Starting phenix.real_space_refine on Sun Feb 18 22:10:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/02_2024/8ioe_35617_updated.pdb" } resolution = 2.86 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= 0.004 sd= 0.053 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 24 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 47820 2.51 5 N 13510 2.21 5 O 13846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 75404 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 787, 6232 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 49, 'TRANS': 737} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 787, 6232 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 49, 'TRANS': 737} Chain breaks: 1 bond proxies already assigned to first conformer: 6384 Chain: "B" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "C" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "D" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "E" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "F" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "G" Number of atoms: 6250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 787, 6232 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 49, 'TRANS': 737} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 787, 6232 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 49, 'TRANS': 737} Chain breaks: 1 bond proxies already assigned to first conformer: 6384 Chain: "H" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "I" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "J" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "K" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "L" Number of atoms: 6258 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6393 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 54.30, per 1000 atoms: 0.72 Number of scatterers: 75404 At special positions: 0 Unit cell: (214.02, 218.94, 99.22, 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 192 16.00 P 24 15.00 Mg 12 11.99 O 13846 8.00 N 13510 7.00 C 47820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.39 Conformation dependent library (CDL) restraints added in 20.8 seconds 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 445 helices and 41 sheets defined 43.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.29 Creating SS restraints... Processing helix chain 'A' and resid 15 through 37 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.604A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.689A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.824A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N HIS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 248 through 275 removed outlier: 3.874A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 324 through 337 removed outlier: 4.115A pdb=" N TYR A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.645A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 402 through 415 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 471 through 482 removed outlier: 3.607A pdb=" N GLU A 478 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 515 removed outlier: 3.515A pdb=" N ASN A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.572A pdb=" N LEU A 552 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.513A pdb=" N ALA A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 652 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.658A pdb=" N ILE A 705 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 782 removed outlier: 4.346A pdb=" N HIS A 763 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 782 " --> pdb=" O ALA A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 790 No H-bonds generated for 'chain 'A' and resid 787 through 790' Processing helix chain 'B' and resid 15 through 37 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.618A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.707A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.669A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 248 through 275 removed outlier: 3.855A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 324 through 337 removed outlier: 4.079A pdb=" N TYR B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.647A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 372 through 375 No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 402 through 415 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.615A pdb=" N LEU B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 515 removed outlier: 3.555A pdb=" N ASN B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.535A pdb=" N LEU B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 553 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.534A pdb=" N ALA B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 652 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.621A pdb=" N ILE B 705 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 4.579A pdb=" N ASN B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 738 removed outlier: 3.543A pdb=" N ALA B 736 " --> pdb=" O PRO B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 782 removed outlier: 4.327A pdb=" N HIS B 763 " --> pdb=" O ARG B 760 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 782 " --> pdb=" O ALA B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 790 No H-bonds generated for 'chain 'B' and resid 787 through 790' Processing helix chain 'C' and resid 15 through 37 removed outlier: 3.553A pdb=" N ALA C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.649A pdb=" N HIS C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.663A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.757A pdb=" N TRP C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASN C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 248 through 275 removed outlier: 3.835A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 324 through 337 removed outlier: 4.078A pdb=" N TYR C 337 " --> pdb=" O TRP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.624A pdb=" N ILE C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 372 through 375 No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 402 through 415 Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.528A pdb=" N ASP C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.660A pdb=" N LEU C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 515 removed outlier: 3.597A pdb=" N ASN C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.537A pdb=" N LEU C 552 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 553 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 579 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.511A pdb=" N ALA C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 652 Processing helix chain 'C' and resid 666 through 669 Processing helix chain 'C' and resid 681 through 687 Processing helix chain 'C' and resid 702 through 708 removed outlier: 3.682A pdb=" N ILE C 705 " --> pdb=" O PRO C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.550A pdb=" N ALA C 736 " --> pdb=" O PRO C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 753 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 782 removed outlier: 4.315A pdb=" N HIS C 763 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 782 " --> pdb=" O ALA C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 790 No H-bonds generated for 'chain 'C' and resid 787 through 790' Processing helix chain 'D' and resid 15 through 37 removed outlier: 3.537A pdb=" N ALA D 19 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.621A pdb=" N HIS D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.690A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.579A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 182' Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.733A pdb=" N TRP D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N HIS D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS D 194 " --> pdb=" O TRP D 190 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE D 195 " --> pdb=" O HIS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 248 through 275 removed outlier: 3.854A pdb=" N GLY D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'D' and resid 324 through 337 removed outlier: 4.068A pdb=" N TYR D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 342 No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.648A pdb=" N ILE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 372 through 375 No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 402 through 415 Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 470 through 482 removed outlier: 3.638A pdb=" N LEU D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 515 removed outlier: 3.554A pdb=" N ASN D 504 " --> pdb=" O ASP D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 555 Processing helix chain 'D' and resid 569 through 579 Processing helix chain 'D' and resid 602 through 611 removed outlier: 3.515A pdb=" N ALA D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 652 Processing helix chain 'D' and resid 666 through 669 Processing helix chain 'D' and resid 681 through 687 Processing helix chain 'D' and resid 703 through 708 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 732 through 738 removed outlier: 3.539A pdb=" N ALA D 736 " --> pdb=" O PRO D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 782 removed outlier: 4.316A pdb=" N HIS D 763 " --> pdb=" O ARG D 760 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 775 " --> pdb=" O ILE D 772 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 782 " --> pdb=" O ALA D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 790 No H-bonds generated for 'chain 'D' and resid 787 through 790' Processing helix chain 'E' and resid 15 through 37 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 64 through 81 removed outlier: 3.619A pdb=" N HIS E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 119 through 128 Processing helix chain 'E' and resid 156 through 164 removed outlier: 3.703A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.765A pdb=" N TRP E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N HIS E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS E 194 " --> pdb=" O TRP E 190 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 195 " --> pdb=" O HIS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 248 through 275 removed outlier: 3.832A pdb=" N GLY E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'E' and resid 324 through 337 removed outlier: 4.141A pdb=" N TYR E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 342 No H-bonds generated for 'chain 'E' and resid 339 through 342' Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.661A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 364 through 366 No H-bonds generated for 'chain 'E' and resid 364 through 366' Processing helix chain 'E' and resid 372 through 375 No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 402 through 415 Processing helix chain 'E' and resid 434 through 438 Processing helix chain 'E' and resid 450 through 455 Processing helix chain 'E' and resid 470 through 482 removed outlier: 3.649A pdb=" N LEU E 477 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 479 " --> pdb=" O GLY E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 497 removed outlier: 4.433A pdb=" N HIS E 497 " --> pdb=" O ALA E 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 494 through 497' Processing helix chain 'E' and resid 500 through 515 removed outlier: 3.504A pdb=" N ASN E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 555 removed outlier: 3.540A pdb=" N LEU E 552 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 579 Processing helix chain 'E' and resid 602 through 611 removed outlier: 3.531A pdb=" N ALA E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 652 Processing helix chain 'E' and resid 666 through 669 Processing helix chain 'E' and resid 681 through 687 Processing helix chain 'E' and resid 702 through 708 removed outlier: 3.596A pdb=" N ILE E 705 " --> pdb=" O PRO E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 717 removed outlier: 4.558A pdb=" N ASN E 716 " --> pdb=" O HIS E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 738 removed outlier: 3.570A pdb=" N ALA E 736 " --> pdb=" O PRO E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 753 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 760 through 782 removed outlier: 4.327A pdb=" N HIS E 763 " --> pdb=" O ARG E 760 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 782 " --> pdb=" O ALA E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 790 No H-bonds generated for 'chain 'E' and resid 787 through 790' Processing helix chain 'F' and resid 15 through 37 removed outlier: 3.544A pdb=" N ALA F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 64 through 81 removed outlier: 3.623A pdb=" N HIS F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 156 through 164 removed outlier: 3.704A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 181 No H-bonds generated for 'chain 'F' and resid 178 through 181' Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.711A pdb=" N TRP F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N HIS F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS F 194 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE F 195 " --> pdb=" O HIS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 235 Processing helix chain 'F' and resid 248 through 275 removed outlier: 3.841A pdb=" N GLY F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 324 through 337 removed outlier: 4.061A pdb=" N TYR F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 342 No H-bonds generated for 'chain 'F' and resid 339 through 342' Processing helix chain 'F' and resid 351 through 356 removed outlier: 3.650A pdb=" N ILE F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 364 through 366 No H-bonds generated for 'chain 'F' and resid 364 through 366' Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 402 through 415 Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 470 through 482 removed outlier: 3.644A pdb=" N LEU F 477 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 479 " --> pdb=" O GLY F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 515 removed outlier: 3.549A pdb=" N ASN F 504 " --> pdb=" O ASP F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 555 removed outlier: 3.572A pdb=" N LEU F 552 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL F 553 " --> pdb=" O ILE F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 579 Processing helix chain 'F' and resid 602 through 611 removed outlier: 3.518A pdb=" N ALA F 606 " --> pdb=" O ALA F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 652 Processing helix chain 'F' and resid 666 through 669 Processing helix chain 'F' and resid 681 through 687 Processing helix chain 'F' and resid 702 through 708 removed outlier: 3.660A pdb=" N ILE F 705 " --> pdb=" O PRO F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 717 removed outlier: 4.615A pdb=" N ASN F 716 " --> pdb=" O HIS F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 738 removed outlier: 3.517A pdb=" N ALA F 736 " --> pdb=" O PRO F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 753 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 760 through 782 removed outlier: 4.344A pdb=" N HIS F 763 " --> pdb=" O ARG F 760 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU F 782 " --> pdb=" O ALA F 779 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 790 No H-bonds generated for 'chain 'F' and resid 787 through 790' Processing helix chain 'G' and resid 15 through 37 Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 64 through 81 removed outlier: 3.642A pdb=" N HIS G 73 " --> pdb=" O PHE G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 removed outlier: 4.989A pdb=" N GLU G 105 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 156 through 164 removed outlier: 3.713A pdb=" N ALA G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 181 No H-bonds generated for 'chain 'G' and resid 178 through 181' Processing helix chain 'G' and resid 184 through 195 removed outlier: 3.853A pdb=" N TRP G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N HIS G 191 " --> pdb=" O ALA G 187 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS G 194 " --> pdb=" O TRP G 190 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE G 195 " --> pdb=" O HIS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 235 Processing helix chain 'G' and resid 248 through 275 removed outlier: 3.883A pdb=" N GLY G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 312 No H-bonds generated for 'chain 'G' and resid 310 through 312' Processing helix chain 'G' and resid 324 through 337 removed outlier: 4.113A pdb=" N TYR G 337 " --> pdb=" O TRP G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 342 No H-bonds generated for 'chain 'G' and resid 339 through 342' Processing helix chain 'G' and resid 351 through 356 removed outlier: 3.620A pdb=" N ILE G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'G' and resid 364 through 366 No H-bonds generated for 'chain 'G' and resid 364 through 366' Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 402 through 415 Processing helix chain 'G' and resid 434 through 438 Processing helix chain 'G' and resid 450 through 455 Processing helix chain 'G' and resid 470 through 482 removed outlier: 3.675A pdb=" N LEU G 477 " --> pdb=" O LEU G 473 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA G 479 " --> pdb=" O GLY G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 515 Processing helix chain 'G' and resid 547 through 555 removed outlier: 3.566A pdb=" N LEU G 552 " --> pdb=" O PHE G 549 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 553 " --> pdb=" O ILE G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 579 Processing helix chain 'G' and resid 602 through 611 removed outlier: 3.519A pdb=" N ALA G 606 " --> pdb=" O ALA G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 652 Processing helix chain 'G' and resid 666 through 669 Processing helix chain 'G' and resid 681 through 687 Processing helix chain 'G' and resid 702 through 708 removed outlier: 3.620A pdb=" N ILE G 705 " --> pdb=" O PRO G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 713 through 717 removed outlier: 4.606A pdb=" N ASN G 716 " --> pdb=" O HIS G 713 " (cutoff:3.500A) Processing helix chain 'G' and resid 732 through 738 removed outlier: 3.531A pdb=" N ALA G 736 " --> pdb=" O PRO G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 743 through 753 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 760 through 782 removed outlier: 4.351A pdb=" N HIS G 763 " --> pdb=" O ARG G 760 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 782 " --> pdb=" O ALA G 779 " (cutoff:3.500A) Processing helix chain 'G' and resid 787 through 790 No H-bonds generated for 'chain 'G' and resid 787 through 790' Processing helix chain 'H' and resid 15 through 37 Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'H' and resid 64 through 81 removed outlier: 3.629A pdb=" N HIS H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 removed outlier: 3.563A pdb=" N LEU H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 100 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU H 105 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 119 through 128 Processing helix chain 'H' and resid 156 through 164 removed outlier: 3.699A pdb=" N ALA H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 184 through 195 removed outlier: 3.672A pdb=" N TRP H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N HIS H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER H 192 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS H 194 " --> pdb=" O TRP H 190 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE H 195 " --> pdb=" O HIS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 235 Processing helix chain 'H' and resid 248 through 275 removed outlier: 3.831A pdb=" N GLY H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 312 No H-bonds generated for 'chain 'H' and resid 310 through 312' Processing helix chain 'H' and resid 324 through 337 removed outlier: 4.100A pdb=" N TYR H 337 " --> pdb=" O TRP H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 342 No H-bonds generated for 'chain 'H' and resid 339 through 342' Processing helix chain 'H' and resid 351 through 356 removed outlier: 3.661A pdb=" N ILE H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 362 No H-bonds generated for 'chain 'H' and resid 360 through 362' Processing helix chain 'H' and resid 364 through 366 No H-bonds generated for 'chain 'H' and resid 364 through 366' Processing helix chain 'H' and resid 372 through 375 No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 402 through 415 Processing helix chain 'H' and resid 434 through 438 Processing helix chain 'H' and resid 450 through 455 Processing helix chain 'H' and resid 470 through 482 removed outlier: 3.661A pdb=" N LEU H 477 " --> pdb=" O LEU H 473 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA H 479 " --> pdb=" O GLY H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 515 Processing helix chain 'H' and resid 547 through 555 removed outlier: 3.567A pdb=" N LEU H 552 " --> pdb=" O PHE H 549 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 553 " --> pdb=" O ILE H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 579 Processing helix chain 'H' and resid 602 through 611 removed outlier: 3.534A pdb=" N ALA H 606 " --> pdb=" O ALA H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 652 Processing helix chain 'H' and resid 666 through 669 Processing helix chain 'H' and resid 681 through 687 Processing helix chain 'H' and resid 702 through 708 removed outlier: 3.642A pdb=" N ILE H 705 " --> pdb=" O PRO H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 713 through 717 removed outlier: 4.555A pdb=" N ASN H 716 " --> pdb=" O HIS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 732 through 738 removed outlier: 3.713A pdb=" N ALA H 736 " --> pdb=" O PRO H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 743 through 753 Processing helix chain 'H' and resid 755 through 757 No H-bonds generated for 'chain 'H' and resid 755 through 757' Processing helix chain 'H' and resid 760 through 782 removed outlier: 4.325A pdb=" N HIS H 763 " --> pdb=" O ARG H 760 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU H 782 " --> pdb=" O ALA H 779 " (cutoff:3.500A) Processing helix chain 'H' and resid 787 through 790 No H-bonds generated for 'chain 'H' and resid 787 through 790' Processing helix chain 'I' and resid 15 through 37 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 64 through 81 removed outlier: 3.620A pdb=" N HIS I 73 " --> pdb=" O PHE I 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG I 80 " --> pdb=" O ARG I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 105 Processing helix chain 'I' and resid 107 through 111 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 156 through 164 removed outlier: 3.679A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 181 No H-bonds generated for 'chain 'I' and resid 178 through 181' Processing helix chain 'I' and resid 184 through 195 removed outlier: 3.840A pdb=" N TRP I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER I 192 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS I 194 " --> pdb=" O TRP I 190 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE I 195 " --> pdb=" O HIS I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 235 Processing helix chain 'I' and resid 248 through 275 removed outlier: 3.880A pdb=" N GLY I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 312 No H-bonds generated for 'chain 'I' and resid 310 through 312' Processing helix chain 'I' and resid 324 through 337 removed outlier: 4.063A pdb=" N TYR I 337 " --> pdb=" O TRP I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 342 No H-bonds generated for 'chain 'I' and resid 339 through 342' Processing helix chain 'I' and resid 351 through 356 removed outlier: 3.649A pdb=" N ILE I 356 " --> pdb=" O GLU I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'I' and resid 364 through 366 No H-bonds generated for 'chain 'I' and resid 364 through 366' Processing helix chain 'I' and resid 372 through 375 No H-bonds generated for 'chain 'I' and resid 372 through 375' Processing helix chain 'I' and resid 384 through 386 No H-bonds generated for 'chain 'I' and resid 384 through 386' Processing helix chain 'I' and resid 402 through 415 Processing helix chain 'I' and resid 436 through 438 No H-bonds generated for 'chain 'I' and resid 436 through 438' Processing helix chain 'I' and resid 450 through 455 Processing helix chain 'I' and resid 470 through 482 removed outlier: 3.567A pdb=" N LEU I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 515 removed outlier: 4.400A pdb=" N SER I 501 " --> pdb=" O VAL I 498 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL I 503 " --> pdb=" O ASP I 500 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN I 504 " --> pdb=" O SER I 501 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 507 " --> pdb=" O ASN I 504 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU I 510 " --> pdb=" O ALA I 507 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL I 512 " --> pdb=" O TRP I 509 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS I 514 " --> pdb=" O ASP I 511 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG I 515 " --> pdb=" O VAL I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 555 removed outlier: 3.518A pdb=" N LEU I 552 " --> pdb=" O PHE I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 579 Processing helix chain 'I' and resid 602 through 611 removed outlier: 3.510A pdb=" N ALA I 606 " --> pdb=" O ALA I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 637 through 652 Processing helix chain 'I' and resid 666 through 669 Processing helix chain 'I' and resid 681 through 687 Processing helix chain 'I' and resid 702 through 708 removed outlier: 3.683A pdb=" N ILE I 705 " --> pdb=" O PRO I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 713 through 715 No H-bonds generated for 'chain 'I' and resid 713 through 715' Processing helix chain 'I' and resid 732 through 738 removed outlier: 3.600A pdb=" N ALA I 736 " --> pdb=" O PRO I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 743 through 753 Processing helix chain 'I' and resid 755 through 757 No H-bonds generated for 'chain 'I' and resid 755 through 757' Processing helix chain 'I' and resid 760 through 782 removed outlier: 4.316A pdb=" N HIS I 763 " --> pdb=" O ARG I 760 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU I 782 " --> pdb=" O ALA I 779 " (cutoff:3.500A) Processing helix chain 'I' and resid 787 through 790 No H-bonds generated for 'chain 'I' and resid 787 through 790' Processing helix chain 'J' and resid 15 through 37 Processing helix chain 'J' and resid 50 through 52 No H-bonds generated for 'chain 'J' and resid 50 through 52' Processing helix chain 'J' and resid 64 through 81 removed outlier: 3.616A pdb=" N HIS J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 80 " --> pdb=" O ARG J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 105 removed outlier: 3.542A pdb=" N LEU J 99 " --> pdb=" O PRO J 96 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU J 105 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 111 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 156 through 164 removed outlier: 3.703A pdb=" N ALA J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 182 No H-bonds generated for 'chain 'J' and resid 180 through 182' Processing helix chain 'J' and resid 184 through 195 removed outlier: 3.695A pdb=" N TRP J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N HIS J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER J 192 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASN J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS J 194 " --> pdb=" O TRP J 190 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE J 195 " --> pdb=" O HIS J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 235 Processing helix chain 'J' and resid 248 through 275 removed outlier: 3.886A pdb=" N GLY J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 312 No H-bonds generated for 'chain 'J' and resid 310 through 