442 MET cc_start: 0.8094 (mmp) cc_final: 0.7823 (mpp) REVERT: E 449 MET cc_start: 0.7685 (tpt) cc_final: 0.7399 (tpp) REVERT: E 764 GLN cc_start: 0.7898 (mt0) cc_final: 0.7692 (mp10) REVERT: F 711 ARG cc_start: 0.8469 (tmm160) cc_final: 0.8206 (ptt90) REVERT: F 720 MET cc_start: 0.7670 (mmm) cc_final: 0.7332 (pmm) REVERT: A 449 MET cc_start: 0.8519 (tpt) cc_final: 0.7624 (tpp) REVERT: A 720 MET cc_start: 0.7516 (mmm) cc_final: 0.7285 (pmm) REVERT: L 39 VAL cc_start: 0.6878 (m) cc_final: 0.6394 (p) REVERT: L 173 TYR cc_start: 0.5867 (p90) cc_final: 0.5661 (p90) REVERT: L 449 MET cc_start: 0.8023 (tpt) cc_final: 0.7718 (tpt) REVERT: G 398 GLN cc_start: 0.8584 (tt0) cc_final: 0.7748 (pt0) REVERT: G 420 LEU cc_start: 0.7579 (mt) cc_final: 0.7316 (tt) REVERT: G 449 MET cc_start: 0.8167 (tpt) cc_final: 0.7879 (mmm) REVERT: H 46 MET cc_start: 0.6671 (ttp) cc_final: 0.6340 (mtt) REVERT: H 222 LEU cc_start: 0.8536 (mt) cc_final: 0.8233 (tt) REVERT: H 449 MET cc_start: 0.8294 (tpt) cc_final: 0.7862 (tpp) REVERT: H 550 MET cc_start: 0.8692 (mtt) cc_final: 0.8475 (mtp) REVERT: I 764 GLN cc_start: 0.8060 (mt0) cc_final: 0.7766 (mp10) REVERT: J 173 TYR cc_start: 0.5154 (p90) cc_final: 0.4828 (p90) REVERT: J 222 LEU cc_start: 0.8660 (mt) cc_final: 0.8414 (tt) REVERT: J 720 MET cc_start: 0.7724 (mmm) cc_final: 0.7455 (ptt) outliers start: 0 outliers final: 0 residues processed: 728 average time/residue: 0.8079 time to fit residues: 933.3205 Evaluate side-chains 415 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 6.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 30.0000 chunk 682 optimal weight: 40.0000 chunk 378 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 460 optimal weight: 30.0000 chunk 364 optimal weight: 0.0070 chunk 705 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 428 optimal weight: 2.9990 chunk 525 optimal weight: 50.0000 chunk 817 optimal weight: 7.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 473 GLN K 538 ASN D 538 ASN E 538 ASN F 538 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN G 760 GLN ** H 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 ASN I 538 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 73176 Z= 0.224 Angle : 0.590 9.331 98964 Z= 0.293 Chirality : 0.044 0.184 11052 Planarity : 0.005 0.051 13068 Dihedral : 8.304 157.230 10272 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.67 % Allowed : 2.58 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.05 (0.08), residues: 9060 helix: -0.34 (0.08), residues: 3840 sheet: -0.17 (0.13), residues: 1344 loop : -1.13 (0.10), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 454 HIS 0.007 0.001 HIS G 735 PHE 0.017 0.002 PHE K 265 TYR 0.023 0.002 TYR J 244 ARG 0.016 0.001 ARG G 711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 427 time to evaluate : 6.531 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: K 46 MET cc_start: 0.6246 (ptm) cc_final: 0.6038 (ptp) REVERT: K 84 MET cc_start: 0.3870 (ptp) cc_final: 0.3599 (ptp) REVERT: K 155 ARG cc_start: 0.6771 (mtt90) cc_final: 0.6298 (ttm110) REVERT: K 183 HIS cc_start: 0.6064 (m170) cc_final: 0.5780 (m170) REVERT: K 420 LEU cc_start: 0.8310 (mt) cc_final: 0.7920 (tt) REVERT: B 173 TYR cc_start: 0.5672 (p90) cc_final: 0.5328 (p90) REVERT: B 199 ASN cc_start: 0.6475 (t0) cc_final: 0.5959 (p0) REVERT: C 46 MET cc_start: 0.5847 (ptm) cc_final: 0.5524 (ptp) REVERT: C 84 MET cc_start: 0.5498 (ptp) cc_final: 0.5168 (ptp) REVERT: C 442 MET cc_start: 0.7396 (mpp) cc_final: 0.6507 (mtt) REVERT: D 46 MET cc_start: 0.6289 (ptm) cc_final: 0.6070 (ptp) REVERT: D 84 MET cc_start: 0.5837 (ptp) cc_final: 0.5618 (ptp) REVERT: D 199 ASN cc_start: 0.6065 (t0) cc_final: 0.5662 (p0) REVERT: D 442 MET cc_start: 0.7272 (mtt) cc_final: 0.6662 (mpp) REVERT: E 46 MET cc_start: 0.5702 (ptp) cc_final: 0.5254 (ptp) REVERT: E 764 GLN cc_start: 0.8098 (mt0) cc_final: 0.7833 (mp10) REVERT: F 199 ASN cc_start: 0.6739 (t0) cc_final: 0.6481 (m-40) REVERT: F 720 MET cc_start: 0.7699 (mmm) cc_final: 0.7323 (pmm) REVERT: A 199 ASN cc_start: 0.6855 (t0) cc_final: 0.6605 (m-40) REVERT: A 720 MET cc_start: 0.7527 (mmm) cc_final: 0.7270 (pmm) REVERT: L 173 TYR cc_start: 0.5882 (p90) cc_final: 0.5619 (p90) REVERT: L 678 MET cc_start: 0.9375 (mmp) cc_final: 0.9169 (mmp) REVERT: G 158 MET cc_start: 0.5427 (ttp) cc_final: 0.4902 (ttp) REVERT: G 314 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: G 398 GLN cc_start: 0.8546 (tt0) cc_final: 0.8035 (pt0) REVERT: G 420 LEU cc_start: 0.7783 (mt) cc_final: 0.7533 (tt) REVERT: G 449 MET cc_start: 0.8296 (tpt) cc_final: 0.7616 (tpt) REVERT: H 46 MET cc_start: 0.6693 (ttp) cc_final: 0.6361 (mtt) REVERT: H 222 LEU cc_start: 0.8696 (mt) cc_final: 0.8460 (tt) REVERT: H 449 MET cc_start: 0.8421 (tpt) cc_final: 0.7733 (tpp) REVERT: H 453 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8200 (ttm110) REVERT: I 84 MET cc_start: 0.6106 (ptp) cc_final: 0.5486 (ppp) REVERT: I 740 MET cc_start: 0.9106 (mmm) cc_final: 0.8814 (mmm) REVERT: I 764 GLN cc_start: 0.7908 (mt0) cc_final: 0.7707 (mp10) REVERT: J 158 MET cc_start: 0.6057 (ttp) cc_final: 0.5441 (ttp) REVERT: J 173 TYR cc_start: 0.5370 (p90) cc_final: 0.4971 (p90) REVERT: J 720 MET cc_start: 0.7672 (mmm) cc_final: 0.7409 (ptt) outliers start: 52 outliers final: 19 residues processed: 463 average time/residue: 0.6980 time to fit residues: 545.2263 Evaluate side-chains 404 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 384 time to evaluate : 6.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 762 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 762 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain J residue 508 MET Chi-restraints excluded: chain J residue 762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 680 optimal weight: 0.4980 chunk 556 optimal weight: 9.9990 chunk 225 optimal weight: 60.0000 chunk 818 optimal weight: 4.9990 chunk 884 optimal weight: 9.9990 chunk 729 optimal weight: 0.0670 chunk 811 optimal weight: 0.0670 chunk 279 optimal weight: 3.9990 chunk 656 optimal weight: 10.0000 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 327 GLN B 327 GLN B 538 ASN C 327 GLN D 327 GLN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN A 183 HIS A 327 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 GLN L 538 ASN G 327 GLN G 538 ASN H 327 GLN ** H 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 GLN J 327 GLN J 538 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 73176 Z= 0.131 Angle : 0.515 10.599 98964 Z= 0.250 Chirality : 0.042 0.154 11052 Planarity : 0.004 0.048 13068 Dihedral : 7.734 160.110 10272 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.67 % Allowed : 3.05 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.28 (0.09), residues: 9060 helix: 0.33 (0.08), residues: 3828 sheet: 0.26 (0.14), residues: 1344 loop : -0.77 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 454 HIS 0.006 0.000 HIS H 183 PHE 0.018 0.001 PHE K 265 TYR 0.020 0.001 TYR H 173 ARG 0.009 0.000 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 399 time to evaluate : 6.473 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: K 46 MET cc_start: 0.6349 (ptm) cc_final: 0.6040 (ptp) REVERT: K 84 MET cc_start: 0.4003 (ptp) cc_final: 0.3746 (ptp) REVERT: K 155 ARG cc_start: 0.6795 (mtt90) cc_final: 0.6309 (ttm110) REVERT: K 183 HIS cc_start: 0.6169 (m170) cc_final: 0.5845 (m170) REVERT: K 420 LEU cc_start: 0.8270 (mt) cc_final: 0.7895 (tt) REVERT: K 442 MET cc_start: 0.7670 (mpp) cc_final: 0.6749 (mtt) REVERT: B 173 TYR cc_start: 0.5595 (p90) cc_final: 0.5216 (p90) REVERT: B 199 ASN cc_start: 0.6485 (t0) cc_final: 0.6179 (p0) REVERT: C 46 MET cc_start: 0.5633 (ptm) cc_final: 0.5312 (ptp) REVERT: C 84 MET cc_start: 0.5514 (ptp) cc_final: 0.5190 (ptp) REVERT: C 561 GLU cc_start: 0.7521 (mp0) cc_final: 0.7320 (mp0) REVERT: D 46 MET cc_start: 0.6161 (ptm) cc_final: 0.5946 (ptp) REVERT: D 199 ASN cc_start: 0.6187 (t0) cc_final: 0.5886 (p0) REVERT: D 449 MET cc_start: 0.8070 (tpp) cc_final: 0.7793 (tpp) REVERT: E 46 MET cc_start: 0.5723 (ptp) cc_final: 0.5238 (ptp) REVERT: E 453 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8113 (ttm110) REVERT: F 720 MET cc_start: 0.7695 (mmm) cc_final: 0.7467 (ptt) REVERT: A 199 ASN cc_start: 0.6893 (t0) cc_final: 0.6627 (m-40) REVERT: A 449 MET cc_start: 0.8483 (tpt) cc_final: 0.8048 (tpp) REVERT: L 46 MET cc_start: 0.5414 (ptp) cc_final: 0.4971 (ptp) REVERT: L 173 TYR cc_start: 0.5954 (p90) cc_final: 0.5242 (p90) REVERT: G 449 MET cc_start: 0.8078 (tpt) cc_final: 0.7653 (tpt) REVERT: H 46 MET cc_start: 