Starting phenix.real_space_refine on Sun Sep 29 19:46:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/09_2024/8ioe_35617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/09_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_35617/09_2024/8ioe_35617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/09_2024/8ioe_35617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/09_2024/8ioe_35617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioe_35617/09_2024/8ioe_35617.cif" } 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. Time to flip 8 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 58.68, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.90 Conformation dependent library (CDL) restraints added in 13.4 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... Secondary structure from input PDB file: 459 helices and 60 sheets defined 51.4% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 63 through 82 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 94 through 105 Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.885A pdb=" N PHE A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 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 182 removed outlier: 3.707A pdb=" N GLU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.824A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 4.314A pdb=" N PHE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 247 through 276 removed outlier: 3.874A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.990A pdb=" N LEU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.645A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.713A pdb=" N ARG A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER A 365 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.060A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.582A pdb=" N VAL A 436 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 439 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 471 through 472 No H-bonds generated for 'chain 'A' and resid 471 through 472' Processing helix chain 'A' and resid 474 through 474 No H-bonds generated for 'chain 'A' and resid 474 through 474' Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.553A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 3.515A pdb=" N ASN A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.764A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 601 through 612 removed outlier: 3.513A pdb=" N ALA A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 680 through 688 Processing helix chain 'A' and resid 702 through 709 removed outlier: 4.235A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.502A pdb=" N HIS A 715 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 716 " --> pdb=" O HIS A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 755 through 758 removed outlier: 3.871A pdb=" N ARG A 758 " --> pdb=" O PRO A 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 758' Processing helix chain 'A' and resid 759 through 760 No H-bonds generated for 'chain 'A' and resid 759 through 760' Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'B' and resid 14 through 38 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 63 through 82 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 94 through 105 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.881A pdb=" N PHE B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 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 179 through 182 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.669A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 4.263A pdb=" N PHE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 247 through 276 removed outlier: 3.855A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.010A pdb=" N LEU B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.647A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.708A pdb=" N ARG B 362 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N MET B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N SER B 365 " --> pdb=" O ARG B 362 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN B 367 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.099A pdb=" N LEU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 401 through 416 removed outlier: 4.018A pdb=" N LEU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.555A pdb=" N VAL B 436 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 439 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 469 through 483 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 499 through 516 removed outlier: 3.555A pdb=" N ASN B 504 " --> pdb=" O ASP B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 removed outlier: 3.768A pdb=" N LYS B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 601 through 612 removed outlier: 3.534A pdb=" N ALA B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 653 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 702 through 709 removed outlier: 4.189A pdb=" N HIS B 706 " --> pdb=" O PRO B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 removed outlier: 4.579A pdb=" N ASN B 716 " --> pdb=" O HIS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 739 removed outlier: 3.543A pdb=" N ALA B 736 " --> pdb=" O PRO B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 754 Processing helix chain 'B' and resid 755 through 758 removed outlier: 3.851A pdb=" N ARG B 758 " --> pdb=" O PRO B 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 758' Processing helix chain 'B' and resid 759 through 760 No H-bonds generated for 'chain 'B' and resid 759 through 760' Processing helix chain 'B' and resid 761 through 783 Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'C' and resid 14 through 38 removed outlier: 3.553A pdb=" N ALA C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.649A pdb=" N HIS C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.865A pdb=" N PHE C 129 " --> pdb=" O PHE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 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 179 through 182 Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.757A pdb=" N TRP C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.257A pdb=" N PHE C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 247 through 276 removed outlier: 3.835A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 338 through 343 removed outlier: 4.027A pdb=" N LEU C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 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 359 through 367 removed outlier: 3.772A pdb=" N ARG C 362 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N MET C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER C 365 " --> pdb=" O ARG C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.084A pdb=" N LEU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.522A pdb=" N ASP C 386 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 416 removed outlier: 4.091A pdb=" N LEU C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 439 removed outlier: 3.649A pdb=" N VAL C 439 " --> pdb=" O VAL C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.528A pdb=" N ASP C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 483 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 499 through 516 removed outlier: 3.597A pdb=" N ASN C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 556 removed outlier: 3.781A pdb=" N LYS C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 580 Processing helix chain 'C' and resid 601 through 612 removed outlier: 3.511A pdb=" N ALA C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 653 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 680 through 688 Processing helix chain 'C' and resid 702 through 709 removed outlier: 4.274A pdb=" N HIS C 706 " --> pdb=" O PRO C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 716 removed outlier: 4.546A pdb=" N ASN C 716 " --> pdb=" O HIS C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 739 removed outlier: 3.550A pdb=" N ALA C 736 " --> pdb=" O PRO C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 754 Processing helix chain 'C' and resid 755 through 758 removed outlier: 3.839A pdb=" N ARG C 758 " --> pdb=" O PRO C 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 758' Processing helix chain 'C' and resid 759 through 760 No H-bonds generated for 'chain 'C' and resid 759 through 760' Processing helix chain 'C' and resid 761 through 783 Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'D' and resid 14 through 38 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 49 through 53 Processing helix chain 'D' and resid 63 through 82 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 94 through 105 Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.892A pdb=" N PHE D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 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 179 through 182 Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.733A pdb=" N TRP D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 removed outlier: 4.265A pdb=" N PHE D 195 " --> pdb=" O HIS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 247 through 276 removed outlier: 3.854A pdb=" N GLY D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 313 Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 338 through 343 removed outlier: 4.021A pdb=" N LEU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.648A pdb=" N ILE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.681A pdb=" N ARG D 362 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N MET D 364 " --> pdb=" O ASP D 361 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER D 365 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 367 " --> pdb=" O MET D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 4.076A pdb=" N LEU D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 401 through 416 removed outlier: 4.092A pdb=" N LEU D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 439 removed outlier: 3.578A pdb=" N VAL D 436 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 439 " --> pdb=" O VAL D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.638A pdb=" N LEU D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 516 removed outlier: 3.554A pdb=" N ASN D 504 " --> pdb=" O ASP D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 556 removed outlier: 3.870A pdb=" N LYS D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 Processing helix chain 'D' and resid 601 through 612 removed outlier: 3.515A pdb=" N ALA D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 653 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 680 through 688 Processing helix chain 'D' and resid 702 through 709 removed outlier: 4.253A pdb=" N HIS D 706 " --> pdb=" O PRO D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 716 removed outlier: 4.552A pdb=" N ASN D 716 " --> pdb=" O HIS D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 739 removed outlier: 3.539A pdb=" N ALA D 736 " --> pdb=" O PRO D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 754 Processing helix chain 'D' and resid 755 through 758 removed outlier: 3.837A pdb=" N ARG D 758 " --> pdb=" O PRO D 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 755 through 758' Processing helix chain 'D' and resid 759 through 760 No H-bonds generated for 'chain 'D' and resid 759 through 760' Processing helix chain 'D' and resid 761 through 783 Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'E' and resid 14 through 38 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 63 through 82 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 94 through 105 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.988A pdb=" N PHE E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 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 182 removed outlier: 3.695A pdb=" N GLU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 178 through 182' Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.765A pdb=" N TRP E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 4.255A pdb=" N PHE E 195 " --> pdb=" O HIS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 247 through 276 removed outlier: 3.832A pdb=" N GLY E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.993A pdb=" N LEU E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 357 removed outlier: 3.661A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 367 removed outlier: 3.649A pdb=" N ARG E 362 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N MET E 364 " --> pdb=" O ASP E 361 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER E 365 " --> pdb=" O ARG E 362 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN E 367 " --> pdb=" O MET E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 376 removed outlier: 4.097A pdb=" N LEU E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 401 through 416 removed outlier: 4.021A pdb=" N LEU E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 439 removed outlier: 3.579A pdb=" N VAL E 436 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL E 439 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 456 Processing helix chain 'E' and resid 469 through 483 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 498 removed outlier: 4.433A pdb=" N HIS E 497 " --> pdb=" O ALA E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 516 removed outlier: 3.504A pdb=" N ASN E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 removed outlier: 3.789A pdb=" N LYS E 556 " --> pdb=" O LEU E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 580 Processing helix chain 'E' and resid 601 through 612 removed outlier: 3.531A pdb=" N ALA E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 653 Processing helix chain 'E' and resid 665 through 670 Processing helix chain 'E' and resid 680 through 688 Processing helix chain 'E' and resid 702 through 709 removed outlier: 4.192A pdb=" N HIS E 706 " --> pdb=" O PRO E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 716 removed outlier: 3.509A pdb=" N HIS E 715 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN E 716 " --> pdb=" O HIS E 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 712 through 716' Processing helix chain 'E' and resid 731 through 739 removed outlier: 3.570A pdb=" N ALA E 736 " --> pdb=" O PRO E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 754 Processing helix chain 'E' and resid 755 through 758 removed outlier: 3.856A pdb=" N ARG E 758 " --> pdb=" O PRO E 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 755 through 758' Processing helix chain 'E' and resid 759 through 760 No H-bonds generated for 'chain 'E' and resid 759 through 760' Processing helix chain 'E' and resid 761 through 783 Processing helix chain 'E' and resid 786 through 791 Processing helix chain 'F' and resid 14 through 38 removed outlier: 3.544A pdb=" N ALA F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 63 through 82 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 94 through 105 Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.900A pdb=" N PHE F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 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 182 removed outlier: 3.630A pdb=" N GLU F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 178 through 182' Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.711A pdb=" N TRP F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.252A pdb=" N PHE F 195 " --> pdb=" O HIS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'F' and resid 247 through 276 removed outlier: 3.841A pdb=" N GLY F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 338 through 343 removed outlier: 4.004A pdb=" N LEU F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 357 removed outlier: 3.650A pdb=" N ILE F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 367 removed outlier: 3.717A pdb=" N ARG F 362 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N MET F 364 " --> pdb=" O ASP F 361 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER F 365 " --> pdb=" O ARG F 362 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F 367 " --> pdb=" O MET F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 401 through 416 removed outlier: 4.041A pdb=" N LEU F 405 " --> pdb=" O SER F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 439 removed outlier: 3.593A pdb=" N VAL F 436 " --> pdb=" O LEU F 433 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 439 " --> pdb=" O VAL F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 456 Processing helix chain 'F' and resid 469 through 483 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 499 through 516 removed outlier: 3.549A pdb=" N ASN F 504 " --> pdb=" O ASP F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 556 removed outlier: 3.759A pdb=" N LYS F 556 " --> pdb=" O LEU F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 580 Processing helix chain 'F' and resid 601 through 612 removed outlier: 3.518A pdb=" N ALA F 606 " --> pdb=" O ALA F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 653 Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 680 through 688 Processing helix chain 'F' and resid 702 through 709 removed outlier: 4.221A pdb=" N HIS F 706 " --> pdb=" O PRO F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 716 removed outlier: 4.615A pdb=" N ASN F 716 " --> pdb=" O HIS F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 739 removed outlier: 3.517A pdb=" N ALA F 736 " --> pdb=" O PRO F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 754 Processing helix chain 'F' and resid 755 through 758 removed outlier: 3.860A pdb=" N ARG F 758 " --> pdb=" O PRO F 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 755 through 758' Processing helix chain 'F' and resid 759 through 760 No H-bonds generated for 'chain 'F' and resid 759 through 760' Processing helix chain 'F' and resid 761 through 783 Processing helix chain 'F' and resid 786 through 791 Processing helix chain 'G' and resid 14 through 38 Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 63 through 82 removed outlier: 3.642A pdb=" N HIS G 73 " --> pdb=" O PHE G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.901A pdb=" N PHE G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 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 182 removed outlier: 3.704A pdb=" N GLU G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 178 through 182' Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.853A pdb=" N TRP G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.282A pdb=" N PHE G 195 " --> pdb=" O HIS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 236 Processing helix chain 'G' and resid 247 through 276 removed outlier: 3.883A pdb=" N GLY G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 313 Processing helix chain 'G' and resid 323 through 336 Processing helix chain 'G' and resid 338 through 343 removed outlier: 3.983A pdb=" N LEU G 342 " --> pdb=" O ARG G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 357 removed outlier: 3.620A pdb=" N ILE G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 367 removed outlier: 3.762A pdb=" N ARG G 362 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET G 364 " --> pdb=" O ASP G 361 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER G 365 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 387 Processing helix chain 'G' and resid 401 through 416 removed outlier: 4.058A pdb=" N LEU G 405 " --> pdb=" O SER G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 439 removed outlier: 3.560A pdb=" N VAL G 436 " --> pdb=" O LEU G 433 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL G 439 " --> pdb=" O VAL G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 456 Processing helix chain 'G' and resid 469 through 483 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 499 through 516 Processing helix chain 'G' and resid 548 through 556 removed outlier: 3.761A pdb=" N LYS G 556 " --> pdb=" O LEU G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 568 through 580 Processing helix chain 'G' and resid 601 through 612 removed outlier: 3.519A pdb=" N ALA G 606 " --> pdb=" O ALA G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 653 Processing helix chain 'G' and resid 665 through 670 Processing helix chain 'G' and resid 680 through 688 Processing helix chain 'G' and resid 702 through 709 removed outlier: 4.212A pdb=" N HIS G 706 " --> pdb=" O PRO G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 712 through 716 removed outlier: 4.606A pdb=" N ASN G 716 " --> pdb=" O HIS G 713 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 739 removed outlier: 3.531A pdb=" N ALA G 736 " --> pdb=" O PRO G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 742 through 754 Processing helix chain 'G' and resid 755 through 758 removed outlier: 3.872A pdb=" N ARG G 758 " --> pdb=" O PRO G 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 755 through 758' Processing helix chain 'G' and resid 759 through 760 No H-bonds generated for 'chain 'G' and resid 759 through 760' Processing helix chain 'G' and resid 761 through 783 Processing helix chain 'G' and resid 786 through 791 Processing helix chain 'H' and resid 14 through 38 Processing helix chain 'H' and resid 49 through 53 Processing helix chain 'H' and resid 63 through 82 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 Processing helix chain 'H' and resid 106 through 112 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.892A pdb=" N PHE H 129 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 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 179 through 182 Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.672A pdb=" N TRP H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 removed outlier: 4.255A pdb=" N PHE H 195 " --> pdb=" O HIS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 236 Processing helix chain 'H' and resid 247 through 276 removed outlier: 3.831A pdb=" N GLY H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 313 Processing helix chain 'H' and resid 323 through 336 Processing helix chain 'H' and resid 338 through 343 removed outlier: 4.009A pdb=" N LEU H 342 " --> pdb=" O ARG H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 357 removed outlier: 3.661A pdb=" N ILE H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 367 removed outlier: 3.652A pdb=" N ARG H 362 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET H 364 " --> pdb=" O ASP H 361 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER H 365 " --> pdb=" O ARG H 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN H 367 " --> pdb=" O MET H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 376 removed outlier: 4.088A pdb=" N LEU H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 387 Processing helix chain 'H' and resid 401 through 416 removed outlier: 4.021A pdb=" N LEU H 405 " --> pdb=" O SER H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 439 removed outlier: 3.559A pdb=" N VAL H 436 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL H 439 " --> pdb=" O VAL H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 456 Processing helix chain 'H' and resid 469 through 483 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 499 through 516 Processing helix chain 'H' and resid 548 through 556 removed outlier: 3.752A pdb=" N LYS H 556 " --> pdb=" O LEU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 568 through 580 Processing helix chain 'H' and resid 601 through 612 removed outlier: 3.534A pdb=" N ALA H 606 " --> pdb=" O ALA H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 636 through 653 Processing helix chain 'H' and resid 665 through 670 Processing helix chain 'H' and resid 680 through 688 Processing helix chain 'H' and resid 702 through 709 removed outlier: 4.173A pdb=" N HIS H 706 " --> pdb=" O PRO H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 712 through 716 removed outlier: 4.555A pdb=" N ASN H 716 " --> pdb=" O HIS H 713 " (cutoff:3.500A) Processing helix chain 'H' and resid 731 through 739 removed outlier: 3.713A pdb=" N ALA H 736 " --> pdb=" O PRO H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 742 through 754 Processing helix chain 'H' and resid 755 through 758 removed outlier: 3.854A pdb=" N ARG H 758 " --> pdb=" O PRO H 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 755 through 758' Processing helix chain 'H' and resid 759 through 760 No H-bonds generated for 'chain 'H' and resid 759 through 760' Processing helix chain 'H' and resid 761 through 783 Processing helix chain 'H' and resid 786 through 791 Processing helix chain 'I' and resid 14 through 38 Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 63 through 82 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 94 through 105 Processing helix chain 'I' and resid 106 through 112 Processing helix chain 'I' and resid 118 through 129 removed outlier: 3.912A pdb=" N PHE I 129 " --> pdb=" O PHE I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 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 182 removed outlier: 3.784A pdb=" N GLU I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 178 through 182' Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.840A pdb=" N TRP I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 196 removed outlier: 4.272A pdb=" N PHE I 195 " --> pdb=" O HIS I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 236 Processing helix chain 'I' and resid 247 through 276 removed outlier: 3.880A pdb=" N GLY I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 313 Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 338 through 343 removed outlier: 4.003A pdb=" N LEU I 342 " --> pdb=" O ARG I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 357 removed outlier: 3.649A pdb=" N ILE I 356 " --> pdb=" O GLU I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 367 removed outlier: 3.715A pdb=" N ARG I 362 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N MET I 364 " --> pdb=" O ASP I 361 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER I 365 " --> pdb=" O ARG