312' Processing helix chain 'J' and resid 324 through 337 removed outlier: 4.060A pdb=" N TYR J 337 " --> pdb=" O TRP J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 342 No H-bonds generated for 'chain 'J' and resid 339 through 342' Processing helix chain 'J' and resid 351 through 355 Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 364 through 366 No H-bonds generated for 'chain 'J' and resid 364 through 366' Processing helix chain 'J' and resid 372 through 375 No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 384 through 386 No H-bonds generated for 'chain 'J' and resid 384 through 386' Processing helix chain 'J' and resid 402 through 415 Processing helix chain 'J' and resid 436 through 438 No H-bonds generated for 'chain 'J' and resid 436 through 438' Processing helix chain 'J' and resid 450 through 455 Processing helix chain 'J' and resid 470 through 482 removed outlier: 3.625A pdb=" N LEU J 477 " --> pdb=" O LEU J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 515 removed outlier: 3.559A pdb=" N ASN J 504 " --> pdb=" O ASP J 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 555 removed outlier: 3.569A pdb=" N LEU J 552 " --> pdb=" O PHE J 549 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 553 " --> pdb=" O ILE J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 579 Processing helix chain 'J' and resid 602 through 611 removed outlier: 3.518A pdb=" N ALA J 606 " --> pdb=" O ALA J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 652 Processing helix chain 'J' and resid 666 through 669 Processing helix chain 'J' and resid 681 through 687 Processing helix chain 'J' and resid 703 through 708 Processing helix chain 'J' and resid 713 through 715 No H-bonds generated for 'chain 'J' and resid 713 through 715' Processing helix chain 'J' and resid 732 through 738 removed outlier: 3.538A pdb=" N ALA J 736 " --> pdb=" O PRO J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 743 through 753 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 760 through 782 removed outlier: 4.315A pdb=" N HIS J 763 " --> pdb=" O ARG J 760 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS J 775 " --> pdb=" O ILE J 772 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU J 782 " --> pdb=" O ALA J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 787 through 790 No H-bonds generated for 'chain 'J' and resid 787 through 790' Processing helix chain 'K' and resid 15 through 36 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 64 through 81 removed outlier: 3.605A pdb=" N HIS K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG K 80 " --> pdb=" O ARG K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 105 Processing helix chain 'K' and resid 107 through 111 Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 156 through 164 removed outlier: 3.682A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 182 No H-bonds generated for 'chain 'K' and resid 180 through 182' Processing helix chain 'K' and resid 184 through 195 removed outlier: 3.675A pdb=" N TRP K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER K 192 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS K 194 " --> pdb=" O TRP K 190 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE K 195 " --> pdb=" O HIS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 223 No H-bonds generated for 'chain 'K' and resid 220 through 223' Processing helix chain 'K' and resid 226 through 235 Processing helix chain 'K' and resid 248 through 275 removed outlier: 3.851A pdb=" N GLY K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 312 No H-bonds generated for 'chain 'K' and resid 310 through 312' Processing helix chain 'K' and resid 324 through 337 removed outlier: 4.112A pdb=" N TYR K 337 " --> pdb=" O TRP K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 342 No H-bonds generated for 'chain 'K' and resid 339 through 342' Processing helix chain 'K' and resid 351 through 356 removed outlier: 3.674A pdb=" N ILE K 356 " --> pdb=" O GLU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 364 through 366 No H-bonds generated for 'chain 'K' and resid 364 through 366' Processing helix chain 'K' and resid 372 through 375 No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 384 through 386 No H-bonds generated for 'chain 'K' and resid 384 through 386' Processing helix chain 'K' and resid 402 through 415 Processing helix chain 'K' and resid 434 through 438 Processing helix chain 'K' and resid 450 through 455 Processing helix chain 'K' and resid 470 through 482 removed outlier: 3.635A pdb=" N LEU K 477 " --> pdb=" O LEU K 473 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA K 479 " --> pdb=" O GLY K 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 500 through 515 removed outlier: 3.502A pdb=" N ASN K 504 " --> pdb=" O ASP K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 547 through 555 removed outlier: 3.543A pdb=" N LEU K 552 " --> pdb=" O PHE K 549 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 553 " --> pdb=" O ILE K 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 579 Processing helix chain 'K' and resid 602 through 611 removed outlier: 3.537A pdb=" N ALA K 606 " --> pdb=" O ALA K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 652 Processing helix chain 'K' and resid 666 through 669 Processing helix chain 'K' and resid 681 through 687 Processing helix chain 'K' and resid 702 through 708 removed outlier: 3.600A pdb=" N ILE K 705 " --> pdb=" O PRO K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 713 through 717 removed outlier: 4.552A pdb=" N ASN K 716 " --> pdb=" O HIS K 713 " (cutoff:3.500A) Processing helix chain 'K' and resid 732 through 738 removed outlier: 3.565A pdb=" N ALA K 736 " --> pdb=" O PRO K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 743 through 753 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 760 through 782 removed outlier: 4.327A pdb=" N HIS K 763 " --> pdb=" O ARG K 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU K 782 " --> pdb=" O ALA K 779 " (cutoff:3.500A) Processing helix chain 'K' and resid 787 through 790 No H-bonds generated for 'chain 'K' and resid 787 through 790' Processing helix chain 'L' and resid 15 through 37 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 64 through 81 removed outlier: 3.627A pdb=" N HIS L 73 " --> pdb=" O PHE L 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 105 Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'L' and resid 156 through 164 removed outlier: 3.731A pdb=" N ALA L 164 " --> pdb=" O ALA L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 181 No H-bonds generated for 'chain 'L' and resid 178 through 181' Processing helix chain 'L' and resid 184 through 195 removed outlier: 3.608A pdb=" N TRP L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N HIS L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER L 192 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN L 193 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS L 194 " --> pdb=" O TRP L 190 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 235 Processing helix chain 'L' and resid 248 through 275 removed outlier: 3.863A pdb=" N GLY L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 312 No H-bonds generated for 'chain 'L' and resid 310 through 312' Processing helix chain 'L' and resid 324 through 337 removed outlier: 4.052A pdb=" N TYR L 337 " --> pdb=" O TRP L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 342 No H-bonds generated for 'chain 'L' and resid 339 through 342' Processing helix chain 'L' and resid 351 through 356 removed outlier: 3.648A pdb=" N ILE L 356 " --> pdb=" O GLU L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 364 through 366 No H-bonds generated for 'chain 'L' and resid 364 through 366' Processing helix chain 'L' and resid 384 through 386 No H-bonds generated for 'chain 'L' and resid 384 through 386' Processing helix chain 'L' and resid 402 through 415 Processing helix chain 'L' and resid 434 through 438 Processing helix chain 'L' and resid 450 through 455 Processing helix chain 'L' and resid 470 through 482 removed outlier: 3.665A pdb=" N LEU L 477 " --> pdb=" O LEU L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 500 through 515 removed outlier: 3.603A pdb=" N ASN L 504 " --> pdb=" O ASP L 500 " (cutoff:3.500A) Processing helix chain 'L' and resid 547 through 555 Processing helix chain 'L' and resid 569 through 579 Processing helix chain 'L' and resid 602 through 611 removed outlier: 3.520A pdb=" N ALA L 606 " --> pdb=" O ALA L 602 " (cutoff:3.500A) Processing helix chain 'L' and resid 637 through 652 Processing helix chain 'L' and resid 666 through 669 Processing helix chain 'L' and resid 681 through 687 Processing helix chain 'L' and resid 702 through 708 removed outlier: 3.657A pdb=" N ILE L 705 " --> pdb=" O PRO L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 713 through 717 removed outlier: 4.580A pdb=" N ASN L 716 " --> pdb=" O HIS L 713 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 739 removed outlier: 3.537A pdb=" N ALA L 736 " --> pdb=" O PRO L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 743 through 753 Processing helix chain 'L' and resid 755 through 757 No H-bonds generated for 'chain 'L' and resid 755 through 757' Processing helix chain 'L' and resid 760 through 782 removed outlier: 4.269A pdb=" N HIS L 763 " --> pdb=" O ARG L 760 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU L 782 " --> pdb=" O ALA L 779 " (cutoff:3.500A) Processing helix chain 'L' and resid 787 through 790 No H-bonds generated for 'chain 'L' and resid 787 through 790' Processing sheet with id= A, first strand: chain 'A' and resid 171 through 177 removed outlier: 6.772A pdb=" N ALA A 203 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N CYS A 174 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 205 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 176 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 207 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 464 through 466 removed outlier: 8.758A pdb=" N MET A 465 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS A 486 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE A 423 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 488 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN A 527 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.576A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA A 632 " --> pdb=" O PRO A 693 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE A 695 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.745A pdb=" N ALA B 203 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N CYS B 174 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 205 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 176 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE B 207 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 464 through 466 removed outlier: 8.608A pdb=" N MET B 465 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS B 486 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE B 423 " --> pdb=" O HIS B 486 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE B 488 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN B 527 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.555A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA B 632 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE B 695 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 171 through 177 removed outlier: 6.634A pdb=" N ALA C 203 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N CYS C 174 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 205 " --> pdb=" O CYS C 174 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE C 176 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 207 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 397 through 399 removed outlier: 4.849A pdb=" N SER C 397 " --> pdb=" O GLN C 598 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS C 596 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 464 through 466 removed outlier: 8.750A pdb=" N MET C 465 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU C 422 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N HIS C 486 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N PHE C 423 " --> pdb=" O HIS C 486 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE C 488 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN C 527 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 613 through 615 removed outlier: 6.561A pdb=" N VAL C 629 " --> pdb=" O ARG C 659 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL C 661 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 631 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 663 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 633 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 171 through 177 removed outlier: 6.719A pdb=" N ALA D 203 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N CYS D 174 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU D 205 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE D 176 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE D 207 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 397 through 399 removed outlier: 4.866A pdb=" N SER D 397 " --> pdb=" O GLN D 598 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS D 596 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 464 through 466 removed outlier: 8.663A pdb=" N MET D 465 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 422 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N HIS D 486 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N PHE D 423 " --> pdb=" O HIS D 486 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE D 488 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN D 527 " --> pdb=" O GLY D 487 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 613 through 615 removed outlier: 6.576A pdb=" N VAL D 629 " --> pdb=" O ARG D 659 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL D 661 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 631 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL D 663 " --> pdb=" O ILE D 631 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 