0.6698 (ttp) cc_final: 0.6325 (mtt) REVERT: H 222 LEU cc_start: 0.8668 (mt) cc_final: 0.8443 (tt) REVERT: H 449 MET cc_start: 0.8400 (tpt) cc_final: 0.7657 (tpp) REVERT: H 453 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8153 (ttm110) REVERT: J 173 TYR cc_start: 0.5387 (p90) cc_final: 0.4974 (p90) REVERT: J 711 ARG cc_start: 0.8395 (tmm160) cc_final: 0.8170 (ptt90) REVERT: J 720 MET cc_start: 0.7640 (mmm) cc_final: 0.7427 (ptt) outliers start: 52 outliers final: 19 residues processed: 437 average time/residue: 0.7064 time to fit residues: 522.0168 Evaluate side-chains 394 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 375 time to evaluate : 6.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 275 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 720 MET Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain L residue 762 LEU Chi-restraints excluded: chain G residue 316 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 555 SER Chi-restraints excluded: chain J residue 555 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 3.9990 chunk 615 optimal weight: 4.9990 chunk 424 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 390 optimal weight: 9.9990 chunk 549 optimal weight: 8.9990 chunk 821 optimal weight: 6.9990 chunk 869 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 778 optimal weight: 6.9990 chunk 234 optimal weight: 30.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 750 ASN C 750 ASN E 750 ASN A 750 ASN ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 73176 Z= 0.237 Angle : 0.553 8.889 98964 Z= 0.271 Chirality : 0.044 0.175 11052 Planarity : 0.004 0.050 13068 Dihedral : 7.481 158.734 10272 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.59 % Allowed : 3.62 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.19 (0.09), residues: 9060 helix: 0.75 (0.08), residues: 3852 sheet: 0.44 (0.14), residues: 1344 loop : -0.52 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 551 HIS 0.009 0.001 HIS F 183 PHE 0.018 0.002 PHE C 516 TYR 0.027 0.002 TYR F 244 ARG 0.014 0.001 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 380 time to evaluate : 6.522 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: K 183 HIS cc_start: 0.6109 (m170) cc_final: 0.5800 (m170) REVERT: K 420 LEU cc_start: 0.8399 (mt) cc_final: 0.8006 (tt) REVERT: B 173 TYR cc_start: 0.5616 (p90) cc_final: 0.5203 (p90) REVERT: B 199 ASN cc_start: 0.6534 (t0) cc_final: 0.6211 (p0) REVERT: C 84 MET cc_start: 0.5563 (ptp) cc_final: 0.5270 (ptp) REVERT: C 183 HIS cc_start: 0.5679 (m-70) cc_final: 0.5294 (m170) REVERT: C 442 MET cc_start: 0.7471 (mpp) cc_final: 0.6507 (mtt) REVERT: D 199 ASN cc_start: 0.6294 (t0) cc_final: 0.6038 (p0) REVERT: D 442 MET cc_start: 0.7205 (mtt) cc_final: 0.6714 (mpp) REVERT: E 46 MET cc_start: 0.5749 (ptp) cc_final: 0.5189 (ptp) REVERT: E 453 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8166 (ttm110) REVERT: F 84 MET cc_start: 0.6164 (ptp) cc_final: 0.5829 (ttp) REVERT: F 244 TYR cc_start: 0.8700 (p90) cc_final: 0.8422 (p90) REVERT: F 338 ARG cc_start: 0.6419 (ttt90) cc_final: 0.6133 (ttt90) REVERT: F 720 MET cc_start: 0.7691 (mmm) cc_final: 0.7438 (ptt) REVERT: A 158 MET cc_start: 0.4988 (ttp) cc_final: 0.4613 (ttp) REVERT: A 199 ASN cc_start: 0.6942 (t0) cc_final: 0.6680 (m-40) REVERT: L 442 MET cc_start: 0.7265 (mtt) cc_final: 0.6507 (mpp) REVERT: L 450 ASP cc_start: 0.8882 (m-30) cc_final: 0.8474 (p0) REVERT: G 46 MET cc_start: 0.6490 (ptm) cc_final: 0.6252 (ptp) REVERT: G 449 MET cc_start: 0.8202 (tpt) cc_final: 0.7900 (tpt) REVERT: H 449 MET cc_start: 0.8536 (tpt) cc_final: 0.8093 (tpp) REVERT: H 453 ARG cc_start: 0.8529 (ttm110) cc_final: 0.8313 (ttm110) REVERT: I 84 MET cc_start: 0.6485 (ptp) cc_final: 0.5950 (ppp) REVERT: I 560 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7870 (ttm170) REVERT: J 173 TYR cc_start: 0.5497 (p90) cc_final: 0.5055 (p90) outliers start: 46 outliers final: 21 residues processed: 413 average time/residue: 0.7163 time to fit residues: 502.0929 Evaluate side-chains 386 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 364 time to evaluate : 6.