I 362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN I 367 " --> pdb=" O MET I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 376 removed outlier: 4.068A pdb=" N LEU I 375 " --> pdb=" O ASN I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 387 Processing helix chain 'I' and resid 401 through 416 removed outlier: 4.112A pdb=" N LEU I 405 " --> pdb=" O SER I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 439 removed outlier: 3.562A pdb=" N VAL I 436 " --> pdb=" O LEU I 433 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL I 439 " --> pdb=" O VAL I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 456 Processing helix chain 'I' and resid 469 through 483 removed outlier: 3.567A pdb=" N LEU I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 516 removed outlier: 3.555A pdb=" N ASN I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 556 removed outlier: 3.758A pdb=" N LYS I 556 " --> pdb=" O LEU I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 580 Processing helix chain 'I' and resid 601 through 612 removed outlier: 3.510A pdb=" N ALA I 606 " --> pdb=" O ALA I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 636 through 653 Processing helix chain 'I' and resid 665 through 670 Processing helix chain 'I' and resid 680 through 688 Processing helix chain 'I' and resid 702 through 709 removed outlier: 4.269A pdb=" N HIS I 706 " --> pdb=" O PRO I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 716 removed outlier: 4.531A pdb=" N ASN I 716 " --> pdb=" O HIS I 713 " (cutoff:3.500A) Processing helix chain 'I' and resid 731 through 739 removed outlier: 3.600A pdb=" N ALA I 736 " --> pdb=" O PRO I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 742 through 754 Processing helix chain 'I' and resid 755 through 758 removed outlier: 3.840A pdb=" N ARG I 758 " --> pdb=" O PRO I 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 755 through 758' Processing helix chain 'I' and resid 759 through 760 No H-bonds generated for 'chain 'I' and resid 759 through 760' Processing helix chain 'I' and resid 761 through 783 Processing helix chain 'I' and resid 786 through 791 Processing helix chain 'J' and resid 14 through 38 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 63 through 82 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 Processing helix chain 'J' and resid 106 through 112 Processing helix chain 'J' and resid 118 through 129 removed outlier: 3.884A pdb=" N PHE J 129 " --> pdb=" O PHE J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 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 179 through 182 Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.695A pdb=" N TRP J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 196 removed outlier: 4.245A pdb=" N PHE J 195 " --> pdb=" O HIS J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 236 Processing helix chain 'J' and resid 247 through 276 removed outlier: 3.886A pdb=" N GLY J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 313 Processing helix chain 'J' and resid 323 through 336 Processing helix chain 'J' and resid 338 through 343 removed outlier: 4.024A pdb=" N LEU J 342 " --> pdb=" O ARG J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 356 removed outlier: 3.645A pdb=" N ILE J 356 " --> pdb=" O GLU J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 367 removed outlier: 3.682A pdb=" N ARG J 362 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N MET J 364 " --> pdb=" O ASP J 361 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N SER J 365 " --> pdb=" O ARG J 362 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN J 367 " --> pdb=" O MET J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 376 removed outlier: 4.108A pdb=" N LEU J 375 " --> pdb=" O ASN J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 387 Processing helix chain 'J' and resid 401 through 416 removed outlier: 4.092A pdb=" N LEU J 405 " --> pdb=" O SER J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 439 removed outlier: 3.616A pdb=" N VAL J 439 " --> pdb=" O VAL J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 Processing helix chain 'J' and resid 469 through 483 removed outlier: 3.625A pdb=" N LEU J 477 " --> pdb=" O LEU J 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 516 removed outlier: 3.559A pdb=" N ASN J 504 " --> pdb=" O ASP J 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 556 removed outlier: 3.777A pdb=" N LYS J 556 " --> pdb=" O LEU J 552 " (cutoff:3.500A) Processing helix chain 'J' and resid 568 through 580 Processing helix chain 'J' and resid 601 through 612 removed outlier: 3.518A pdb=" N ALA J 606 " --> pdb=" O ALA J 602 " (cutoff:3.500A) Processing helix chain 'J' and resid 636 through 653 Processing helix chain 'J' and resid 665 through 670 Processing helix chain 'J' and resid 680 through 688 Processing helix chain 'J' and resid 702 through 709 removed outlier: 4.246A pdb=" N HIS J 706 " --> pdb=" O PRO J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 712 through 716 removed outlier: 4.555A pdb=" N ASN J 716 " --> pdb=" O HIS J 713 " (cutoff:3.500A) Processing helix chain 'J' and resid 731 through 739 removed outlier: 3.538A pdb=" N ALA J 736 " --> pdb=" O PRO J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 754 Processing helix chain 'J' and resid 755 through 758 removed outlier: 3.837A pdb=" N ARG J 758 " --> pdb=" O PRO J 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 755 through 758' Processing helix chain 'J' and resid 759 through 760 No H-bonds generated for 'chain 'J' and resid 759 through 760' Processing helix chain 'J' and resid 761 through 783 Processing helix chain 'J' and resid 786 through 791 Processing helix chain 'K' and resid 14 through 37 Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 63 through 82 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 94 through 105 Processing helix chain 'K' and resid 106 through 112 Processing helix chain 'K' and resid 118 through 129 removed outlier: 3.945A pdb=" N PHE K 129 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 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 179 through 182 Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.675A pdb=" N TRP K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 removed outlier: 4.237A pdb=" N PHE K 195 " --> pdb=" O HIS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 224 removed outlier: 3.547A pdb=" N ARG K 223 " --> pdb=" O THR K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 236 Processing helix chain 'K' and resid 247 through 276 removed outlier: 3.851A pdb=" N GLY K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 313 Processing helix chain 'K' and resid 323 through 336 Processing helix chain 'K' and resid 338 through 343 removed outlier: 3.995A pdb=" N LEU K 342 " --> pdb=" O ARG K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 357 removed outlier: 3.674A pdb=" N ILE K 356 " --> pdb=" O GLU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 367 removed outlier: 3.646A pdb=" N ARG K 362 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N MET K 364 " --> pdb=" O ASP K 361 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER K 365 " --> pdb=" O ARG K 362 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN K 367 " --> pdb=" O MET K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 376 removed outlier: 4.092A pdb=" N LEU K 375 " --> pdb=" O ASN K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 387 Processing helix chain 'K' and resid 401 through 416 removed outlier: 4.038A pdb=" N LEU K 405 " --> pdb=" O SER K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 439 removed outlier: 3.579A pdb=" N VAL K 436 " --> pdb=" O LEU K 433 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL K 439 " --> pdb=" O VAL K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 449 through 456 Processing helix chain 'K' and resid 469 through 483 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 499 through 516 removed outlier: 3.502A pdb=" N ASN K 504 " --> pdb=" O ASP K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 556 removed outlier: 3.807A pdb=" N LYS K 556 " --> pdb=" O LEU K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 580 Processing helix chain 'K' and resid 601 through 612 removed outlier: 3.537A pdb=" N ALA K 606 " --> pdb=" O ALA K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 653 Processing helix chain 'K' and resid 665 through 670 Processing helix chain 'K' and resid 680 through 688 Processing helix chain 'K' and resid 702 through 709 removed outlier: 4.207A pdb=" N HIS K 706 " --> pdb=" O PRO K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 712 through 716 removed outlier: 4.552A pdb=" N ASN K 716 " --> pdb=" O HIS K 713 " (cutoff:3.500A) Processing helix chain 'K' and resid 731 through 739 removed outlier: 3.565A pdb=" N ALA K 736 " --> pdb=" O PRO K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 742 through 754 Processing helix chain 'K' and resid 755 through 758 removed outlier: 3.856A pdb=" N ARG K 758 " --> pdb=" O PRO K 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 755 through 758' Processing helix chain 'K' and resid 759 through 760 No H-bonds generated for 'chain 'K' and resid 759 through 760' Processing helix chain 'K' and resid 761 through 783 Processing helix chain 'K' and resid 786 through 791 Processing helix chain 'L' and resid 14 through 38 Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 63 through 82 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 94 through 105 Processing helix chain 'L' and resid 106 through 112 Processing helix chain 'L' and resid 118 through 129 removed outlier: 3.918A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 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 182 removed outlier: 3.670A pdb=" N GLU L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 178 through 182' Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.608A pdb=" N TRP L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 196 removed outlier: 4.243A pdb=" N PHE L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 236 Processing helix chain 'L' and resid 247 through 276 removed outlier: 3.863A pdb=" N GLY L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 309 through 313 Processing helix chain 'L' and resid 323 through 336 Processing helix chain 'L' and resid 338 through 343 removed outlier: 4.008A pdb=" N LEU L 342 " --> pdb=" O ARG L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 3.648A pdb=" N ILE L 356 " --> pdb=" O GLU L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 367 removed outlier: 3.716A pdb=" N ARG L 362 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N MET L 364 " --> pdb=" O ASP L 361 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER L 365 " --> pdb=" O ARG L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 375 Processing helix chain 'L' and resid 383 through 387 Processing helix chain 'L' and resid 401 through 416 removed outlier: 4.062A pdb=" N LEU L 405 " --> pdb=" O SER L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 439 removed outlier: 3.589A pdb=" N VAL L 436 " --> pdb=" O LEU L 433 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 439 " --> pdb=" O VAL L 436 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 456 Processing helix chain 'L' and resid 469 through 483 removed outlier: 3.665A pdb=" N LEU L 477 " --> pdb=" O LEU L 473 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 516 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 556 removed outlier: 4.290A pdb=" N ASP L 551 " --> pdb=" O PRO L 547 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS L 556 " --> pdb=" O LEU L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 568 through 580 Processing helix chain 'L' and resid 601 through 612 removed outlier: 3.520A pdb=" N ALA L 606 " --> pdb=" O ALA L 602 " (cutoff:3.500A) Processing helix chain 'L' and resid 636 through 653 Processing helix chain 'L' and resid 665 through 670 Processing helix chain 'L' and resid 680 through 688 Processing helix chain 'L' and resid 702 through 709 removed outlier: 4.209A pdb=" N HIS L 706 " --> pdb=" O PRO L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 712 through 716 removed outlier: 4.580A pdb=" N ASN L 716 " --> pdb=" O HIS L 713 " (cutoff:3.500A) Processing helix chain 'L' and resid 731 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 742 through 754 Processing helix chain 'L' and resid 755 through 758 removed outlier: 3.777A pdb=" N ARG L 758 " --> pdb=" O PRO L 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 755 through 758' Processing helix chain 'L' and resid 759 through 760 No H-bonds generated for 'chain 'L' and resid 759 through 760' Processing helix chain 'L' and resid 761 through 783 Processing helix chain 'L' and resid 786 through 791 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.661A pdb=" N HIS A 596 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 6.725A pdb=" N ARG A 421 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA A 490 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 423 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N TYR A 492 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY A 487 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LEU A 529 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE A 489 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 531 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 491 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 526 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 589 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 528 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 443 removed outlier: 5.843A pdb=" N LYS A 442 " --> pdb=" O SER A 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.770A pdb=" N VAL A 630 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASN A 697 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 632 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 177 removed outlier: 6.468A pdb=" N VAL B 172 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE B 207 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N HIS B 209 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 176 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 398 through 399 removed outlier: 3.623A pdb=" N HIS B 596 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing sheet with id=AA8, 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: 7.147A pdb=" N GLY B 487 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU B 529 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 489 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER B 531 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 491 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 5.847A pdb=" N LYS B 442 " --> pdb=" O SER B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 615 removed outlier: 6.815A pdb=" N VAL B 630 " --> pdb=" O ILE B 695 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN B 697 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 632 " --> pdb=" O ASN B 697 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 171 through 177 Processing sheet with id=AB3, 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=AB4, 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: 6.651A pdb=" N ARG C 421 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA C 490 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE C 423 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR C 492 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY C 487 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N LEU C 529 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE C 489 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER C 531 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR C 491 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 442 through 443 removed outlier: 5.766A pdb=" N LYS C 442 " --> pdb=" O SER C 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 613 through 615 removed outlier: 6.767A pdb=" N VAL C 630 " --> pdb=" O ILE C 695 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN C 697 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 632 " --> pdb=" O ASN C 697 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 171 through 177 removed outlier: 6.445A pdb=" N VAL D 172 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE D 207 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS D 174 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N HIS D 209 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 176 " --> pdb=" O HIS D 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 398 through 399 removed outlier: 3.651A pdb=" N HIS D 596 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing sheet with id=AB9, 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: 6.658A pdb=" N ARG D 421 " --> pdb=" O PHE D 488 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA D 490 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE D 423 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR D 492 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY D 487 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU D 529 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE D 489 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER D 531 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR D 491 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 442 through 443 removed outlier: 5.834A pdb=" N LYS D 442 " --> pdb=" O SER D 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 613 through 615 removed outlier: 6.766A pdb=" N VAL D 630 " --> pdb=" O ILE D 695 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN D 697 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA D 632 " --> pdb=" O ASN D 697 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 171 through 177 removed outlier: 6.521A pdb=" N VAL E 172 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE E 207 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS E 174 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N HIS E 209 " --> pdb=" O CYS E 174 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 176 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 287 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 398 through 399 removed outlier: 3.624A pdb=" N HIS E 596 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 6.770A pdb=" N ARG E 421 " --> pdb=" O PHE E 488 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ALA E 490 " --> pdb=" O ARG E 421 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE E 423 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N TYR E 492 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY E 487 " --> pdb=" O ASN E 527 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU E 529 " --> pdb=" O GLY E 487 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE E 489 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER E 531 " --> pdb=" O PHE E 489 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR E 491 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 442 through 443 removed outlier: 5.791A pdb=" N LYS E 442 " --> pdb=" O SER E 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 613 through 615 removed outlier: 6.758A pdb=" N VAL E 630 " --> pdb=" O ILE E 695 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN E 697 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA E 632 " --> pdb=" O ASN E 697 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 171 through 177 Processing sheet with id=AC9, first strand: chain 'F' and resid 398 through 399 removed outlier: 3.631A pdb=" N HIS F 596 " --> pdb=" O ALA F 399 " (cutoff:3.500A) Processing sheet with id=AD1, 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: 6.687A pdb=" N ARG F 421 " --> pdb=" O PHE F 488 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA F 490 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE F 423 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N TYR F 492 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY F 487 " --> pdb=" O ASN F 527 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N LEU F 529 " --> pdb=" O GLY F 487 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE F 489 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER F 531 " --> pdb=" O PHE F 489 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR F 491 " --> pdb=" O SER F 531 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU F 526 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE F 589 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE F 528 " --> pdb=" O ILE F 589 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 442 through 443 removed outlier: 5.847A pdb=" N LYS F 442 " --> pdb=" O SER F 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 613 through 615 removed outlier: 6.735A pdb=" N VAL F 630 " --> pdb=" O ILE F 695 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN F 697 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA F 632 " --> pdb=" O ASN F 697 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 171 through 177 Processing sheet with id=AD5, first strand: chain 'G' and resid 398 through 399 removed outlier: 3.643A pdb=" N HIS G 596 " --> pdb=" O ALA G 399 " (cutoff:3.500A) Processing sheet with id=AD6, 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: 6.682A pdb=" N ARG G 421 " --> pdb=" O PHE G 488 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA G 490 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE G 423 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR G 492 " --> pdb=" O PHE G 423 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY G 487 " --> pdb=" O ASN G 527 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N LEU G 529 " --> pdb=" O GLY G 487 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE G 489 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER G 531 " --> pdb=" O PHE G 489 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR G 491 " --> pdb=" O SER G 531 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU G 526 " --> pdb=" O ASN G 587 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE G 589 " --> pdb=" O LEU G 526 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE G 528 " --> pdb=" O ILE G 589 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 442 through 443 removed outlier: 5.737A pdb=" N LYS G 442 " --> pdb=" O SER G 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 613 through 615 removed outlier: 6.767A pdb=" N VAL G 630 " --> pdb=" O ILE G 695 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN G 697 " --> pdb=" O VAL G 630 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA G 632 " --> pdb=" O ASN G 697 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 171 through 177 removed outlier: 3.506A pdb=" N ILE H 287 " --> pdb=" O PRO H 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 398 through 399 removed outlier: 3.619A pdb=" N HIS H 596 " --> pdb=" O ALA H 399 " (cutoff:3.500A) Processing sheet with id=AE2, 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: 6.741A pdb=" N ARG H 421 " --> pdb=" O PHE H 488 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ALA H 490 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE H 423 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N TYR H 492 " --> pdb=" O PHE H 423 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLY H 487 " --> pdb=" O ASN H 527 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU H 529 " --> pdb=" O GLY H 487 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE H 489 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N SER H 531 " --> pdb=" O PHE H 489 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR H 491 " --> pdb=" O SER H 531 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 442 through 443 removed outlier: 5.791A pdb=" N LYS H 442 " --> pdb=" O SER H 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 613 through 615 removed outlier: 6.801A pdb=" N VAL H 630 " --> pdb=" O ILE H 695 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASN H 697 " --> pdb=" O VAL H 630 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA H 632 " --> pdb=" O ASN H 697 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 88 through 89 removed outlier: 7.459A pdb=" N VAL I 88 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLY I 177 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 398 through 399 removed outlier: 3.648A pdb=" N HIS I 596 " --> pdb=" O ALA I 399 " (cutoff:3.500A) Processing sheet with id=AE7, 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: 7.164A pdb=" N GLY I 487 " --> pdb=" O ASN I 527 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LEU I 529 " --> pdb=" O GLY I 487 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE I 489 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER I 531 " --> pdb=" O PHE I 489 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR I 491 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 442 through 443 removed outlier: 5.700A pdb=" N LYS I 442 " --> pdb=" O SER I 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'I' and resid 613 through 615 removed outlier: 6.750A pdb=" N VAL I 630 " --> pdb=" O ILE I 695 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN I 697 " --> pdb=" O VAL I 630 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA I 632 " --> pdb=" O ASN I 697 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 171 through 177 Processing sheet with id=AF2, first strand: chain 'J' and resid 398 through 399 removed outlier: 3.644A pdb=" N HIS J 596 " --> pdb=" O ALA J 399 " (cutoff:3.500A) Processing sheet with id=AF3, 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: 6.598A pdb=" N ARG J 421 " --> pdb=" O PHE J 488 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA J 490 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE J 423 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N TYR J 492 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY J 487 " --> pdb=" O ASN J 527 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N LEU J 529 " --> pdb=" O GLY J 487 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE J 489 " --> pdb=" O LEU J 529 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER J 531 " --> pdb=" O PHE J 489 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR J 491 " --> pdb=" O SER J 531 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU J 526 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE J 589 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE J 528 " --> pdb=" O ILE J 589 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 442 through 443 removed outlier: 5.734A pdb=" N LYS J 442 " --> pdb=" O SER J 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'J' and resid 613 through 615 removed outlier: 6.744A pdb=" N VAL J 630 " --> pdb=" O ILE J 695 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN J 697 " --> pdb=" O VAL J 630 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA J 632 " --> pdb=" O ASN J 697 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 171 through 177 removed outlier: 6.481A pdb=" N VAL K 172 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE K 207 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS K 174 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS K 209 " --> pdb=" O CYS K 174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE K 176 " --> pdb=" O HIS K 209 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 398 through 399 removed outlier: 3.574A pdb=" N HIS K 596 " --> pdb=" O ALA K 399 " (cutoff:3.500A) Processing sheet with id=AF8, 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: 6.767A pdb=" N ARG K 421 " --> pdb=" O PHE K 488 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA K 490 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE K 423 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N TYR K 492 " --> pdb=" O PHE K 423 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY K 487 " --> pdb=" O ASN K 527 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU K 529 " --> pdb=" O GLY K 487 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE K 489 " --> pdb=" O LEU K 529 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER K 531 " --> pdb=" O PHE K 489 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR K 491 " --> pdb=" O SER K 531 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 442 through 443 removed outlier: 5.802A pdb=" N LYS K 442 " --> pdb=" O SER K 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'K' and resid 613 through 615 removed outlier: 6.754A pdb=" N VAL K 630 " --> pdb=" O ILE K 695 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN K 697 " --> pdb=" O VAL K 630 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA K 632 " --> pdb=" O ASN K 697 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 171 through 177 Processing sheet with id=AG3, first strand: chain 'L' and resid 398 through 399 removed outlier: 3.585A pdb=" N HIS L 596 " --> pdb=" O ALA L 399 " (cutoff:3.500A) Processing sheet with id=AG4, 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: 6.637A pdb=" N ARG L 421 " --> pdb=" O PHE L 488 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA L 490 " --> pdb=" O ARG L 421 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE L 423 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N TYR L 492 " --> pdb=" O PHE L 423 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY L 487 " --> pdb=" O ASN L 527 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU L 529 " --> pdb=" O GLY L 487 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE L 489 " --> pdb=" O LEU L 529 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N SER L 531 " --> pdb=" O PHE L 489 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR L 491 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU L 526 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE L 589 " --> pdb=" O LEU L 526 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE L 528 " --> pdb=" O ILE L 589 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 442 through 443 removed outlier: 5.762A pdb=" N LYS L 442 " --> pdb=" O SER L 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'L' and resid 613 through 615 removed outlier: 6.746A pdb=" N VAL L 630 " --> pdb=" O ILE L 695 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN L 697 " --> pdb=" O VAL L 630 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA L 632 " --> pdb=" O ASN L 697 " (cutoff:3.500A) 3206 hydrogen bonds defined for protein. 9066 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: 31.36 Time building geometry restraints manager: 15.67 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: 0.00 - 1.47: 104008 1.47 - 2.95: 1483 2.95 - 4.42: 323 4.42 - 5.89: 70 5.89 - 7.36: 24 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 - 17.97: 43079 17.97 - 35.93: 2170 35.93 - 53.90: 301 53.90 - 71.87: 20 71.87 - 89.84: 6 Dihedral angle restraints: 45576 sinusoidal: 18236 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 45573 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: 1197 2.62 - 3.19: 66682 3.19 - 3.76: 125642 3.76 - 4.33: 176545 4.33 - 4.90: 291083 Nonbonded interactions: 661149 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 661144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 2.750 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: 2.200 Check model and map are aligned: 0.420 Set scattering table: 0.530 Process input model: 168.030 Find NCS groups from input model: 4.440 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.680 ------------------------------------------------------------------------------- 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= 0.239 Angle : 0.493 7.365 105908 Z= 0.254 Chirality : 0.042 0.186 11324 Planarity : 0.005 0.059 13940 Dihedral : 10.430 89.835 27988 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 : 6.331 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: 1.2629 time to fit residues: 1099.0681 Evaluate side-chains 291 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 283 time to evaluate : 6.251 ------------------------------------------------------------------------------- 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: 3.9990 chunk 393 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 chunk 478 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 733 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 chunk 446 optimal weight: 7.9990 chunk 546 optimal weight: 50.0000 chunk 849 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 167 ASN B 209 HIS C 167 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS D 167 ASN ** D 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN D 537 GLN E 35 GLN E 101 ASN E 167 ASN E 209 HIS ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 717 ASN F 167 ASN F 537 GLN G 35 GLN G 167 ASN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN H 35 GLN H 167 ASN H 209 HIS H 730 ASN I 167 ASN ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 505 GLN J 101 ASN J 167 ASN J 326 HIS J 505 GLN J 537 GLN K 35 GLN K 101 ASN K 167 ASN K 209 HIS L 101 ASN L 537 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 77574 Z= 0.271 Angle : 0.555 8.415 105908 Z= 0.282 Chirality : 0.044 0.165 11324 Planarity : 0.005 0.054 13940 Dihedral : 5.710 87.279 10488 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.63 % Allowed : 7.87 % Favored : 90.50 % 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: 0.65 (0.09), residues: 9450 helix: 1.23 (0.08), residues: 4213 sheet: 0.48 (0.16), residues: 1144 loop : -0.35 (0.09), residues: 4093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 25 HIS 0.009 0.001 HIS H 539 PHE 0.012 0.001 PHE I 195 TYR 0.011 0.001 TYR H 71 ARG 0.009 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 467 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 337 time to evaluate : 6.284 Fit side-chains REVERT: A 500 ASP cc_start: 0.8426 (t0) cc_final: 0.8212 (t0) REVERT: A 674 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: A 734 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7605 (tm-30) REVERT: B 86 ILE cc_start: 0.8332 (mm) cc_final: 0.7820 (tt) REVERT: B 474 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 283 MET cc_start: 0.8232 (mpp) cc_final: 0.7933 (mmp) REVERT: C 474 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 683 ASP cc_start: 0.8237 (m-30) cc_final: 0.8033 (m-30) REVERT: D 474 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 500 ASP cc_start: 0.8360 (t0) cc_final: 0.8141 (t0) REVERT: D 516 GLU cc_start: 0.8050 (mp0) cc_final: 0.7758 (mm-30) REVERT: D 683 ASP cc_start: 0.8197 (m-30) cc_final: 0.7991 (m-30) REVERT: D 781 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: E 86 ILE cc_start: 0.8264 (mm) cc_final: 0.7743 (tt) REVERT: E 474 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7661 (tm-30) REVERT: F 86 ILE cc_start: 0.8189 (mm) cc_final: 0.7960 (mt) REVERT: F 474 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7545 (tm-30) REVERT: F 674 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: F 683 ASP cc_start: 0.8267 (m-30) cc_final: 0.8050 (m-30) REVERT: G 13 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5655 (pp) REVERT: G 86 ILE cc_start: 0.8175 (mm) cc_final: 0.7687 (tt) REVERT: G 474 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 674 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: G 683 ASP cc_start: 0.8261 (m-30) cc_final: 0.8053 (m-30) REVERT: G 734 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7618 (tm-30) REVERT: H 474 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7626 (tm-30) REVERT: H 683 ASP cc_start: 0.8176 (m-30) cc_final: 0.7972 (m-30) REVERT: I 283 MET cc_start: 0.8246 (mpp) cc_final: 0.8037 (mmp) REVERT: I 516 GLU cc_start: 0.8006 (mp0) cc_final: 0.7761 (mm-30) REVERT: I 683 ASP cc_start: 0.8205 (m-30) cc_final: 0.8002 (m-30) REVERT: J 283 MET cc_start: 0.8284 (mpp) cc_final: 0.8011 (mmp) REVERT: J 474 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7549 (tm-30) REVERT: J 683 ASP cc_start: 0.8191 (m-30) cc_final: 0.7982 (m-30) REVERT: K 86 ILE cc_start: 0.8256 (mm) cc_final: 0.7735 (tt) REVERT: K 283 MET cc_start: 0.8244 (mpp) cc_final: 0.8044 (mmp) REVERT: K 474 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7691 (tm-30) REVERT: L 465 MET cc_start: 0.8709 (mpp) cc_final: 0.8499 (mmm) REVERT: L 474 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7450 (tm-30) REVERT: L 674 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: L 683 ASP cc_start: 0.8260 (m-30) cc_final: 0.8044 (m-30) outliers start: 130 outliers final: 55 residues processed: 436 average time/residue: 1.1516 time to fit residues: 728.4463 Evaluate side-chains 344 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 283 time to evaluate : 6.267 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 674 GLU 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 613 ILE Chi-restraints excluded: chain B residue 733 LEU 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 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 781 GLN Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 674 GLU Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain G residue 13 LEU 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 G residue 674 GLU 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 613 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 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 729 ILE 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 733 LEU Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 674 GLU 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: 8.9990 chunk 263 optimal weight: 20.0000 chunk 707 optimal weight: 3.9990 chunk 578 optimal weight: 10.0000 chunk 234 optimal weight: 50.0000 chunk 851 optimal weight: 6.9990 chunk 919 optimal weight: 2.9990 chunk 758 optimal weight: 0.9980 chunk 844 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 683 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 HIS ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 HIS L 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1614 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= 0.220 Angle : 0.522 8.524 105908 Z= 0.259 Chirality : 0.042 0.195 11324 Planarity : 0.004 0.051 13940 Dihedral : 5.555 83.849 10476 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.63 % Allowed : 8.65 % Favored : 89.72 % 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: 0.88 (0.09), residues: 9450 helix: 1.64 (0.08), residues: 4127 sheet: 0.25 (0.16), residues: 1142 loop : -0.34 (0.09), residues: 4181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 25 HIS 0.007 0.001 HIS H 539 PHE 0.009 0.001 PHE K 125 TYR 0.010 0.001 TYR G 71 ARG 0.007 0.000 ARG K 738 *********************** 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 431 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 301 time to evaluate : 6.496 Fit side-chains REVERT: A 674 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: A 734 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 86 ILE cc_start: 0.8363 (mm) cc_final: 0.7828 (tt) REVERT: B 474 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 86 ILE cc_start: 0.8295 (mm) cc_final: 0.7717 (tt) REVERT: C 283 MET cc_start: 0.8237 (mpp) cc_final: 0.7911 (mmp) REVERT: C 474 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 683 ASP cc_start: 0.8226 (m-30) cc_final: 0.8020 (m-30) REVERT: C 734 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 86 ILE cc_start: 0.8313 (mm) cc_final: 0.7734 (tt) REVERT: D 474 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7516 (tm-30) REVERT: D 516 GLU cc_start: 0.8046 (mp0) cc_final: 0.7768 (mm-30) REVERT: D 734 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 781 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: E 86 ILE cc_start: 0.8303 (mm) cc_final: 0.7782 (tt) REVERT: E 474 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7625 (tm-30) REVERT: F 465 MET cc_start: 0.8671 (mmm) cc_final: 0.8188 (mmt) REVERT: F 474 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7540 (tm-30) REVERT: F 674 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: F 734 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7599 (tm-30) REVERT: G 474 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7448 (tm-30) REVERT: G 674 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: G 734 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7664 (tm-30) REVERT: H 86 ILE cc_start: 0.8305 (mm) cc_final: 0.7764 (tt) REVERT: H 474 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7620 (tm-30) REVERT: I 86 ILE cc_start: 0.8303 (mm) cc_final: 0.7709 (tt) REVERT: I 205 LEU cc_start: 0.9128 (tp) cc_final: 0.8707 (mp) REVERT: I 283 MET cc_start: 0.8352 (mpp) cc_final: 0.8116 (mmp) REVERT: I 516 GLU cc_start: 0.8020 (mp0) cc_final: 0.7693 (mm-30) REVERT: J 86 ILE cc_start: 0.8322 (mm) cc_final: 0.7734 (tt) REVERT: J 205 LEU cc_start: 0.9129 (tp) cc_final: 0.8724 (mp) REVERT: J 283 MET cc_start: 0.8326 (mpp) cc_final: 0.8039 (mmp) REVERT: J 474 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7495 (tm-30) REVERT: J 683 ASP cc_start: 0.8191 (m-30) cc_final: 0.7988 (m-30) REVERT: J 734 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7578 (tm-30) REVERT: K 86 ILE cc_start: 0.8319 (mm) cc_final: 0.7806 (tt) REVERT: K 283 MET cc_start: 0.8270 (mpp) cc_final: 0.8028 (mmp) REVERT: K 474 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7631 (tm-30) REVERT: L 474 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7456 (tm-30) REVERT: L 674 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: L 734 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7603 (tm-30) outliers start: 130 outliers final: 57 residues processed: 404 average time/residue: 1.2045 time to fit residues: 706.6580 Evaluate side-chains 325 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 6.339 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 674 GLU Chi-restraints excluded: chain B residue 135 ILE 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 B residue 733 LEU Chi-restraints excluded: chain C residue 266 ILE 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 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 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 613 ILE Chi-restraints excluded: chain F residue 674 GLU 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 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 381 LEU Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 613 ILE Chi-restraints excluded: chain H residue 733 LEU 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 534 VAL Chi-restraints excluded: chain I residue 613 ILE 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 729 ILE 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 613 ILE Chi-restraints excluded: chain L residue 674 GLU 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: 0.9980 chunk 640 optimal weight: 4.9990 chunk 441 optimal weight: 0.0270 chunk 94 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 571 optimal weight: 6.9990 chunk 854 optimal weight: 1.9990 chunk 904 optimal weight: 5.9990 chunk 446 optimal weight: 0.9980 chunk 809 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 209 HIS B 209 HIS ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 730 ASN K 209 HIS K 505 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 77574 Z= 0.162 Angle : 0.506 8.807 105908 Z= 0.249 Chirality : 0.041 0.162 11324 Planarity : 0.004 0.051 13940 Dihedral : 5.350 86.181 10476 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.54 % Allowed : 9.13 % Favored : 89.33 % 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: 1.01 (0.09), residues: 9450 helix: 1.84 (0.08), residues: 4123 sheet: 0.17 (0.16), residues: 1144 loop : -0.33 (0.09), residues: 4183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 25 HIS 0.005 0.001 HIS H 539 PHE 0.010 0.001 PHE K 125 TYR 0.009 0.001 TYR F 71 ARG 0.008 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 423 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 300 time to evaluate : 6.445 Fit side-chains REVERT: A 734 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 86 ILE cc_start: 0.8367 (mm) cc_final: 0.7833 (tt) REVERT: B 474 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 674 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: C 86 ILE cc_start: 0.8245 (mm) cc_final: 0.7645 (tt) REVERT: C 186 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8443 (tm) REVERT: C 205 LEU cc_start: 0.9205 (tp) cc_final: 0.8744 (mp) REVERT: C 290 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7103 (mmt180) REVERT: C 474 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 734 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 86 ILE cc_start: 0.8294 (mm) cc_final: 0.7724 (tt) REVERT: D 186 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8456 (tm) REVERT: D 290 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7135 (mmt180) REVERT: D 474 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 516 GLU cc_start: 0.8008 (mp0) cc_final: 0.7723 (mm-30) REVERT: D 683 ASP cc_start: 0.8202 (m-30) cc_final: 0.7999 (m-30) REVERT: D 734 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 781 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: E 474 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7582 (tm-30) REVERT: E 502 MET cc_start: 0.8316 (mtp) cc_final: 0.8090 (mtt) REVERT: F 286 MET cc_start: 0.4846 (OUTLIER) cc_final: 0.4618 (pp-130) REVERT: F 474 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 734 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7638 (tm-30) REVERT: G 286 MET cc_start: 0.4783 (OUTLIER) cc_final: 0.4575 (pp-130) REVERT: G 474 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7504 (tm-30) REVERT: G 674 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: G 734 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 87 TYR cc_start: 0.8402 (t80) cc_final: 0.8188 (t80) REVERT: H 474 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7584 (tm-30) REVERT: H 674 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: I 86 ILE cc_start: 0.8261 (mm) cc_final: 0.7647 (tt) REVERT: I 205 LEU cc_start: 0.9128 (tp) cc_final: 0.8771 (mp) REVERT: I 283 MET cc_start: 0.8396 (mpp) cc_final: 0.8147 (mmp) REVERT: I 290 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7095 (mmt180) REVERT: I 516 GLU cc_start: 0.8031 (mp0) cc_final: 0.7648 (mm-30) REVERT: J 86 ILE cc_start: 0.8252 (mm) cc_final: 0.7652 (tt) REVERT: J 186 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8450 (tm) REVERT: J 205 LEU cc_start: 0.9097 (tp) cc_final: 0.8706 (mp) REVERT: J 290 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7070 (mmt180) REVERT: J 474 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7496 (tm-30) REVERT: J 734 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7609 (tm-30) REVERT: K 86 ILE cc_start: 0.8337 (mm) cc_final: 0.7825 (tt) REVERT: K 87 TYR cc_start: 0.8373 (t80) cc_final: 0.8099 (t80) REVERT: K 283 MET cc_start: 0.8319 (mpp) cc_final: 0.8041 (mmp) REVERT: K 474 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7607 (tm-30) REVERT: K 674 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: L 474 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7450 (tm-30) REVERT: L 734 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7650 (tm-30) outliers start: 123 outliers final: 63 residues processed: 396 average time/residue: 1.3139 time to fit residues: 750.1760 Evaluate side-chains 343 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 266 time to evaluate : 6.362 ------------------------------------------------------------------------------- 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 534 VAL 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 571 CYS Chi-restraints excluded: chain B residue 674 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 186 LEU 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 D residue 186 LEU 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 726 VAL Chi-restraints excluded: chain D residue 774 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 571 CYS Chi-restraints excluded: chain E residue 613 ILE 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 286 MET Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain F residue 774 ASP 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 286 MET Chi-restraints excluded: chain G residue 499 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 381 LEU Chi-restraints excluded: chain H residue 674 GLU 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 J residue 186 LEU 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 499 ILE Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 726 VAL Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 613 ILE Chi-restraints excluded: chain K residue 674 GLU Chi-restraints excluded: chain L residue 251 LEU Chi-restraints excluded: chain L residue 266 ILE Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 726 VAL Chi-restraints excluded: chain L residue 733 LEU Chi-restraints excluded: chain L residue 774 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 3.9990 chunk 513 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 673 optimal weight: 1.9990 chunk 373 optimal weight: 0.1980 chunk 772 optimal weight: 3.9990 chunk 625 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 chunk 812 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 209 HIS ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 GLN H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 77574 Z= 0.198 Angle : 0.517 12.347 105908 Z= 0.254 Chirality : 0.042 0.162 11324 Planarity : 0.004 0.050 13940 Dihedral : 5.283 88.845 10472 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.83 % Allowed : 9.18 % Favored : 88.99 % 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: 1.02 (0.09), residues: 9450 helix: 1.89 (0.08), residues: 4130 sheet: 0.06 (0.16), residues: 1145 loop : -0.33 (0.09), residues: 4175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 25 HIS 0.005 0.001 HIS H 539 PHE 0.040 0.001 PHE E 233 TYR 0.011 0.001 TYR J 155 ARG 0.007 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 426 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 280 time to evaluate : 6.350 Fit side-chains REVERT: A 286 MET cc_start: 0.4770 (OUTLIER) cc_final: 0.4569 (pp-130) REVERT: A 734 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 86 ILE cc_start: 0.8425 (mm) cc_final: 0.7843 (tt) REVERT: B 474 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 186 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (tm) REVERT: C 283 MET cc_start: 0.8160 (mpp) cc_final: 0.7905 (mmp) REVERT: C 290 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7165 (mmt180) REVERT: C 474 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 683 ASP cc_start: 0.8108 (m-30) cc_final: 0.7825 (m-30) REVERT: C 734 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 86 ILE cc_start: 0.8292 (mm) cc_final: 0.7733 (tt) REVERT: D 186 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8512 (tm) REVERT: D 290 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7197 (mmt180) REVERT: D 474 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 516 GLU cc_start: 0.7980 (mp0) cc_final: 0.7630 (mm-30) REVERT: D 683 ASP cc_start: 0.8214 (m-30) cc_final: 0.8009 (m-30) REVERT: D 734 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 781 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: E 86 ILE cc_start: 0.8303 (mm) cc_final: 0.7746 (tt) REVERT: E 474 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7622 (tm-30) REVERT: F 286 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.4648 (pp-130) REVERT: F 474 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 681 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7513 (t0) REVERT: F 734 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 286 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.4594 (pp-130) REVERT: G 474 