633 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 171 through 177 removed outlier: 6.718A pdb=" N ALA E 203 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS E 174 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 205 " --> pdb=" O CYS E 174 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE E 176 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE E 207 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N LEU E 208 " --> pdb=" O PRO E 285 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 287 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 464 through 466 removed outlier: 8.574A pdb=" N MET E 465 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 422 " --> pdb=" O MET E 465 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS E 486 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N PHE E 423 " --> pdb=" O HIS E 486 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE E 488 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN E 527 " --> pdb=" O GLY E 487 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 613 through 615 removed outlier: 6.555A pdb=" N VAL E 629 " --> pdb=" O ARG E 659 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 661 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 631 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL E 663 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER E 633 " --> pdb=" O VAL E 663 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 171 through 177 removed outlier: 6.729A pdb=" N ALA F 203 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N CYS F 174 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU F 205 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE F 176 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE F 207 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 464 through 466 removed outlier: 8.457A pdb=" N MET F 465 " --> pdb=" O PHE F 420 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 422 " --> pdb=" O MET F 465 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS F 486 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE F 423 " --> pdb=" O HIS F 486 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE F 488 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN F 527 " --> pdb=" O GLY F 487 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 613 through 615 removed outlier: 6.579A pdb=" N VAL F 629 " --> pdb=" O ARG F 659 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL F 661 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE F 631 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL F 663 " --> pdb=" O ILE F 631 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER F 633 " --> pdb=" O VAL F 663 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 171 through 177 removed outlier: 6.726A pdb=" N ALA G 203 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N CYS G 174 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU G 205 " --> pdb=" O CYS G 174 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE G 176 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE G 207 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 397 through 399 removed outlier: 4.843A pdb=" N SER G 397 " --> pdb=" O GLN G 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS G 596 " --> pdb=" O ALA G 399 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 464 through 466 removed outlier: 8.799A pdb=" N MET G 465 " --> pdb=" O PHE G 420 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU G 422 " --> pdb=" O MET G 465 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N HIS G 486 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE G 423 " --> pdb=" O HIS G 486 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE G 488 " --> pdb=" O PHE G 423 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN G 527 " --> pdb=" O GLY G 487 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 613 through 615 removed outlier: 6.578A pdb=" N VAL G 629 " --> pdb=" O ARG G 659 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL G 661 " --> pdb=" O VAL G 629 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE G 631 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL G 663 " --> pdb=" O ILE G 631 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER G 633 " --> pdb=" O VAL G 663 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 171 through 177 removed outlier: 6.745A pdb=" N ALA H 203 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS H 174 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU H 205 " --> pdb=" O CYS H 174 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE H 176 " --> pdb=" O LEU H 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 207 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 287 " --> pdb=" O PRO H 206 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 397 through 399 removed outlier: 4.833A pdb=" N SER H 397 " --> pdb=" O GLN H 598 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS H 596 " --> pdb=" O ALA H 399 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 464 through 466 removed outlier: 8.551A pdb=" N MET H 465 " --> pdb=" O PHE H 420 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU H 422 " --> pdb=" O MET H 465 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N HIS H 486 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N PHE H 423 " --> pdb=" O HIS H 486 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE H 488 " --> pdb=" O PHE H 423 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN H 527 " --> pdb=" O GLY H 487 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 613 through 615 removed outlier: 6.553A pdb=" N VAL H 629 " --> pdb=" O ARG H 659 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL H 661 " --> pdb=" O VAL H 629 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE H 631 " --> pdb=" O VAL H 661 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL H 663 " --> pdb=" O ILE H 631 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER H 633 " --> pdb=" O VAL H 663 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA H 632 " --> pdb=" O PRO H 693 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE H 695 " --> pdb=" O ALA H 632 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 171 through 177 removed outlier: 6.717A pdb=" N ALA I 203 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS I 174 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU I 205 " --> pdb=" O CYS I 174 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE I 176 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE I 207 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 397 through 399 removed outlier: 4.854A pdb=" N SER I 397 " --> pdb=" O GLN I 598 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS I 596 " --> pdb=" O ALA I 399 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 464 through 466 removed outlier: 8.622A pdb=" N MET I 465 " --> pdb=" O PHE I 420 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU I 422 " --> pdb=" O MET I 465 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS I 486 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE I 423 " --> pdb=" O HIS I 486 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE I 488 " --> pdb=" O PHE I 423 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN I 527 " --> pdb=" O GLY I 487 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 613 through 615 removed outlier: 6.585A pdb=" N VAL I 629 " --> pdb=" O ARG I 659 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL I 661 " --> pdb=" O VAL I 629 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE I 631 " --> pdb=" O VAL I 661 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL I 663 " --> pdb=" O ILE I 631 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER I 633 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 171 through 177 removed outlier: 6.709A pdb=" N ALA J 203 " --> pdb=" O VAL J 172 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS J 174 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU J 205 " --> pdb=" O CYS J 174 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE J 176 " --> pdb=" O LEU J 205 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE J 207 " --> pdb=" O ILE J 176 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 464 through 466 removed outlier: 8.576A pdb=" N MET J 465 " --> pdb=" O PHE J 420 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU J 422 " --> pdb=" O MET J 465 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS J 486 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N PHE J 423 " --> pdb=" O HIS J 486 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE J 488 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN J 527 " --> pdb=" O GLY J 487 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 613 through 615 removed outlier: 6.574A pdb=" N VAL J 629 " --> pdb=" O ARG J 659 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL J 661 " --> pdb=" O VAL J 629 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE J 631 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL J 663 " --> pdb=" O ILE J 631 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER J 633 " --> pdb=" O VAL J 663 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 171 through 177 removed outlier: 6.748A pdb=" N ALA K 203 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N CYS K 174 " --> pdb=" O ALA K 203 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU K 205 " --> pdb=" O CYS K 174 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE K 176 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE K 207 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 464 through 466 removed outlier: 8.533A pdb=" N MET K 465 " --> pdb=" O PHE K 420 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU K 422 " --> pdb=" O MET K 465 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS K 486 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N PHE K 423 " --> pdb=" O HIS K 486 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE K 488 " --> pdb=" O PHE K 423 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN K 527 " --> pdb=" O GLY K 487 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 613 through 615 removed outlier: 6.556A pdb=" N VAL K 629 " --> pdb=" O ARG K 659 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL K 661 " --> pdb=" O VAL K 629 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 631 " --> pdb=" O VAL K 661 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL K 663 " --> pdb=" O ILE K 631 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER K 633 " --> pdb=" O VAL K 663 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 171 through 177 removed outlier: 6.709A pdb=" N ALA L 203 " --> pdb=" O VAL L 172 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS L 174 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU L 205 " --> pdb=" O CYS L 174 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE L 176 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE L 207 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 464 through 466 removed outlier: 8.526A pdb=" N MET L 465 " --> pdb=" O PHE L 420 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU L 422 " --> pdb=" O MET L 465 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS L 486 " --> pdb=" O ARG L 421 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N PHE L 423 " --> pdb=" O HIS L 486 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE L 488 " --> pdb=" O PHE L 423 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN L 527 " --> pdb=" O GLY L 487 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 613 through 615 removed outlier: 6.580A pdb=" N VAL L 629 " --> pdb=" O ARG L 659 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL L 661 " --> pdb=" O VAL L 629 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE L 631 " --> pdb=" O VAL L 661 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL L 663 " --> pdb=" O ILE L 631 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER L 633 " --> pdb=" O VAL L 663 " (cutoff:3.500A) 2534 hydrogen bonds defined for protein. 6534 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: 29.49 Time building geometry restraints manager: 27.