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 316 THR Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain I residue 468 VAL Chi-restraints excluded: chain I residue 560 ARG Chi-restraints excluded: chain J residue 592 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 5.9990 chunk 493 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 647 optimal weight: 0.8980 chunk 358 optimal weight: 0.9980 chunk 742 optimal weight: 1.9990 chunk 601 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 444 optimal weight: 4.9990 chunk 780 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 GLN I 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 73176 Z= 0.123 Angle : 0.494 9.527 98964 Z= 0.237 Chirality : 0.042 0.193 11052 Planarity : 0.003 0.047 13068 Dihedral : 7.180 150.698 10272 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.35 % Allowed : 4.26 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.56 (0.09), residues: 9060 helix: 1.07 (0.09), residues: 3840 sheet: 0.66 (0.14), residues: 1344 loop : -0.36 (0.10), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 454 HIS 0.006 0.000 HIS J 183 PHE 0.022 0.001 PHE C 265 TYR 0.021 0.001 TYR A 244 ARG 0.009 0.000 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 377 time to evaluate : 6.601 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: K 84 MET cc_start: 0.4254 (ptp) cc_final: 0.4034 (ptp) REVERT: K 183 HIS cc_start: 0.6083 (m170) cc_final: 0.5763 (m170) REVERT: K 420 LEU cc_start: 0.8330 (mt) cc_final: 0.7964 (tt) REVERT: K 442 MET cc_start: 0.7461 (mpp) cc_final: 0.6494 (mtt) REVERT: B 173 TYR cc_start: 0.5649 (p90) cc_final: 0.5201 (p90) REVERT: B 199 ASN cc_start: 0.6558 (t0) cc_final: 0.6237 (p0) REVERT: C 84 MET cc_start: 0.5556 (ptp) cc_final: 0.5235 (ptp) REVERT: C 183 HIS cc_start: 0.5456 (m-70) cc_final: 0.5130 (m170) REVERT: C 244 TYR cc_start: 0.8833 (p90) cc_final: 0.8461 (p90) REVERT: C 442 MET cc_start: 0.7534 (mpp) cc_final: 0.6596 (mtt) REVERT: D 199 ASN cc_start: 0.6219 (t0) cc_final: 0.5996 (p0) REVERT: D 442 MET cc_start: 0.7225 (mtt) cc_final: 0.6812 (mpp) REVERT: E 46 MET cc_start: 0.5755 (ptp) cc_final: 0.5189 (ptp) REVERT: E 453 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8143 (ttm110) REVERT: F 84 MET cc_start: 0.6259 (ptp) cc_final: 0.5921 (ttp) REVERT: F 244 TYR cc_start: 0.8635 (p90) cc_final: 0.8430 (p90) REVERT: F 720 MET cc_start: 0.7665 (mmm) cc_final: 0.7460 (ptt) REVERT: A 158 MET cc_start: 0.4692 (ttp) cc_final: 0.4384 (ttp) REVERT: A 199 ASN cc_start: 0.6909 (t0) cc_final: 0.6663 (m-40) REVERT: A 449 MET cc_start: 0.8573 (tpt) cc_final: 0.8187 (tpp) REVERT: L 442 MET cc_start: 0.7147 (mtt) cc_final: 0.6391 (mpp) REVERT: L 450 ASP cc_start: 0.8851 (m-30) cc_final: 0.8452 (p0) REVERT: L 678 MET cc_start: 0.9367 (mmp) cc_final: 0.9021 (mmp) REVERT: G 46 MET cc_start: 0.6434 (ptm) cc_final: 0.6184 (ptp) REVERT: G 183 HIS cc_start: 0.5295 (m-70) cc_final: 0.4458 (m170) REVERT: G 449 MET cc_start: 0.8085 (tpt) cc_final: 0.7728 (tpt) REVERT: H 84 MET cc_start: 0.6065 (ptp) cc_final: 0.5847 (ttp) REVERT: H 449 MET cc_start: 0.8549 (tpt) cc_final: 0.8147 (tpp) REVERT: H 453 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8286 (ttm110) REVERT: I 84 MET cc_start: 0.6485 (ptp) cc_final: 0.6002 (ppp) REVERT: J 173 TYR cc_start: 0.5668 (p90) cc_final: 0.5228 (p90) REVERT: J 442 MET cc_start: 0.7591 (mpp) cc_final: 0.6660 (mtt) outliers start: 27 outliers final: 19 residues processed: 395 average time/residue: 0.7019 time to fit residues: 468.0289 Evaluate side-chains 377 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain L residue 720 MET Chi-restraints excluded: chain L residue 762 LEU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain I residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 3.9990 chunk 783 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 510 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 870 optimal weight: 10.0000 chunk 722 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 457 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 73176 Z= 0.285 Angle : 0.566 9.554 98964 Z= 0.279 Chirality : 0.044 0.169 11052 Planarity : 0.004 0.049 13068 Dihedral : 7.238 147.876 10272 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.49 % Allowed : 4.65 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.62 (0.09), residues: 9060 helix: 1.06 (0.08), residues: 3852 sheet: 0.62 (0.14), residues: 