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 25477 1.34 - 1.46: 12183 1.46 - 1.57: 39592 1.57 - 1.69: 46 1.69 - 1.81: 276 Bond restraints: 77574 Sorted by residual: bond pdb=" O1A TPP H 801 " pdb=" PA TPP H 801 " ideal model delta sigma weight residual 1.479 1.530 -0.051 1.00e-02 1.00e+04 2.61e+01 bond pdb=" O1A TPP D 801 " pdb=" PA TPP D 801 " ideal model delta sigma weight residual 1.479 1.526 -0.047 1.00e-02 1.00e+04 2.25e+01 bond pdb=" O1A TPP C 801 " pdb=" PA TPP C 801 " ideal model delta sigma weight residual 1.479 1.526 -0.047 1.00e-02 1.00e+04 2.21e+01 bond pdb=" O1A TPP A 801 " pdb=" PA TPP A 801 " ideal model delta sigma weight residual 1.479 1.526 -0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" O1A TPP E 801 " pdb=" PA TPP E 801 " ideal model delta sigma weight residual 1.479 1.526 -0.047 1.00e-02 1.00e+04 2.17e+01 ... (remaining 77569 not shown) Histogram of bond angle deviations from ideal: 91.12 - 100.88: 82 100.88 - 110.64: 25960 110.64 - 120.40: 48275 120.40 - 130.15: 30685 130.15 - 139.91: 906 Bond angle restraints: 105908 Sorted by residual: angle pdb=" O3A TPP D 801 " pdb=" PB TPP D 801 " pdb=" O3B TPP D 801 " ideal model delta sigma weight residual 104.26 111.30 -7.04 1.33e+00 5.64e-01 2.79e+01 angle pdb=" O2B TPP B 801 " pdb=" PB TPP B 801 " pdb=" O3A TPP B 801 " ideal model delta sigma weight residual 104.26 111.27 -7.01 1.33e+00 5.64e-01 2.77e+01 angle pdb=" O2B TPP F 801 " pdb=" PB TPP F 801 " pdb=" O3A TPP F 801 " ideal model delta sigma weight residual 104.26 111.27 -7.01 1.33e+00 5.64e-01 2.77e+01 angle pdb=" O2B TPP J 801 " pdb=" PB TPP J 801 " pdb=" O3A TPP J 801 " ideal model delta sigma weight residual 104.26 111.08 -6.82 1.33e+00 5.64e-01 2.62e+01 angle pdb=" O3A TPP G 801 " pdb=" PB TPP G 801 " pdb=" O3B TPP G 801 " ideal model delta sigma weight residual 104.26 111.08 -6.82 1.33e+00 5.64e-01 2.62e+01 ... (remaining 105903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 41422 12.89 - 25.78: 3016 25.78 - 38.66: 889 38.66 - 51.55: 173 51.55 - 64.44: 28 Dihedral angle restraints: 45528 sinusoidal: 18188 harmonic: 27340 Sorted by residual: dihedral pdb=" CA HIS L 313 " pdb=" C HIS L 313 " pdb=" N GLN L 314 " pdb=" CA GLN L 314 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 315 " pdb=" C VAL K 315 " pdb=" N PRO K 316 " pdb=" CA PRO K 316 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA HIS B 313 " pdb=" C HIS B 313 " pdb=" N GLN B 314 " pdb=" CA GLN B 314 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 45525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 7943 0.037 - 0.074: 2380 0.074 - 0.111: 779 0.111 - 0.148: 219 0.148 - 0.186: 3 Chirality restraints: 11324 Sorted by residual: chirality pdb=" CA GLN K 314 " pdb=" N GLN K 314 " pdb=" C GLN K 314 " pdb=" CB GLN K 314 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE L 613 " pdb=" N ILE L 613 " pdb=" C ILE L 613 " pdb=" CB ILE L 613 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA HIS K 313 " pdb=" N HIS K 313 " pdb=" C HIS K 313 " pdb=" CB HIS K 313 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 11321 not shown) Planarity restraints: 13940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 140 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO D 141 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 140 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO J 141 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 141 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 141 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 140 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO C 141 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 141 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 13937 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 1195 2.62 - 3.19: 67257 3.19 - 3.76: 126044 3.76 - 4.33: 177880 4.33 - 4.90: 291461 Nonbonded interactions: 663837 Sorted by model distance: nonbonded pdb=" O1B TPP H 801 " pdb="MG MG H 802 " model vdw 2.048 2.170 nonbonded pdb=" O2B TPP I 801 " pdb="MG MG I 802 " model vdw 2.050 2.170 nonbonded pdb=" O2B TPP D 801 " pdb="MG MG D 802 " model vdw 2.054 2.170 nonbonded pdb=" O1B TPP F 801 " pdb="MG MG F 802 " model vdw 2.057 2.170 nonbonded pdb=" O1B TPP B 801 " pdb="MG MG B 802 " model vdw 2.066 2.170 ... (remaining 663832 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' and (resid 9 through 103 or resid 105 through 702 or resid 704 throug \ h 718 or resid 720 through 796 or resid 801 through 802)) selection = (chain 'B' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'C' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'D' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'E' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'F' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'G' and (resid 9 through 472 or resid 474 through 702 or resid 704 throug \ h 718 or resid 720 through 796 or resid 801 through 802)) selection = (chain 'H' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'I' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'J' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'K' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) selection = (chain 'L' and (resid 9 through 103 or resid 105 through 472 or resid 474 throug \ h 702 or resid 704 through 718 or resid 720 through 796 or resid 801 through 802 \ )) } 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=0.50 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: 4.010 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: 0.080 Extract box with map and model: 14.430 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 202.150 Find NCS groups from input model: 5.300 Set up NCS constraints: 0.360 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 77574 Z= 0.241 Angle : 0.493 7.365 105908 Z= 0.254 Chirality : 0.042 0.186 11324 Planarity : 0.005 0.059 13940 Dihedral : 10.291 64.439 27940 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.78 % Allowed : 5.20 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.08), residues: 9450 helix: 0.28 (0.07), residues: 4018 sheet: 0.96 (0.16), residues: 1144 loop : -0.39 (0.09), residues: 4288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 61 HIS 0.005 0.001 HIS B 699 PHE 0.009 0.001 PHE G 233 TYR 0.010 0.001 TYR G 710 ARG 0.003 0.000 ARG G 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 568 time to evaluate : 6.407 Fit side-chains REVERT: A 683 ASP cc_start: 0.8099 (m-30) cc_final: 0.7876 (m-30) REVERT: A 734 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 474 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 552 LEU cc_start: 0.8771 (pp) cc_final: 0.8172 (pp) REVERT: C 422 LEU cc_start: 0.9125 (tp) cc_final: 0.8877 (mm) REVERT: C 465 MET cc_start: 0.7769 (mpp) cc_final: 0.7103 (mpt) REVERT: C 474 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7736 (tm-30) REVERT: C 516 GLU cc_start: 0.7860 (mp0) cc_final: 0.7606 (mp0) REVERT: C 552 LEU cc_start: 0.8750 (pp) cc_final: 0.8053 (pp) REVERT: C 734 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 474 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7713 (tm-30) REVERT: D 552 LEU cc_start: 0.8617 (pp) cc_final: 0.8406 (pp) REVERT: E 474 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7712 (tm-30) REVERT: E 552 LEU cc_start: 0.8771 (pp) cc_final: 0.8163 (pp) REVERT: F 474 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7805 (tm-30) REVERT: F 683 ASP cc_start: 0.8122 (m-30) cc_final: 0.7884 (m-30) REVERT: G 474 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7758 (tm-30) REVERT: G 683 ASP cc_start: 0.8104 (m-30) cc_final: 0.7876 (m-30) REVERT: G 734 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7830 (tm-30) REVERT: H 474 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7797 (tm-30) REVERT: H 552 LEU cc_start: 0.8685 (pp) cc_final: 0.8330 (pp) REVERT: I 552 LEU cc_start: 0.8803 (pp) cc_final: 0.8047 (pp) REVERT: I 738 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7938 (mmt90) REVERT: J 465 MET cc_start: 0.7794 (mpp) cc_final: 0.7377 (mpm) REVERT: J 474 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7713 (tm-30) REVERT: J 516 GLU cc_start: 0.7894 (mp0) cc_final: 0.7503 (mp0) REVERT: J 552 LEU cc_start: 0.8640 (pp) cc_final: 0.8390 (pp) REVERT: K 474 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7697 (tm-30) REVERT: K 552 LEU cc_start: 0.8737 (pp) cc_final: 0.8181 (pp) REVERT: K 738 ARG cc_start: 0.8292 (mmt90) cc_final: 0.8029 (mmt90) REVERT: L 474 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7757 (tm-30) REVERT: L 683 ASP cc_start: 0.8120 (m-30) cc_final: 0.7882 (m-30) outliers start: 62 outliers final: 8 residues processed: 619 average time/residue: 1.2766 time to fit residues: 1105.9024 Evaluate side-chains 291 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 283 time to evaluate : 6.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 691 ASP Chi-restraints excluded: chain L residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 5.9990 chunk 709 optimal weight: 0.0570 chunk 393 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 478 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 733 optimal weight: 0.0170 chunk 283 optimal weight: 0.9990 chunk 446 optimal weight: 6.9990 chunk 546 optimal weight: 50.0000 chunk 849 optimal weight: 0.7980 overall best weight: 1.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN D 717 ASN E 35 GLN ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN H 35 GLN H 101 ASN H 730 ASN ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 GLN K 35 GLN K 209 HIS L 101 ASN ** L 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 77574 Z= 0.169 Angle : 0.492 8.020 105908 Z= 0.245 Chirality : 0.041 0.166 11324 Planarity : 0.005 0.053 13940 Dihedral : 4.551 59.446 10440 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 8.79 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.08), residues: 9450 helix: 1.15 (0.08), residues: 4096 sheet: 0.70 (0.16), residues: 1153 loop : -0.31 (0.09), residues: 4201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 25 HIS 0.008 0.001 HIS H 539 PHE 0.013 0.001 PHE K 125 TYR 0.011 0.001 TYR E 71 ARG 0.010 0.000 ARG G 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 321 time to evaluate : 7.403 Fit side-chains REVERT: A 86 ILE cc_start: 0.8177 (mm) cc_final: 0.7676 (tp) REVERT: A 734 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 86 ILE cc_start: 0.8295 (mm) cc_final: 0.7771 (tt) REVERT: B 283 MET cc_start: 0.8279 (mpp) cc_final: 0.8059 (mmp) REVERT: B 474 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 283 MET cc_start: 0.8291 (mpp) cc_final: 0.7970 (mmp) REVERT: C 465 MET cc_start: 0.8304 (mpp) cc_final: 0.7827 (mpm) REVERT: C 474 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 474 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 500 ASP cc_start: 0.8431 (t0) cc_final: 0.8226 (t0) REVERT: E 86 ILE cc_start: 0.8191 (mm) cc_final: 0.7658 (tt) REVERT: E 474 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7595 (tm-30) REVERT: E 681 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7138 (t0) REVERT: F 86 ILE cc_start: 0.8166 (mm) cc_final: 0.7929 (mt) REVERT: F 465 MET cc_start: 0.8193 (mpp) cc_final: 0.7966 (mmm) REVERT: F 474 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 683 ASP cc_start: 0.8076 (m-30) cc_final: 0.7874 (m-30) REVERT: G 13 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5711 (pp) REVERT: G 86 ILE cc_start: 0.8068 (mm) cc_final: 0.7572 (tt) REVERT: G 474 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7362 (tm-30) REVERT: G 734 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7654 (tm-30) REVERT: H 86 ILE cc_start: 0.8218 (mm) cc_final: 0.7654 (tt) REVERT: H 283 MET cc_start: 0.8282 (mpp) cc_final: 0.8059 (mmp) REVERT: H 474 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7710 (tm-30) REVERT: I 283 MET cc_start: 0.8315 (mpp) cc_final: 0.8050 (mmp) REVERT: J 283 MET cc_start: 0.8381 (mpp) cc_final: 0.8112 (mmp) REVERT: J 474 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7393 (tm-30) REVERT: K 86 ILE cc_start: 0.8176 (mm) cc_final: 0.7643 (tt) REVERT: K 283 MET cc_start: 0.8309 (mpp) cc_final: 0.8093 (mmp) REVERT: K 474 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7572 (tm-30) REVERT: L 86 ILE cc_start: 0.8132 (mm) cc_final: 0.7898 (mt) REVERT: L 465 MET cc_start: 0.8567 (mpp) cc_final: 0.8313 (mmm) REVERT: L 474 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7363 (tm-30) outliers start: 123 outliers final: 59 residues processed: 414 average time/residue: 1.1966 time to fit residues: 720.0577 Evaluate side-chains 333 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 272 time to evaluate : 6.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 733 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 733 LEU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 733 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 544 HIS Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 707 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 234 optimal weight: 40.0000 chunk 851 optimal weight: 6.9990 chunk 919 optimal weight: 6.9990 chunk 758 optimal weight: 4.9990 chunk 844 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 683 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN H 505 GLN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 ASN ** I 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 328 GLN ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN K 209 HIS K 328 GLN K 497 HIS L 29 ASN ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 77574 Z= 0.350 Angle : 0.548 8.895 105908 Z= 0.275 Chirality : 0.044 0.236 11324 Planarity : 0.005 0.050 13940 Dihedral : 4.794 59.970 10436 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.67 % Allowed : 9.80 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 9450 helix: 1.25 (0.08), residues: 4083 sheet: 0.32 (0.16), residues: 1150 loop : -0.32 (0.09), residues: 4217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 25 HIS 0.008 0.001 HIS H 539 PHE 0.011 0.001 PHE K 233 TYR 0.009 0.001 TYR F 71 ARG 0.007 0.000 ARG G 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 260 time to evaluate : 6.662 Fit side-chains REVERT: A 86 ILE cc_start: 0.8270 (mm) cc_final: 0.7740 (tt) REVERT: A 734 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 283 MET cc_start: 0.8246 (mpp) cc_final: 0.8012 (mmp) REVERT: B 474 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 508 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8745 (ttmt) REVERT: B 681 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7099 (t0) REVERT: C 474 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7520 (tm-30) REVERT: D 86 ILE cc_start: 0.8360 (mm) cc_final: 0.7804 (tt) REVERT: D 474 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7486 (tm-30) REVERT: D 683 ASP cc_start: 0.7956 (m-30) cc_final: 0.7681 (m-30) REVERT: D 781 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: E 13 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5775 (pp) REVERT: E 86 ILE cc_start: 0.8334 (mm) cc_final: 0.7867 (tt) REVERT: E 474 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7632 (tm-30) REVERT: E 681 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7116 (t0) REVERT: F 86 ILE cc_start: 0.8238 (mm) cc_final: 0.7712 (tt) REVERT: F 465 MET cc_start: 0.8256 (mpp) cc_final: 0.8045 (mmm) REVERT: F 474 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 683 ASP cc_start: 0.8118 (m-30) cc_final: 0.7916 (m-30) REVERT: G 86 ILE cc_start: 0.8135 (mm) cc_final: 0.7653 (tt) REVERT: G 474 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7484 (tm-30) REVERT: G 734 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7722 (tm-30) REVERT: H 283 MET cc_start: 0.8255 (mpp) cc_final: 0.8020 (mmp) REVERT: H 474 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7619 (tm-30) REVERT: I 86 ILE cc_start: 0.8366 (mm) cc_final: 0.7815 (tt) REVERT: I 283 MET cc_start: 0.8388 (mpp) cc_final: 0.8161 (mmp) REVERT: J 86 ILE cc_start: 0.8369 (mm) cc_final: 0.7826 (tt) REVERT: J 283 MET cc_start: 0.8323 (mpp) cc_final: 0.8078 (mmp) REVERT: J 290 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7187 (mmt-90) REVERT: J 474 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7492 (tm-30) REVERT: J 681 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7423 (t0) REVERT: K 86 ILE cc_start: 0.8358 (mm) cc_final: 0.7911 (tt) REVERT: K 283 MET cc_start: 0.8259 (mpp) cc_final: 0.8025 (mmp) REVERT: K 474 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7615 (tm-30) REVERT: L 86 ILE cc_start: 0.8229 (mm) cc_final: 0.7688 (tt) REVERT: L 474 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7467 (tm-30) outliers start: 133 outliers final: 57 residues processed: 371 average time/residue: 1.2236 time to fit residues: 650.6929 Evaluate side-chains 306 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 6.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 544 HIS Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 544 HIS Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 733 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 4.9990 chunk 640 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 571 optimal weight: 5.9990 chunk 854 optimal weight: 1.9990 chunk 904 optimal weight: 5.9990 chunk 446 optimal weight: 3.9990 chunk 809 optimal weight: 30.0000 chunk 243 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 209 HIS B 328 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 209 HIS ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 505 GLN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 77574 Z= 0.334 Angle : 0.541 10.685 105908 Z= 0.269 Chirality : 0.043 0.238 11324 Planarity : 0.005 0.050 13940 Dihedral : 4.825 54.638 10430 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.01 % Allowed : 9.80 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.09), residues: 9450 helix: 1.17 (0.08), residues: 4119 sheet: 0.10 (0.16), residues: 1144 loop : -0.30 (0.09), residues: 4187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 25 HIS 0.008 0.001 HIS H 539 PHE 0.020 0.001 PHE E 233 TYR 0.010 0.001 TYR A 87 ARG 0.006 0.000 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 266 time to evaluate : 6.722 Fit side-chains REVERT: A 86 ILE cc_start: 0.8290 (mm) cc_final: 0.7802 (tt) REVERT: A 465 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.6410 (mpt) REVERT: A 674 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 734 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 86 ILE cc_start: 0.8368 (mm) cc_final: 0.7867 (tt) REVERT: B 283 MET cc_start: 0.8212 (mpp) cc_final: 0.7999 (mmp) REVERT: B 474 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 681 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7085 (t0) REVERT: C 86 ILE cc_start: 0.8234 (mm) cc_final: 0.7695 (tt) REVERT: C 283 MET cc_start: 0.8175 (mpp) cc_final: 0.7954 (mmp) REVERT: C 290 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7086 (mmt-90) REVERT: C 474 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 734 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 86 ILE cc_start: 0.8368 (mm) cc_final: 0.7829 (tt) REVERT: D 290 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7137 (mmt-90) REVERT: D 474 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7472 (tm-30) REVERT: D 781 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: E 13 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5716 (pp) REVERT: E 86 ILE cc_start: 0.8321 (mm) cc_final: 0.7801 (tt) REVERT: E 250 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8730 (pp) REVERT: E 286 MET cc_start: 0.6543 (tpt) cc_final: 0.6122 (tpt) REVERT: E 474 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7594 (tm-30) REVERT: E 681 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7090 (t0) REVERT: F 86 ILE cc_start: 0.8252 (mm) cc_final: 0.7752 (tt) REVERT: F 286 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4841 (pp-130) REVERT: F 474 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7521 (tm-30) REVERT: F 674 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: F 734 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7733 (tm-30) REVERT: G 86 ILE cc_start: 0.8234 (mm) cc_final: 0.7722 (tt) REVERT: G 286 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4818 (pp-130) REVERT: G 474 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 674 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: G 734 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7749 (tm-30) REVERT: H 86 ILE cc_start: 0.8343 (mm) cc_final: 0.7880 (tt) REVERT: H 283 MET cc_start: 0.8150 (mpp) cc_final: 0.7927 (mmp) REVERT: H 474 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7570 (tm-30) REVERT: I 86 ILE cc_start: 0.8360 (mm) cc_final: 0.7825 (tt) REVERT: I 186 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (tm) REVERT: J 86 ILE cc_start: 0.8399 (mm) cc_final: 0.7874 (tt) REVERT: J 283 MET cc_start: 0.8336 (mpp) cc_final: 0.8126 (mmp) REVERT: J 474 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7480 (tm-30) REVERT: J 681 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7335 (t0) REVERT: K 86 ILE cc_start: 0.8378 (mm) cc_final: 0.7859 (tt) REVERT: K 283 MET cc_start: 0.8151 (mpp) cc_final: 0.7925 (mmp) REVERT: K 474 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7621 (tm-30) REVERT: K 514 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8881 (ttpt) REVERT: L 86 ILE cc_start: 0.8250 (mm) cc_final: 0.7750 (tt) REVERT: L 474 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7456 (tm-30) REVERT: L 674 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: L 734 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7673 (tm-30) outliers start: 160 outliers final: 69 residues processed: 389 average time/residue: 1.2511 time to fit residues: 692.6258 Evaluate side-chains 333 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 248 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 544 HIS Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 674 GLU Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 691 ASP Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 286 MET Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 691 ASP Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 544 HIS Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 674 GLU Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 0.4980 chunk 513 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 673 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 772 optimal weight: 8.9990 chunk 625 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 461 optimal weight: 3.9990 chunk 812 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS B B 209 HIS C 167 ASN D 167 ASN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 77574 Z= 0.229 Angle : 0.508 12.907 105908 Z= 0.249 Chirality : 0.042 0.251 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.667 50.991 10428 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.74 % Allowed : 10.39 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 9450 helix: 1.37 (0.08), residues: 4046 sheet: -0.00 (0.16), residues: 1144 loop : -0.30 (0.09), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 25 HIS 0.006 0.001 HIS D 539 PHE 0.024 0.001 PHE H 233 TYR 0.009 0.001 TYR J 155 ARG 0.006 0.000 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 274 time to evaluate : 6.432 Fit side-chains REVERT: A 86 ILE cc_start: 0.8245 (mm) cc_final: 0.7738 (tt) REVERT: A 286 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4833 (pp-130) REVERT: A 465 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.6410 (mpt) REVERT: A 734 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7817 (tm-30) REVERT: B 86 ILE cc_start: 0.8379 (mm) cc_final: 0.7860 (tt) REVERT: B 283 MET cc_start: 0.8200 (mpp) cc_final: 0.7974 (mmp) REVERT: B 317 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6364 (mpt) REVERT: B 474 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 681 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 86 ILE cc_start: 0.8228 (mm) cc_final: 0.7687 (tt) REVERT: C 283 MET cc_start: 0.8201 (mpp) cc_final: 0.7889 (mmp) REVERT: C 290 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7217 (mmt-90) REVERT: C 474 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 734 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7596 (tm-30) REVERT: D 86 ILE cc_start: 0.8331 (mm) cc_final: 0.7797 (tt) REVERT: D 290 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7230 (mmt-90) REVERT: D 474 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 781 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: E 86 ILE cc_start: 0.8249 (mm) cc_final: 0.7788 (tt) REVERT: E 474 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7581 (tm-30) REVERT: E 502 MET cc_start: 0.8425 (mtp) cc_final: 0.8216 (mtt) REVERT: E 681 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7081 (t0) REVERT: F 86 ILE cc_start: 0.8232 (mm) cc_final: 0.7706 (tt) REVERT: F 286 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4744 (pp-130) REVERT: F 474 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7502 (tm-30) REVERT: F 502 MET cc_start: 0.8368 (mtp) cc_final: 0.8133 (mtt) REVERT: F 674 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: F 734 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7736 (tm-30) REVERT: G 86 ILE cc_start: 0.8257 (mm) cc_final: 0.7747 (tt) REVERT: G 286 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4741 (pp-130) REVERT: G 465 MET cc_start: 0.7698 (mpt) cc_final: 0.7461 (mmt) REVERT: G 474 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7458 (tm-30) REVERT: G 734 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7741 (tm-30) REVERT: H 86 ILE cc_start: 0.8287 (mm) cc_final: 0.7796 (tt) REVERT: H 474 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7548 (tm-30) REVERT: I 86 ILE cc_start: 0.8328 (mm) cc_final: 0.7779 (tt) REVERT: I 283 MET cc_start: 0.8214 (mpp) cc_final: 0.8012 (mmp) REVERT: I 290 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7197 (mmt-90) REVERT: I 681 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7376 (t0) REVERT: I 689 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8534 (p) REVERT: J 86 ILE cc_start: 0.8345 (mm) cc_final: 0.7826 (tt) REVERT: J 283 MET cc_start: 0.8342 (mpp) cc_final: 0.8095 (mmp) REVERT: J 290 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7131 (mmt180) REVERT: J 474 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7474 (tm-30) REVERT: J 681 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7347 (t0) REVERT: J 734 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7657 (tm-30) REVERT: K 86 ILE cc_start: 0.8313 (mm) cc_final: 0.7881 (tt) REVERT: K 283 MET cc_start: 0.8109 (mpp) cc_final: 0.7875 (mmp) REVERT: K 474 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7565 (tm-30) REVERT: L 86 ILE cc_start: 0.8248 (mm) cc_final: 0.7784 (tt) REVERT: L 286 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4883 (pp-130) REVERT: L 474 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7430 (tm-30) REVERT: L 674 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: L 734 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7653 (tm-30) outliers start: 139 outliers final: 72 residues processed: 382 average time/residue: 1.2721 time to fit residues: 695.0762 Evaluate side-chains 353 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 263 time to evaluate : 6.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 674 GLU Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 317 MET Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 691 ASP Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 691 ASP Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 674 GLU Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 304 optimal weight: 9.9990 chunk 814 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 531 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 905 optimal weight: 8.9990 chunk 751 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 299 optimal weight: 1.9990 chunk 475 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN D 537 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 505 GLN G 101 ASN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 77574 Z= 0.146 Angle : 0.488 12.651 105908 Z= 0.236 Chirality : 0.040 0.172 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.440 49.550 10428 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.65 % Allowed : 10.69 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.09), residues: 9450 helix: 1.64 (0.08), residues: 3956 sheet: -0.01 (0.16), residues: 1149 loop : -0.34 (0.09), residues: 4345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 25 HIS 0.004 0.000 HIS H 539 PHE 0.025 0.001 PHE E 233 TYR 0.010 0.001 TYR C 155 ARG 0.007 0.000 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 287 time to evaluate : 6.483 Fit side-chains REVERT: A 286 MET cc_start: 0.5000 (OUTLIER) cc_final: 0.4618 (pp-130) REVERT: A 290 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6940 (mmt180) REVERT: A 734 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 86 ILE cc_start: 0.8399 (mm) cc_final: 0.7838 (tt) REVERT: B 317 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6290 (mpt) REVERT: B 474 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 681 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7113 (t0) REVERT: C 86 ILE cc_start: 0.8236 (mm) cc_final: 0.7683 (tt) REVERT: C 283 MET cc_start: 0.8236 (mpp) cc_final: 0.7922 (mmp) REVERT: C 290 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7092 (mmt180) REVERT: C 474 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 734 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 86 ILE cc_start: 0.8279 (mm) cc_final: 0.7759 (tt) REVERT: D 290 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7147 (mmt-90) REVERT: D 474 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7403 (tm-30) REVERT: D 683 ASP cc_start: 0.7946 (m-30) cc_final: 0.7657 (m-30) REVERT: D 734 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7640 (tm-30) REVERT: D 781 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: E 86 ILE cc_start: 0.8306 (mm) cc_final: 0.7793 (tt) REVERT: E 474 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7538 (tm-30) REVERT: E 502 MET cc_start: 