1368 loop : -0.24 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 551 HIS 0.007 0.001 HIS K 340 PHE 0.022 0.002 PHE K 265 TYR 0.024 0.002 TYR A 244 ARG 0.010 0.001 ARG K 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 368 time to evaluate : 6.511 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: K 84 MET cc_start: 0.4569 (ptp) cc_final: 0.4328 (ptp) REVERT: K 183 HIS cc_start: 0.6168 (m170) cc_final: 0.5922 (m170) REVERT: K 420 LEU cc_start: 0.8462 (mt) cc_final: 0.8056 (tt) REVERT: K 442 MET cc_start: 0.7437 (mpp) cc_final: 0.6475 (mtt) REVERT: B 158 MET cc_start: 0.4864 (ttp) cc_final: 0.4403 (ttp) REVERT: B 173 TYR cc_start: 0.5690 (p90) cc_final: 0.5248 (p90) REVERT: B 199 ASN cc_start: 0.6538 (t0) cc_final: 0.6043 (p0) REVERT: B 338 ARG cc_start: 0.6328 (ttt180) cc_final: 0.6018 (ttt90) REVERT: C 84 MET cc_start: 0.5628 (ptp) cc_final: 0.5307 (ptp) REVERT: C 183 HIS cc_start: 0.5630 (m-70) cc_final: 0.5225 (m170) REVERT: C 442 MET cc_start: 0.7453 (mpp) cc_final: 0.6407 (mtt) REVERT: D 199 ASN cc_start: 0.6317 (t0) cc_final: 0.6043 (p0) REVERT: D 442 MET cc_start: 0.7251 (mtt) cc_final: 0.6750 (mpp) REVERT: E 46 MET cc_start: 0.5721 (ptp) cc_final: 0.5154 (ptp) REVERT: E 224 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8388 (mt) REVERT: F 84 MET cc_start: 0.6338 (ptp) cc_final: 0.5970 (ttp) REVERT: F 244 TYR cc_start: 0.8732 (p90) cc_final: 0.8471 (p90) REVERT: F 720 MET cc_start: 0.7510 (mmm) cc_final: 0.7310 (ptt) REVERT: A 158 MET cc_start: 0.4826 (ttp) cc_final: 0.4523 (ttp) REVERT: A 199 ASN cc_start: 0.6877 (t0) cc_final: 0.6615 (m-40) REVERT: L 442 MET cc_start: 0.7329 (mtt) cc_final: 0.6577 (mpp) REVERT: L 450 ASP cc_start: 0.8862 (m-30) cc_final: 0.8490 (p0) REVERT: L 678 MET cc_start: 0.9372 (mmp) cc_final: 0.9070 (mmp) REVERT: G 46 MET cc_start: 0.6448 (ptm) cc_final: 0.6213 (ptp) REVERT: G 449 MET cc_start: 0.8281 (tpt) cc_final: 0.7797 (tpp) REVERT: H 449 MET cc_start: 0.8563 (tpt) cc_final: 0.8087 (tpp) REVERT: H 453 ARG cc_start: 0.8534 (ttm110) cc_final: 0.8297 (ttm110) REVERT: I 84 MET cc_start: 0.6447 (ptp) cc_final: 0.6164 (ttp) REVERT: I 560 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (ttm170) REVERT: J 158 MET cc_start: 0.6001 (ttm) cc_final: 0.5638 (ttp) REVERT: J 173 TYR cc_start: 0.5618 (p90) cc_final: 0.5156 (p90) outliers start: 38 outliers final: 20 residues processed: 395 average time/residue: 0.7121 time to fit residues: 475.7149 Evaluate side-chains 381 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 359 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain I residue 560 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 496 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 492 optimal weight: 30.0000 chunk 733 optimal weight: 0.8980 chunk 486 optimal weight: 6.9990 chunk 867 optimal weight: 8.9990 chunk 542 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 340 HIS C 340 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 73176 Z= 0.379 Angle : 0.593 10.186 98964 Z= 0.294 Chirality : 0.045 0.153 11052 Planarity : 0.004 0.051 13068 Dihedral : 7.333 150.398 10272 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.50 % Allowed : 4.83 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.49 (0.09), residues: 9060 helix: 0.89 (0.08), residues: 3852 sheet: 0.59 (0.14), residues: 1368 loop : -0.22 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 551 HIS 0.008 0.001 HIS K 340 PHE 0.024 0.002 PHE A 516 TYR 0.023 0.002 TYR G 244 ARG 0.010 0.001 ARG E 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 360 time to evaluate : 6.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 MET cc_start: 0.4950 (ptp) cc_final: 0.4721 (ptp) REVERT: K 244 TYR cc_start: 0.8692 (p90) cc_final: 0.8484 (p90) REVERT: B 173 TYR cc_start: 0.5693 (p90) cc_final: 0.5227 (p90) REVERT: B 199 ASN cc_start: 0.6588 (t0) cc_final: 0.6237 (p0) REVERT: B 678 MET cc_start: 0.9307 (mmp) cc_final: 0.8999 (mmp) REVERT: C 84 MET cc_start: 0.5569 (ptp) cc_final: 0.5232 (ptp) REVERT: C 183 HIS cc_start: 0.5620 (m-70) cc_final: 0.5232 (m170) REVERT: C 442 MET cc_start: 0.7528 (mpp) cc_final: 0.6415 (mtt) REVERT: D 199 ASN cc_start: 0.6394 (t0) cc_final: 0.6093 (p0) REVERT: D 442 MET cc_start: 0.7236 (mtt) cc_final: 0.6699 (mpp) REVERT: E 46 MET