0.8292 (mtp) cc_final: 0.8078 (mtt) REVERT: F 86 ILE cc_start: 0.8193 (mm) cc_final: 0.7663 (tt) REVERT: F 286 MET cc_start: 0.4897 (OUTLIER) cc_final: 0.4551 (pp-130) REVERT: F 290 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7148 (mmt-90) REVERT: F 474 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 734 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7730 (tm-30) REVERT: G 86 ILE cc_start: 0.8255 (mm) cc_final: 0.7763 (tt) REVERT: G 286 MET cc_start: 0.4888 (OUTLIER) cc_final: 0.4493 (pp-130) REVERT: G 290 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7095 (mmt-90) REVERT: G 317 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6334 (mpt) REVERT: G 465 MET cc_start: 0.7696 (mpt) cc_final: 0.7303 (mmt) REVERT: G 474 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7478 (tm-30) REVERT: G 734 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7731 (tm-30) REVERT: H 86 ILE cc_start: 0.8301 (mm) cc_final: 0.7827 (tt) REVERT: H 283 MET cc_start: 0.7928 (mmp) cc_final: 0.7531 (mmp) REVERT: H 290 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6976 (mmt-90) REVERT: H 474 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7529 (tm-30) REVERT: I 86 ILE cc_start: 0.8305 (mm) cc_final: 0.7793 (tt) REVERT: I 186 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8447 (tm) REVERT: I 283 MET cc_start: 0.8209 (mpp) cc_final: 0.7997 (mmp) REVERT: I 290 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7130 (mmt-90) REVERT: I 681 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7367 (t0) REVERT: I 689 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8416 (p) REVERT: J 86 ILE cc_start: 0.8295 (mm) cc_final: 0.7787 (tt) REVERT: J 290 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7144 (mmt-90) REVERT: J 474 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7437 (tm-30) REVERT: J 681 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7335 (t0) REVERT: J 734 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7679 (tm-30) REVERT: K 86 ILE cc_start: 0.8332 (mm) cc_final: 0.7808 (tt) REVERT: K 474 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7586 (tm-30) REVERT: K 499 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9144 (OUTLIER) REVERT: K 502 MET cc_start: 0.8403 (mtm) cc_final: 0.7897 (mtm) REVERT: L 86 ILE cc_start: 0.8283 (mm) cc_final: 0.7761 (tt) REVERT: L 286 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4554 (pp-130) REVERT: L 474 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7421 (tm-30) REVERT: L 734 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7676 (tm-30) outliers start: 132 outliers final: 85 residues processed: 381 average time/residue: 1.2653 time to fit residues: 686.1821 Evaluate side-chains 371 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 266 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain D residue 781 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 290 ARG Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 763 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 290 ARG Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 689 THR Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 763 HIS Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 290 ARG Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain H residue 763 HIS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 763 HIS Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 763 HIS Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 763 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 515 optimal weight: 9.9990 chunk 661 optimal weight: 7.9990 chunk 512 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 505 optimal weight: 6.9990 chunk 902 optimal weight: 4.9990 chunk 564 optimal weight: 1.9990 chunk 550 optimal weight: 4.9990 chunk 416 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN G 167 ASN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 719 HIS B Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 77574 Z= 0.360 Angle : 0.560 14.882 105908 Z= 0.277 Chirality : 0.043 0.184 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.725 52.142 10428 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.83 % Allowed : 10.74 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 9450 helix: 1.32 (0.08), residues: 4036 sheet: -0.18 (0.16), residues: 1134 loop : -0.30 (0.09), residues: 4280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 25 HIS 0.007 0.001 HIS B 699 PHE 0.023 0.001 PHE B 233 TYR 0.009 0.001 TYR F 71 ARG 0.007 0.000 ARG I 738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 250 time to evaluate : 6.731 Fit side-chains REVERT: A 286 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.4830 (pp-130) REVERT: A 734 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 86 ILE cc_start: 0.8427 (mm) cc_final: 0.7952 (tt) REVERT: B 286 MET cc_start: 0.7665 (tpt) cc_final: 0.7443 (tpt) REVERT: B 317 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6418 (mpt) REVERT: B 474 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 681 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7090 (t0) REVERT: C 86 ILE cc_start: 0.8341 (mm) cc_final: 0.7858 (tt) REVERT: C 290 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7183 (mmt-90) REVERT: C 474 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 734 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 86 ILE cc_start: 0.8419 (mm) cc_final: 0.7903 (tt) REVERT: D 290 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7160 (mmt-90) REVERT: D 474 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 86 ILE cc_start: 0.8397 (mm) cc_final: 0.7907 (tt) REVERT: E 474 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7662 (tm-30) REVERT: E 681 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7106 (t0) REVERT: F 86 ILE cc_start: 0.8282 (mm) cc_final: 0.7810 (tt) REVERT: F 290 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7168 (mmt90) REVERT: F 474 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7600 (tm-30) REVERT: F 734 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7722 (tm-30) REVERT: G 86 ILE cc_start: 0.8385 (mm) cc_final: 0.7930 (tt) REVERT: G 317 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6280 (mpt) REVERT: G 474 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7568 (tm-30) REVERT: G 734 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7717 (tm-30) REVERT: H 86 ILE cc_start: 0.8383 (mm) cc_final: 0.7907 (tt) REVERT: H 290 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6965 (mmt-90) REVERT: H 474 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7649 (tm-30) REVERT: H 508 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8768 (ttmt) REVERT: I 86 ILE cc_start: 0.8432 (mm) cc_final: 0.7934 (tt) REVERT: I 186 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8600 (tm) REVERT: I 283 MET cc_start: 0.8196 (mpp) cc_final: 0.7989 (mmp) REVERT: I 290 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7154 (mmt-90) REVERT: I 681 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7368 (t0) REVERT: I 689 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8594 (p) REVERT: J 86 ILE cc_start: 0.8431 (mm) cc_final: 0.7931 (tt) REVERT: J 290 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7118 (mmt-90) REVERT: J 474 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7550 (tm-30) REVERT: J 681 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7332 (t0) REVERT: J 734 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7603 (tm-30) REVERT: K 86 ILE cc_start: 0.8401 (mm) cc_final: 0.7903 (tt) REVERT: K 474 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7638 (tm-30) REVERT: K 689 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8609 (p) REVERT: L 86 ILE cc_start: 0.8307 (mm) cc_final: 0.7830 (tt) REVERT: L 286 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4841 (pp-130) REVERT: L 474 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7491 (tm-30) REVERT: L 734 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7625 (tm-30) outliers start: 146 outliers final: 95 residues processed: 364 average time/residue: 1.3536 time to fit residues: 700.2327 Evaluate side-chains 359 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 246 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 290 ARG Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 763 HIS Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 689 THR Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 763 HIS Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 290 ARG Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 508 LYS Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain H residue 763 HIS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 691 ASP Chi-restraints excluded: chain I residue 763 HIS Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 364 MET Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 364 MET Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 689 THR Chi-restraints excluded: chain K residue 691 ASP Chi-restraints excluded: chain K residue 763 HIS Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 364 MET Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 763 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 0.0870 chunk 360 optimal weight: 5.9990 chunk 538 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 573 optimal weight: 0.0770 chunk 614 optimal weight: 0.9990 chunk 446 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 709 optimal weight: 20.0000 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 77574 Z= 0.176 Angle : 0.505 12.571 105908 Z= 0.246 Chirality : 0.041 0.163 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.513 50.838 10426 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.49 % Allowed : 11.09 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 9450 helix: 1.57 (0.08), residues: 3962 sheet: -0.36 (0.15), residues: 1190 loop : -0.37 (0.09), residues: 4298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 25 HIS 0.005 0.000 HIS H 539 PHE 0.026 0.001 PHE K 233 TYR 0.009 0.001 TYR A 71 ARG 0.007 0.000 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 267 time to evaluate : 6.536 Fit side-chains REVERT: A 286 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4769 (pp-130) REVERT: A 734 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 86 ILE cc_start: 0.8390 (mm) cc_final: 0.7882 (tt) REVERT: B 317 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6338 (mpt) REVERT: B 474 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 502 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8009 (mtt) REVERT: B 508 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8669 (ttmt) REVERT: B 681 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7101 (t0) REVERT: C 86 ILE cc_start: 0.8308 (mm) cc_final: 0.7838 (tt) REVERT: C 283 MET cc_start: 0.8118 (mpp) cc_final: 0.7902 (mmp) REVERT: C 290 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7195 (mmt-90) REVERT: C 474 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 734 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 86 ILE cc_start: 0.8381 (mm) cc_final: 0.7900 (tt) REVERT: D 290 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7215 (mmt-90) REVERT: D 474 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 502 MET cc_start: 0.8255 (mtp) cc_final: 0.8032 (mtt) REVERT: D 734 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7666 (tm-30) REVERT: E 86 ILE cc_start: 0.8326 (mm) cc_final: 0.7851 (tt) REVERT: E 474 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 86 ILE cc_start: 0.8255 (mm) cc_final: 0.7741 (tt) REVERT: F 290 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7276 (mmt90) REVERT: F 474 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7518 (tm-30) REVERT: F 734 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7737 (tm-30) REVERT: G 86 ILE cc_start: 0.8342 (mm) cc_final: 0.7865 (tt) REVERT: G 317 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6344 (mpt) REVERT: G 474 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7479 (tm-30) REVERT: G 734 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7727 (tm-30) REVERT: H 86 ILE cc_start: 0.8346 (mm) cc_final: 0.7836 (tt) REVERT: H 290 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6965 (mmt-90) REVERT: H 474 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7558 (tm-30) REVERT: I 86 ILE cc_start: 0.8389 (mm) cc_final: 0.7929 (tt) REVERT: I 186 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (tm) REVERT: I 283 MET cc_start: 0.8238 (mpp) cc_final: 0.8020 (mmp) REVERT: I 290 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7205 (mmt-90) REVERT: I 681 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7354 (t0) REVERT: I 689 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8449 (p) REVERT: J 86 ILE cc_start: 0.8379 (mm) cc_final: 0.7908 (tt) REVERT: J 290 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7162 (mmt-90) REVERT: J 474 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7470 (tm-30) REVERT: J 681 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7339 (t0) REVERT: J 734 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7673 (tm-30) REVERT: K 86 ILE cc_start: 0.8365 (mm) cc_final: 0.7846 (tt) REVERT: K 474 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7565 (tm-30) REVERT: L 86 ILE cc_start: 0.8280 (mm) cc_final: 0.7807 (tt) REVERT: L 286 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.4847 (pp-130) REVERT: L 290 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7045 (mmt-90) REVERT: L 474 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7390 (tm-30) REVERT: L 734 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7687 (tm-30) outliers start: 119 outliers final: 80 residues processed: 349 average time/residue: 1.2925 time to fit residues: 640.2849 Evaluate side-chains 357 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 259 time to evaluate : 6.