cc_start: 0.5765 (ptp) cc_final: 0.5323 (ptp) REVERT: F 84 MET cc_start: 0.6334 (ptp) cc_final: 0.6001 (ttp) REVERT: F 244 TYR cc_start: 0.8792 (p90) cc_final: 0.8473 (p90) REVERT: A 158 MET cc_start: 0.4806 (ttp) cc_final: 0.4408 (ttp) REVERT: A 199 ASN cc_start: 0.6886 (t0) cc_final: 0.6620 (m-40) REVERT: L 442 MET cc_start: 0.7416 (mtt) cc_final: 0.6654 (mpp) REVERT: L 450 ASP cc_start: 0.8873 (m-30) cc_final: 0.8485 (p0) REVERT: G 46 MET cc_start: 0.6593 (ptm) cc_final: 0.6359 (ptp) REVERT: G 244 TYR cc_start: 0.8831 (p90) cc_final: 0.8585 (p90) REVERT: G 449 MET cc_start: 0.8308 (tpt) cc_final: 0.7813 (tpp) REVERT: H 199 ASN cc_start: 0.6471 (t0) cc_final: 0.5890 (m-40) REVERT: H 449 MET cc_start: 0.8617 (tpt) cc_final: 0.8147 (tpp) REVERT: H 453 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8284 (ttm110) REVERT: I 84 MET cc_start: 0.6442 (ptp) cc_final: 0.6181 (ttp) REVERT: J 173 TYR cc_start: 0.5626 (p90) cc_final: 0.5117 (p90) REVERT: J 442 MET cc_start: 0.7315 (mpp) cc_final: 0.6399 (mtt) outliers start: 39 outliers final: 25 residues processed: 385 average time/residue: 0.7079 time to fit residues: 461.9791 Evaluate side-chains 380 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 355 time to evaluate : 6.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain I residue 450 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 518 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 551 optimal weight: 7.9990 chunk 590 optimal weight: 5.9990 chunk 428 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 681 optimal weight: 20.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 558 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 73176 Z= 0.376 Angle : 0.601 10.786 98964 Z= 0.298 Chirality : 0.046 0.193 11052 Planarity : 0.004 0.091 13068 Dihedral : 7.384 154.012 10272 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.48 % Allowed : 5.10 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.50 (0.09), residues: 9060 helix: 0.97 (0.08), residues: 3708 sheet: 0.42 (0.14), residues: 1392 loop : -0.20 (0.10), residues: 3960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 551 HIS 0.009 0.001 HIS C 340 PHE 0.024 0.002 PHE K 265 TYR 0.020 0.002 TYR L 244 ARG 0.027 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 359 time to evaluate : 6.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 MET cc_start: 0.5001 (ptp) cc_final: 0.4756 (ptp) REVERT: K 158 MET cc_start: 0.5592 (mtm) cc_final: 0.4805 (ttp) REVERT: K 244 TYR cc_start: 0.8712 (p90) cc_final: 0.8497 (p90) REVERT: B 84 MET cc_start: 0.6154 (ptp) cc_final: 0.5370 (ppp) REVERT: B 173 TYR cc_start: 0.5594 (p90) cc_final: 0.5056 (p90) REVERT: B 199 ASN cc_start: 0.6597 (t0) cc_final: 0.6231 (p0) REVERT: C 183 HIS cc_start: 0.5453 (m-70) cc_final: 0.5100 (m170) REVERT: C 442 MET cc_start: 0.7516 (mpp) cc_final: 0.6409 (mtt) REVERT: D 199 ASN cc_start: 0.6510 (t0) cc_final: 0.6191 (p0) REVERT: D 442 MET cc_start: 0.7292 (mtt) cc_final: 0.6732 (mpp) REVERT: E 46 MET cc_start: 0.5821 (ptp) cc_final: 0.5427 (ptp) REVERT: E 442 MET cc_start: 0.7345 (mtt) cc_final: 0.6669 (mpp) REVERT: F 84 MET cc_start: 0.6216 (ptp) cc_final: 0.6005 (ttp) REVERT: F 244 TYR cc_start: 0.8796 (p90) cc_final: 0.8433 (p90) REVERT: A 158 MET cc_start: 0.4871 (ttp) cc_final: 0.4433 (ttp) REVERT: A 199 ASN cc_start: 0.6874 (t0) cc_final: 0.6616 (m-40) REVERT: L 46 MET cc_start: 0.5326 (ptp) cc_final: 0.5008 (ptp) REVERT: L 442 MET cc_start: 0.7495 (mtt) cc_final: 0.6877 (mpp) REVERT: L 450 ASP cc_start: 0.8851 (m-30) cc_final: 0.8480 (p0) REVERT: G 46 MET cc_start: 0.6548 (ptm) cc_final: 0.6296 (ptp) REVERT: G 449 MET cc_start: 0.8354 (tpt) cc_final: 0.7874 (tpp) REVERT: H 199 ASN cc_start: 0.6526 (t0) cc_final: 0.5918 (m-40) REVERT: H 449 MET cc_start: 0.8617 (tpt) cc_final: 0.8165 (tpp) REVERT: H 453 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8295 (ttm110) REVERT: I 84 MET cc_start: 0.6436 (ptp) cc_final: 0.6184 (ttp) REVERT: I 560 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: J 173 TYR cc_start: 0.5696 (p90) cc_final: 0.5155 (p90) REVERT: J 442 MET cc_start: 0.7402 (mpp) cc_final: 0.6410 (mtt) outliers start: 37 outliers final: 26 residues processed: 382 average time/residue: 0.6970 time to fit residues: 451.8694 Evaluate side-chains 383 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 356 time to evaluate : 6.