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 290 ARG Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 763 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 689 THR Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 763 HIS Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 290 ARG Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain H residue 763 HIS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 499 ILE Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 763 HIS Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 763 HIS Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 290 ARG Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 763 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 5.9990 chunk 864 optimal weight: 6.9990 chunk 788 optimal weight: 10.0000 chunk 840 optimal weight: 7.9990 chunk 506 optimal weight: 4.9990 chunk 366 optimal weight: 0.9990 chunk 660 optimal weight: 0.0770 chunk 257 optimal weight: 3.9990 chunk 759 optimal weight: 9.9990 chunk 795 optimal weight: 2.9990 chunk 837 optimal weight: 0.4980 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 77574 Z= 0.169 Angle : 0.498 12.249 105908 Z= 0.241 Chirality : 0.040 0.160 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.365 52.116 10426 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.48 % Allowed : 11.11 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.09), residues: 9450 helix: 1.67 (0.08), residues: 3949 sheet: -0.28 (0.16), residues: 1172 loop : -0.36 (0.09), residues: 4329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 25 HIS 0.004 0.001 HIS H 539 PHE 0.024 0.001 PHE B 233 TYR 0.012 0.001 TYR C 71 ARG 0.007 0.000 ARG K 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 269 time to evaluate : 6.595 Fit side-chains REVERT: A 286 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4791 (pp-130) REVERT: A 734 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 86 ILE cc_start: 0.8383 (mm) cc_final: 0.7894 (tt) REVERT: B 474 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 508 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8699 (ttmt) REVERT: B 681 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7116 (t0) REVERT: C 86 ILE cc_start: 0.8337 (mm) cc_final: 0.7886 (tt) REVERT: C 283 MET cc_start: 0.8097 (mpp) cc_final: 0.7853 (mmp) REVERT: C 290 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7099 (mmt-90) REVERT: C 474 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 734 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7625 (tm-30) REVERT: D 86 ILE cc_start: 0.8368 (mm) cc_final: 0.7890 (tt) REVERT: D 290 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7139 (mmt-90) REVERT: D 474 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 734 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 86 ILE cc_start: 0.8343 (mm) cc_final: 0.7876 (tt) REVERT: E 474 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7587 (tm-30) REVERT: E 689 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8424 (p) REVERT: F 86 ILE cc_start: 0.8310 (mm) cc_final: 0.7781 (tt) REVERT: F 290 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7305 (mmt90) REVERT: F 474 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7527 (tm-30) REVERT: F 734 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7733 (tm-30) REVERT: G 86 ILE cc_start: 0.8385 (mm) cc_final: 0.7880 (tt) REVERT: G 317 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6168 (mpt) REVERT: G 474 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7467 (tm-30) REVERT: G 734 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7715 (tm-30) REVERT: H 86 ILE cc_start: 0.8322 (mm) cc_final: 0.7829 (tt) REVERT: H 290 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6872 (mmt-90) REVERT: H 465 MET cc_start: 0.7824 (mpt) cc_final: 0.7370 (mpt) REVERT: H 474 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7481 (tm-30) REVERT: H 499 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9211 (pp) REVERT: I 86 ILE cc_start: 0.8388 (mm) cc_final: 0.7936 (tt) REVERT: I 186 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (tm) REVERT: I 283 MET cc_start: 0.8256 (mpp) cc_final: 0.8028 (mmp) REVERT: I 290 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7140 (mmt-90) REVERT: I 681 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7383 (t0) REVERT: I 689 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8410 (p) REVERT: J 86 ILE cc_start: 0.8391 (mm) cc_final: 0.7930 (tt) REVERT: J 290 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7134 (mmt-90) REVERT: J 474 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7455 (tm-30) REVERT: J 681 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7369 (t0) REVERT: J 734 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7686 (tm-30) REVERT: K 86 ILE cc_start: 0.8357 (mm) cc_final: 0.7888 (tt) REVERT: K 474 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7591 (tm-30) REVERT: K 689 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8478 (p) REVERT: L 86 ILE cc_start: 0.8311 (mm) cc_final: 0.7792 (tt) REVERT: L 286 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4844 (pp-130) REVERT: L 290 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7029 (mmt-90) REVERT: L 474 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7381 (tm-30) REVERT: L 734 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 118 outliers final: 78 residues processed: 356 average time/residue: 1.3110 time to fit residues: 671.9190 Evaluate side-chains 355 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 258 time to evaluate : 6.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 290 ARG Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 763 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 689 THR Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 763 HIS Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 290 ARG Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain H residue 763 HIS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 763 HIS Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 689 THR Chi-restraints excluded: chain K residue 763 HIS Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 290 ARG Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 763 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 7.9990 chunk 888 optimal weight: 20.0000 chunk 542 optimal weight: 5.9990 chunk 421 optimal weight: 0.4980 chunk 617 optimal weight: 5.9990 chunk 932 optimal weight: 0.9990 chunk 858 optimal weight: 30.0000 chunk 742 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 573 optimal weight: 0.0060 chunk 455 optimal weight: 7.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 77574 Z= 0.190 Angle : 0.513 16.578 105908 Z= 0.248 Chirality : 0.041 0.161 11324 Planarity : 0.004 0.049 13940 Dihedral : 4.369 53.018 10426 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.33 % Allowed : 11.39 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 9450 helix: 1.66 (0.08), residues: 3949 sheet: -0.18 (0.16), residues: 1142 loop : -0.34 (0.09), residues: 4359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 25 HIS 0.004 0.001 HIS H 539 PHE 0.028 0.001 PHE K 233 TYR 0.012 0.001 TYR B 155 ARG 0.007 0.000 ARG K 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18900 Ramachandran restraints generated. 9450 Oldfield, 0 Emsley, 9450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 261 time to evaluate : 6.439 Fit side-chains REVERT: A 286 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4863 (pp-130) REVERT: A 734 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 86 ILE cc_start: 0.8346 (mm) cc_final: 0.7846 (tt) REVERT: B 474 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 508 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8669 (ttmt) REVERT: B 681 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7119 (t0) REVERT: C 86 ILE cc_start: 0.8319 (mm) cc_final: 0.7850 (tt) REVERT: C 283 MET cc_start: 0.8088 (mpp) cc_final: 0.7840 (mmp) REVERT: C 290 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7116 (mmt180) REVERT: C 474 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 734 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7622 (tm-30) REVERT: D 86 ILE cc_start: 0.8393 (mm) cc_final: 0.7923 (tt) REVERT: D 290 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7208 (mmt-90) REVERT: D 474 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7486 (tm-30) REVERT: D 734 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7648 (tm-30) REVERT: E 86 ILE cc_start: 0.8325 (mm) cc_final: 0.7814 (tt) REVERT: E 474 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7583 (tm-30) REVERT: E 502 MET cc_start: 0.8416 (mtm) cc_final: 0.8093 (mtt) REVERT: E 681 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7169 (t0) REVERT: F 86 ILE cc_start: 0.8275 (mm) cc_final: 0.7735 (tt) REVERT: F 290 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7306 (mmt90) REVERT: F 474 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7520 (tm-30) REVERT: F 734 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7731 (tm-30) REVERT: G 86 ILE cc_start: 0.8373 (mm) cc_final: 0.7910 (tt) REVERT: G 317 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6264 (mpt) REVERT: G 474 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 734 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 86 ILE cc_start: 0.8312 (mm) cc_final: 0.7821 (tt) REVERT: H 290 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6929 (mmt-90) REVERT: H 474 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7567 (tm-30) REVERT: H 508 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (ttmt) REVERT: I 86 ILE cc_start: 0.8403 (mm) cc_final: 0.7940 (tt) REVERT: I 283 MET cc_start: 0.8242 (mpp) cc_final: 0.8014 (mmp) REVERT: I 290 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7165 (mmt-90) REVERT: I 681 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7382 (t0) REVERT: I 689 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (p) REVERT: J 86 ILE cc_start: 0.8423 (mm) cc_final: 0.7972 (tt) REVERT: J 290 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7215 (mmt-90) REVERT: J 474 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7467 (tm-30) REVERT: J 681 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7392 (t0) REVERT: J 734 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7674 (tm-30) REVERT: K 86 ILE cc_start: 0.8321 (mm) cc_final: 0.7848 (tt) REVERT: K 465 MET cc_start: 0.7968 (mpt) cc_final: 0.7359 (mpt) REVERT: K 474 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7597 (tm-30) REVERT: L 86 ILE cc_start: 0.8270 (mm) cc_final: 0.7779 (tt) REVERT: L 286 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4852 (pp-130) REVERT: L 290 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7062 (mmt-90) REVERT: L 474 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7393 (tm-30) REVERT: L 734 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7676 (tm-30) outliers start: 106 outliers final: 80 residues processed: 344 average time/residue: 1.2653 time to fit residues: 623.0093 Evaluate side-chains 354 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 257 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 763 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 681 ASP Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 763 HIS Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 571 CYS Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 681 ASP Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 763 HIS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 290 ARG Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 689 THR Chi-restraints excluded: chain F residue 691 ASP Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 763 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 317 MET Chi-restraints excluded: chain G residue 613 ILE Chi-restraints excluded: chain G residue 689 THR Chi-restraints excluded: chain G residue 691 ASP Chi-restraints excluded: chain G residue 763 HIS Chi-restraints excluded: chain G residue 785 ASP Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 290 ARG Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 508 LYS Chi-restraints excluded: chain H residue 571 CYS Chi-restraints excluded: chain H residue 691 ASP Chi-restraints excluded: chain H residue 763 HIS Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 266 ILE Chi-restraints excluded: chain I residue 290 ARG Chi-restraints excluded: chain I residue 474 GLU Chi-restraints excluded: chain I residue 534 VAL Chi-restraints excluded: chain I residue 613 ILE Chi-restraints excluded: chain I residue 681 ASP Chi-restraints excluded: chain I residue 689 THR Chi-restraints excluded: chain I residue 763 HIS Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 251 LEU Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 290 ARG Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 689 THR Chi-restraints excluded: chain K residue 763 HIS Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 286 MET Chi-restraints excluded: chain L residue 290 ARG Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 689 THR Chi-restraints excluded: chain L residue 691 ASP Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 763 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 8.9990 chunk 790 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 684 optimal weight: 0.0770 chunk 109 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 743 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 763 optimal weight: 0.0010 chunk 94 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.106196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073017 restraints weight = 369936.003| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 5.10 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 77574 Z= 0.206 Angle : 0.518 15.207 105908 Z= 0.249 Chirality : 0.041 0.160 11324 Planarity : 0.004 0.050 13940 Dihedral : 4.397 54.433 10426 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.38 % Allowed : 11.32 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 9450 helix: 1.65 (0.08), residues: 3945 sheet: -0.20 (0.16), residues: 1140 loop : -0.35 (0.09), residues: 4365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 25 HIS 0.004 0.001 HIS H 539 PHE 0.028 0.001 PHE K 233 TYR 0.012 0.001 TYR D 71 ARG 0.007 0.000 ARG K 738 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14506.13 seconds wall clock time: 258 minutes 41.72 seconds (15521.72 seconds total)