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 592 ASP Chi-restraints excluded: chain G residue 761 THR Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 560 ARG Chi-restraints excluded: chain I residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 10.0000 chunk 831 optimal weight: 30.0000 chunk 758 optimal weight: 5.9990 chunk 808 optimal weight: 0.9980 chunk 830 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 352 optimal weight: 0.7980 chunk 634 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 730 optimal weight: 0.6980 chunk 764 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 73176 Z= 0.171 Angle : 0.527 12.102 98964 Z= 0.256 Chirality : 0.043 0.144 11052 Planarity : 0.003 0.050 13068 Dihedral : 7.131 152.699 10272 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.74 (0.09), residues: 9060 helix: 1.14 (0.09), residues: 3780 sheet: 0.57 (0.14), residues: 1380 loop : -0.07 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.003 0.001 HIS L 735 PHE 0.019 0.001 PHE K 265 TYR 0.021 0.001 TYR A 244 ARG 0.007 0.000 ARG K 711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 359 time to evaluate : 6.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 MET cc_start: 0.5060 (ptp) cc_final: 0.4809 (ptp) REVERT: K 158 MET cc_start: 0.5597 (mtm) cc_final: 0.4799 (ttp) REVERT: B 173 TYR cc_start: 0.5565 (p90) cc_final: 0.5001 (p90) REVERT: B 199 ASN cc_start: 0.6611 (t0) cc_final: 0.6256 (p0) REVERT: C 183 HIS cc_start: 0.5420 (m-70) cc_final: 0.5068 (m170) REVERT: C 442 MET cc_start: 0.7496 (mpp) cc_final: 0.6404 (mtt) REVERT: D 199 ASN cc_start: 0.6564 (t0) cc_final: 0.6142 (p0) REVERT: D 244 TYR cc_start: 0.8710 (p90) cc_final: 0.8487 (p90) REVERT: D 442 MET cc_start: 0.7298 (mtt) cc_final: 0.6825 (mpp) REVERT: E 46 MET cc_start: 0.6008 (ptp) cc_final: 0.5611 (ptp) REVERT: E 442 MET cc_start: 0.7436 (mtt) cc_final: 0.6774 (mpp) REVERT: F 84 MET cc_start: 0.6275 (ptp) cc_final: 0.6011 (ttp) REVERT: F 244 TYR cc_start: 0.8745 (p90) cc_final: 0.8519 (p90) REVERT: A 84 MET cc_start: 0.5756 (ptp) cc_final: 0.5344 (ppp) REVERT: A 158 MET cc_start: 0.4824 (ttp) cc_final: 0.4359 (ttp) REVERT: A 199 ASN cc_start: 0.6892 (t0) cc_final: 0.6624 (m-40) REVERT: A 711 ARG cc_start: 0.8497 (tmm160) cc_final: 0.8230 (ttp80) REVERT: L 46 MET cc_start: 0.5413 (ptp) cc_final: 0.5212 (ptp) REVERT: L 442 MET cc_start: 0.7433 (mtt) cc_final: 0.7061 (mpp) REVERT: L 450 ASP cc_start: 0.8855 (m-30) cc_final: 0.8643 (p0) REVERT: L 678 MET cc_start: 0.9306 (mmp) cc_final: 0.8958 (mmp) REVERT: G 46 MET cc_start: 0.6473 (ptm) cc_final: 0.6212 (ptp) REVERT: G 449 MET cc_start: 0.8292 (tpt) cc_final: 0.7842 (tpp) REVERT: H 199 ASN cc_start: 0.6593 (t0) cc_final: 0.5984 (m-40) REVERT: H 449 MET cc_start: 0.8580 (tpt) cc_final: 0.8182 (tpp) REVERT: H 453 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8274 (ttm110) REVERT: I 84 MET cc_start: 0.6458 (ptp) cc_final: 0.6189 (ttp) REVERT: J 173 TYR cc_start: 0.5706 (p90) cc_final: 0.5154 (p90) REVERT: J 442 MET cc_start: 0.7390 (mpp) cc_final: 0.6519 (mtt) outliers start: 26 outliers final: 23 residues processed: 374 average time/residue: 0.7293 time to fit residues: 462.6194 Evaluate side-chains 368 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 345 time to evaluate : 7.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 761 THR Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 678 MET Chi-restraints excluded: chain J residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 0.6980 chunk 530 optimal weight: 0.9990 chunk 854 optimal weight: 8.9990 chunk 521 optimal weight: 5.9990 chunk 405 optimal weight: 0.9980 chunk 594 optimal weight: 5.9990 chunk 896 optimal weight: 8.9990 chunk 825 optimal weight: 40.0000 chunk 713 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 551 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 73176 Z= 0.164 Angle : 0.523 12.847 98964 Z= 0.252 Chirality : 0.043 0.299 11052 Planarity : 0.003 0.050 13068 Dihedral : 6.982 150.236 10272 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.34 % Allowed : 5.28 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.84 (0.09), residues: 9060 helix: 1.17 (0.09), residues: 3852 sheet: 0.85 (0.14), residues: 1344 loop : -0.06 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.004 0.001 HIS E 340 PHE 0.021 0.001 PHE B 363 TYR 0.021 0.001 TYR A 244 ARG 0.019 0.000 ARG L 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18120 Ramachandran restraints generated. 9060 Oldfield, 0 Emsley, 9060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 355 time to evaluate : 6.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 158 MET cc_start: 0.5608 (mtm) cc_final: 0.4831 (ttp) REVERT: B 84 MET cc_start: 0.5967 (ptp) cc_final: 0.5146 (ppp) REVERT: B 173 TYR cc_start: 0.5686 (p90) cc_final: 0.5162 (p90) REVERT: C 183 HIS cc_start: 0.5413 (m-70) cc_final: 0.5059 (m170) REVERT: C 199 ASN cc_start: 0.6803 (t0) cc_final: 0.6464 (p0) REVERT: C 442 MET cc_start: 0.7565 (mpp) cc_final: 0.6576 (mtt) REVERT: D 46 MET cc_start: 0.6320 (ptm) cc_final: 0.6027 (ptp) REVERT: D 199 ASN cc_start: 0.6534 (t0) cc_final: 0.6203 (p0) REVERT: D 244 TYR cc_start: 0.8671 (p90) cc_final: 0.8441 (p90) REVERT: D 442 MET cc_start: 0.7322 (mtt) cc_final: 0.6929 (mpp) REVERT: E 46 MET cc_start: 0.6020 (ptp) cc_final: 0.5629 (ptp) REVERT: E 442 MET cc_start: 0.7363 (mtt) cc_final: 0.6693 (mpp) REVERT: F 84 MET cc_start: 0.6275 (ptp) cc_final: 0.6013 (ttp) REVERT: A 84 MET cc_start: 0.5748 (ptp) cc_final: 0.5342 (ppp) REVERT: A 158 MET cc_start: 0.4788 (ttp) cc_final: 0.4344 (ttp) REVERT: A 199 ASN cc_start: 0.6897 (t0) cc_final: 0.6634 (m-40) REVERT: A 711 ARG cc_start: 0.8491 (tmm160) cc_final: 0.8266 (ttp80) REVERT: L 199 ASN cc_start: 0.6809 (t0) cc_final: 0.6455 (p0) REVERT: L 442 MET cc_start: 0.7468 (mtt) cc_final: 0.7145 (mpp) REVERT: L 450 ASP cc_start: 0.8801 (m-30) cc_final: 0.8518 (p0) REVERT: L 678 MET cc_start: 0.9319 (mmp) cc_final: 0.9031 (mmp) REVERT: G 46 MET cc_start: 0.6466 (ptm) cc_final: 0.6200 (ptp) REVERT: G 183 HIS cc_start: 0.5669 (m-70) cc_final: 0.4879 (m170) REVERT: G 449 MET cc_start: 0.8319 (tpt) cc_final: 0.7833 (tpp) REVERT: H 449 MET cc_start: 0.8596 (tpt) cc_final: 0.8074 (tpp) REVERT: H 453 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8310 (ttm110) REVERT: I 84 MET cc_start: 0.6427 (ptp) cc_final: 0.6171 (ttp) REVERT: J 173 TYR cc_start: 0.5701 (p90) cc_final: 0.5151 (p90) REVERT: J 442 MET cc_start: 0.7386 (mpp) cc_final: 0.6507 (mtt) outliers start: 26 outliers final: 22 residues processed: 371 average time/residue: 0.7157 time to fit residues: 449.0556 Evaluate side-chains 365 residues out of total 7740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 343 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 173 TYR Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 762 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 478 ASP Chi-restraints excluded: chain G residue 761 THR Chi-restraints excluded: chain H residue 508 MET Chi-restraints excluded: chain H residue 614 LYS Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain I residue 678 MET Chi-restraints excluded: chain J residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.0980 chunk 567 optimal weight: 40.0000 chunk 760 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 658 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 715 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 734 optimal weight: 7.9990 chunk 90 optimal weight: 50.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.145089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101527 restraints weight = 159981.624| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.15 r_work: 0.2994 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 73176 Z= 0.241 Angle : 0.545 11.911 98964 Z= 0.264 Chirality : 0.044 0.309 11052 Planarity : 0.004 0.050 13068 Dihedral : 7.003 149.654 10272 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.39 % Allowed : 5.34 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.86 (0.09), residues: 9060 helix: 1.16 (0.09), residues: 3876 sheet: 0.84 (0.14), residues: 1344 loop : -0.01 (0.10), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.004 0.001 HIS A 735 PHE 0.021 0.001 PHE K 265 TYR 0.019 0.001 TYR L 244 ARG 0.007 0.000 ARG K 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12385.23 seconds wall clock time: 220 minutes 24.82 seconds (13224.82 seconds total)