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7560 (tm-30) REVERT: G 559 ARG cc_start: 0.8441 (ptt-90) cc_final: 0.8156 (mtm110) REVERT: G 674 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: G 734 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7671 (tm-30) REVERT: H 290 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6925 (mmt180) REVERT: H 474 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7725 (tm-30) REVERT: I 86 ILE cc_start: 0.8309 (mm) cc_final: 0.7713 (tt) REVERT: I 205 LEU cc_start: 0.9154 (tp) cc_final: 0.8766 (mp) REVERT: I 290 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7125 (mmt180) REVERT: I 516 GLU cc_start: 0.8039 (mp0) cc_final: 0.7728 (mm-30) REVERT: I 683 ASP cc_start: 0.8096 (m-30) cc_final: 0.7824 (m-30) REVERT: J 86 ILE cc_start: 0.8303 (mm) cc_final: 0.7704 (tt) REVERT: J 186 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8521 (tm) REVERT: J 205 LEU cc_start: 0.9128 (tp) cc_final: 0.8717 (mp) REVERT: J 283 MET cc_start: 0.8203 (mpp) cc_final: 0.7985 (mmp) REVERT: J 290 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7069 (mmt180) REVERT: J 474 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7717 (tm-30) REVERT: J 734 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7583 (tm-30) REVERT: K 86 ILE cc_start: 0.8392 (mm) cc_final: 0.7879 (tt) REVERT: K 87 TYR cc_start: 0.8472 (t80) cc_final: 0.8231 (t80) REVERT: K 283 MET cc_start: 0.8278 (mpp) cc_final: 0.8004 (mmp) REVERT: K 474 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7721 (tm-30) REVERT: L 286 MET cc_start: 0.4860 (OUTLIER) cc_final: 0.4614 (pp-130) REVERT: L 474 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7524 (tm-30) REVERT: L 681 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7520 (t0) REVERT: L 734 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7637 (tm-30) outliers start: 146 outliers final: 61 residues processed: 391 average time/residue: 1.3021 time to fit residues: 720.0901 Evaluate side-chains 332 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 255 time to evaluate : 6.316 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL 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 571 CYS Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 186 LEU 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 D residue 186 LEU 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 726 VAL 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 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 286 MET Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 681 ASP 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 286 MET Chi-restraints excluded: chain G residue 499 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 290 ARG 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 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 J residue 186 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 726 VAL Chi-restraints excluded: chain J residue 729 ILE 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 534 VAL 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 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 681 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: 2.9990 chunk 814 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 531 optimal weight: 4.9990 chunk 223 optimal weight: 8.9990 chunk 905 optimal weight: 9.9990 chunk 751 optimal weight: 5.9990 chunk 419 optimal weight: 30.0000 chunk 75 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 475 optimal weight: 1.9990 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 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 719 HIS B B 209 HIS B 328 GLN C 328 GLN D 328 GLN E 328 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** G 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 719 HIS B ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN J 328 GLN K 209 HIS K 328 GLN L 167 ASN L 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 GLN L 719 HIS B Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1902 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= 0.336 Angle : 0.571 16.897 105908 Z= 0.283 Chirality : 0.044 0.177 11324 Planarity : 0.004 0.050 13940 Dihedral : 5.476 89.372 10472 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.74 % Allowed : 9.43 % Favored : 88.83 % 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: 0.90 (0.09), residues: 9450 helix: 1.76 (0.08), residues: 4118 sheet: -0.04 (0.16), residues: 1126 loop : -0.34 (0.09), residues: 4206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 25 HIS 0.007 0.001 HIS H 539 PHE 0.025 0.001 PHE E 233 TYR 0.009 0.001 TYR E 87 ARG 0.007 0.000 ARG B 515 *********************** 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 404 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 265 time to evaluate : 6.507 Fit side-chains REVERT: A 286 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4767 (pp-130) REVERT: A 734 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 86 ILE cc_start: 0.8439 (mm) cc_final: 0.7900 (tt) REVERT: B 474 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 508 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8734 (ttmt) REVERT: B 681 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7162 (t0) REVERT: C 86 ILE cc_start: 0.8319 (mm) cc_final: 0.7788 (tt) REVERT: C 186 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8618 (tm) REVERT: C 283 MET cc_start: 0.8131 (mpp) cc_final: 0.7850 (mmp) REVERT: C 290 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7108 (mmt-90) REVERT: C 474 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 683 ASP cc_start: 0.8154 (m-30) cc_final: 0.7852 (m-30) REVERT: C 734 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 86 ILE cc_start: 0.8402 (mm) cc_final: 0.7863 (tt) REVERT: D 186 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8664 (tm) REVERT: D 290 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7152 (mmt-90) REVERT: D 474 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7592 (tm-30) REVERT: D 516 GLU cc_start: 0.8048 (mp0) cc_final: 0.7578 (mm-30) REVERT: D 683 ASP cc_start: 0.8252 (m-30) cc_final: 0.8044 (m-30) REVERT: D 734 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 781 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: E 86 ILE cc_start: 0.8363 (mm) cc_final: 0.7813 (tt) REVERT: E 474 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7713 (tm-30) REVERT: F 86 ILE cc_start: 0.8325 (mm) cc_final: 0.7793 (tt) REVERT: F 286 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4731 (pp-130) REVERT: F 474 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7565 (tm-30) REVERT: F 734 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 286 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.4647 (pp-130) REVERT: G 474 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7557 (tm-30) REVERT: G 502 MET cc_start: 0.8418 (mtm) cc_final: 0.8147 (mtp) REVERT: G 552 LEU cc_start: 0.8956 (tt) cc_final: 0.8730 (tm) REVERT: G 674 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 734 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7702 (tm-30) REVERT: H 290 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6917 (mmt-90) REVERT: H 474 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7752 (tm-30) REVERT: H 502 MET cc_start: 0.8661 (mtm) cc_final: 0.8393 (mtt) REVERT: H 508 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8742 (ttmt) REVERT: I 86 ILE cc_start: 0.8415 (mm) cc_final: 0.7855 (tt) REVERT: I 205 LEU cc_start: 0.9190 (tp) cc_final: 0.8717 (mp) REVERT: I 290 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7133 (mmt-90) REVERT: I 516 GLU cc_start: 0.8034 (mp0) cc_final: 0.7610 (mm-30) REVERT: I 683 ASP cc_start: 0.8150 (m-30) cc_final: 0.7862 (m-30) REVERT: J 86 ILE cc_start: 0.8412 (mm) cc_final: 0.7842 (tt) REVERT: J 186 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8646 (tm) REVERT: J 205 LEU cc_start: 0.9161 (tp) cc_final: 0.8675 (mp) REVERT: J 283 MET cc_start: 0.8168 (mpp) cc_final: 0.7958 (mmp) REVERT: J 290 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7166 (mmt-90) REVERT: J 474 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7620 (tm-30) REVERT: J 734 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7557 (tm-30) REVERT: K 86 ILE cc_start: 0.8395 (mm) cc_final: 0.7876 (tt) REVERT: K 283 MET cc_start: 0.8170 (mpp) cc_final: 0.7949 (mmp) REVERT: K 286 MET cc_start: 0.7351 (tpt) cc_final: 0.6633 (tpt) REVERT: K 474 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7720 (tm-30) REVERT: L 286 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4685 (pp-130) REVERT: L 474 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7548 (tm-30) REVERT: L 734 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7654 (tm-30) outliers start: 139 outliers final: 73 residues processed: 373 average time/residue: 1.3159 time to fit residues: 690.2680 Evaluate side-chains 332 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 242 time to evaluate : 6.302 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL 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 508 LYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 186 LEU 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 D residue 88 VAL Chi-restraints excluded: chain D residue 186 LEU 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 364 MET 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 726 VAL 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 364 MET Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 613 ILE 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 286 MET 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 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 286 MET 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 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 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 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 J residue 88 VAL Chi-restraints excluded: chain J residue 186 LEU 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 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 726 VAL Chi-restraints excluded: chain J residue 729 ILE 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 499 ILE Chi-restraints excluded: chain K residue 534 VAL 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 286 MET Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 515 optimal weight: 6.9990 chunk 661 optimal weight: 1.9990 chunk 512 optimal weight: 20.0000 chunk 762 optimal weight: 1.9990 chunk 505 optimal weight: 5.9990 chunk 902 optimal weight: 8.9990 chunk 564 optimal weight: 4.9990 chunk 550 optimal weight: 3.9990 chunk 416 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS L 167 ASN ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 77574 Z= 0.285 Angle : 0.559 17.558 105908 Z= 0.277 Chirality : 0.043 0.174 11324 Planarity : 0.004 0.050 13940 Dihedral : 5.476 88.211 10472 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.58 % Allowed : 9.78 % Favored : 88.64 % 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: 0.85 (0.09), residues: 9450 helix: 1.75 (0.08), residues: 4119 sheet: -0.14 (0.16), residues: 1126 loop : -0.38 (0.09), residues: 4205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 25 HIS 0.006 0.001 HIS H 539 PHE 0.023 0.001 PHE E 233 TYR 0.009 0.001 TYR E 87 ARG 0.008 0.000 ARG K 515 *********************** 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 392 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 266 time to evaluate : 6.395 Fit side-chains REVERT: A 286 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4709 (pp-130) REVERT: A 734 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 86 ILE cc_start: 0.8449 (mm) cc_final: 0.7915 (tt) REVERT: B 474 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 508 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8718 (ttmt) REVERT: B 681 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7191 (t0) REVERT: C 86 ILE cc_start: 0.8307 (mm) cc_final: 0.7773 (tt) REVERT: C 186 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8591 (tm) REVERT: C 283 MET cc_start: 0.8127 (mpp) cc_final: 0.7908 (mmp) REVERT: C 290 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7145 (mmt-90) REVERT: C 474 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 683 ASP cc_start: 0.8163 (m-30) cc_final: 0.7882 (m-30) REVERT: C 734 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 86 ILE cc_start: 0.8406 (mm) cc_final: 0.7912 (tt) REVERT: D 186 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (tm) REVERT: D 290 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7154 (mmt180) REVERT: D 474 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 516 GLU cc_start: 0.8080 (mp0) cc_final: 0.7635 (mm-30) REVERT: D 683 ASP cc_start: 0.8244 (m-30) cc_final: 0.8042 (m-30) REVERT: D 734 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7658 (tm-30) REVERT: D 781 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: E 86 ILE cc_start: 0.8351 (mm) cc_final: 0.7799 (tt) REVERT: E 474 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7684 (tm-30) REVERT: F 86 ILE cc_start: 0.8343 (mm) cc_final: 0.7836 (tt) REVERT: F 286 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4638 (pp-130) REVERT: F 290 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7016 (mmt-90) REVERT: F 474 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7527 (tm-30) REVERT: F 734 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7696 (tm-30) REVERT: G 286 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4599 (pp-130) REVERT: G 474 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7540 (tm-30) REVERT: G 500 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (t0) REVERT: G 674 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: G 734 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7727 (tm-30) REVERT: H 13 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5788 (pp) REVERT: H 290 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6912 (mmt-90) REVERT: H 474 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7724 (tm-30) REVERT: H 502 MET cc_start: 0.8664 (mtm) cc_final: 0.8398 (mtt) REVERT: H 508 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8720 (ttmt) REVERT: I 86 ILE cc_start: 0.8391 (mm) cc_final: 0.7841 (tt) REVERT: I 205 LEU cc_start: 0.9183 (tp) cc_final: 0.8699 (mp) REVERT: I 290 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7134 (mmt-90) REVERT: I 516 GLU cc_start: 0.8031 (mp0) cc_final: 0.7557 (mm-30) REVERT: I 683 ASP cc_start: 0.8148 (m-30) cc_final: 0.7874 (m-30) REVERT: I 689 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8756 (p) REVERT: J 86 ILE cc_start: 0.8408 (mm) cc_final: 0.7859 (tt) REVERT: J 186 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8607 (tm) REVERT: J 205 LEU cc_start: 0.9170 (tp) cc_final: 0.8650 (mp) REVERT: J 283 MET cc_start: 0.8138 (mpp) cc_final: 0.7896 (mmp) REVERT: J 290 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7143 (mmt-90) REVERT: J 474 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7592 (tm-30) REVERT: J 734 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7668 (tm-30) REVERT: K 86 ILE cc_start: 0.8389 (mm) cc_final: 0.7879 (tt) REVERT: K 286 MET cc_start: 0.7491 (tpt) cc_final: 0.7244 (tpt) REVERT: K 474 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7695 (tm-30) REVERT: L 286 MET cc_start: 0.5101 (OUTLIER) cc_final: 0.4667 (pp-130) REVERT: L 474 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7542 (tm-30) REVERT: L 734 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 126 outliers final: 70 residues processed: 366 average time/residue: 1.3268 time to fit residues: 683.2144 Evaluate side-chains 338 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 247 time to evaluate : 6.378 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL 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 508 LYS Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 186 LEU 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 D residue 88 VAL Chi-restraints excluded: chain D residue 186 LEU 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 726 VAL 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 534 VAL Chi-restraints excluded: chain E residue 613 ILE 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 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 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 286 MET Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 500 ASP Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 13 LEU 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 508 LYS 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 J residue 88 VAL Chi-restraints excluded: chain J residue 186 LEU 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 499 ILE Chi-restraints excluded: chain J residue 613 ILE Chi-restraints excluded: chain J residue 681 ASP Chi-restraints excluded: chain J residue 729 ILE 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 534 VAL 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 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 689 THR Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 10.0000 chunk 360 optimal weight: 3.9990 chunk 538 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 573 optimal weight: 7.9990 chunk 614 optimal weight: 0.9990 chunk 446 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 709 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 209 HIS ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS ** L 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2043 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= 0.315 Angle : 0.575 16.829 105908 Z= 0.286 Chirality : 0.043 0.180 11324 Planarity : 0.004 0.050 13940 Dihedral : 5.512 86.416 10472 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.58 % Allowed : 9.90 % Favored : 88.52 % 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: 0.79 (0.09), residues: 9450 helix: 1.70 (0.08), residues: 4114 sheet: -0.24 (0.16), residues: 1127 loop : -0.39 (0.09), residues: 4209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 25 HIS 0.006 0.001 HIS D 539 PHE 0.024 0.001 PHE B 233 TYR 0.010 0.001 TYR H 71 ARG 0.008 0.000 ARG K 515 *********************** 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 389 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 263 time to evaluate : 6.367 Fit side-chains REVERT: A 286 MET cc_start: 0.5354 (OUTLIER) cc_final: 0.4797 (pp-130) REVERT: A 734 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 86 ILE cc_start: 0.8442 (mm) cc_final: 0.7957 (tt) REVERT: B 474 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 508 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8720 (ttmt) REVERT: B 681 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7179 (t0) REVERT: C 86 ILE cc_start: 0.8365 (mm) cc_final: 0.7881 (tt) REVERT: C 186 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8623 (tm) REVERT: C 283 MET cc_start: 0.8112 (mpp) cc_final: 0.7905 (mmp) REVERT: C 290 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7146 (mmt-90) REVERT: C 474 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 734 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 86 ILE cc_start: 0.8431 (mm) cc_final: 0.7950 (tt) REVERT: D 186 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8650 (tm) REVERT: D 290 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7172 (mmt-90) REVERT: D 474 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 516 GLU cc_start: 0.8101 (mp0) cc_final: 0.7605 (mm-30) REVERT: D 683 ASP cc_start: 0.8243 (m-30) cc_final: 0.8038 (m-30) REVERT: D 734 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 781 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: E 474 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7709 (tm-30) REVERT: F 86 ILE cc_start: 0.8343 (mm) cc_final: 0.7817 (tt) REVERT: F 286 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4677 (pp-130) REVERT: F 474 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 734 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7703 (tm-30) REVERT: G 286 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4700 (pp-130) REVERT: G 474 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7559 (tm-30) REVERT: G 674 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: G 734 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 290 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6876 (mmt-90) REVERT: H 474 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7723 (tm-30) REVERT: H 502 MET cc_start: 0.8694 (mtm) cc_final: 0.8435 (mtt) REVERT: H 508 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (ttmt) REVERT: I 86 ILE cc_start: 0.8427 (mm) cc_final: 0.7908 (tt) REVERT: I 205 LEU cc_start: 0.9197 (tp) cc_final: 0.8678 (mp) REVERT: I 290 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7117 (mmt-90) REVERT: I 516 GLU cc_start: 0.8057 (mp0) cc_final: 0.7569 (mm-30) REVERT: I 689 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8766 (p) REVERT: J 86 ILE cc_start: 0.8398 (mm) cc_final: 0.7865 (tt) REVERT: J 186 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8688 (tm) REVERT: J 290 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7133 (mmt-90) REVERT: J 474 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7584 (tm-30) REVERT: J 734 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7647 (tm-30) REVERT: K 86 ILE cc_start: 0.8405 (mm) cc_final: 0.7891 (tt) REVERT: K 87 TYR cc_start: 0.8467 (t80) cc_final: 0.8191 (t80) REVERT: K 283 MET cc_start: 0.7652 (mmp) cc_final: 0.7291 (mmp) REVERT: K 474 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7700 (tm-30) REVERT: L 286 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.4781 (pp-130) REVERT: L 465 MET cc_start: 0.9029 (mpt) cc_final: 0.7921 (mpt) REVERT: L 474 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7567 (tm-30) REVERT: L 734 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7688 (tm-30) outliers start: 126 outliers final: 73 residues processed: 357 average time/residue: 1.3137 time to fit residues: 665.8496 Evaluate side-chains 339 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 248 time to evaluate : 6.355 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE 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 508 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 186 LEU 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 D residue 88 VAL Chi-restraints excluded: chain D residue 186 LEU 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 726 VAL 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 364 MET Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 613 ILE 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 534 VAL 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 286 MET Chi-restraints excluded: chain G residue 534 VAL 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 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 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 422 LEU 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 J residue 88 VAL Chi-restraints excluded: chain J residue 186 LEU 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 726 VAL Chi-restraints excluded: chain J residue 729 ILE 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 534 VAL 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 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 689 THR Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 0.9990 chunk 864 optimal weight: 1.9990 chunk 788 optimal weight: 8.9990 chunk 840 optimal weight: 0.9980 chunk 506 optimal weight: 0.0770 chunk 366 optimal weight: 3.9990 chunk 660 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 759 optimal weight: 0.8980 chunk 795 optimal weight: 0.9990 chunk 837 optimal weight: 7.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 HIS K 730 ASN L 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 77574 Z= 0.145 Angle : 0.533 15.240 105908 Z= 0.261 Chirality : 0.041 0.171 11324 Planarity : 0.004 0.050 13940 Dihedral : 5.243 87.633 10472 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.07 % Allowed : 10.50 % Favored : 88.43 % 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: 1.01 (0.09), residues: 9450 helix: 1.98 (0.08), residues: 4092 sheet: -0.11 (0.16), residues: 1125 loop : -0.37 (0.09), residues: 4233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 295 HIS 0.004 0.001 HIS E 252 PHE 0.034 0.001 PHE B 233 TYR 0.010 0.001 TYR H 71 ARG 0.008 0.000 ARG K 515 *********************** 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 394 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 309 time to evaluate : 6.590 Fit side-chains REVERT: A 87 TYR cc_start: 0.7834 (t80) cc_final: 0.7622 (t80) REVERT: A 286 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4707 (pp-130) REVERT: A 734 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 86 ILE cc_start: 0.8398 (mm) cc_final: 0.7856 (tt) REVERT: B 87 TYR cc_start: 0.8278 (t80) cc_final: 0.7989 (t80) REVERT: B 290 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6801 (mmt-90) REVERT: B 474 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 502 MET cc_start: 0.8538 (mtt) cc_final: 0.8282 (mtp) REVERT: C 86 ILE cc_start: 0.8335 (mm) cc_final: 0.7821 (tt) REVERT: C 290 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6970 (mmt-90) REVERT: C 474 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 683 ASP cc_start: 0.8102 (m-30) cc_final: 0.7838 (m-30) REVERT: C 734 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 86 ILE cc_start: 0.8357 (mm) cc_final: 0.7902 (tt) REVERT: D 87 TYR cc_start: 0.8299 (t80) cc_final: 0.8062 (t80) REVERT: D 186 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8449 (tm) REVERT: D 290 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7087 (mmt180) REVERT: D 474 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7549 (tm-30) REVERT: D 516 GLU cc_start: 0.8009 (mp0) cc_final: 0.7555 (mm-30) REVERT: D 734 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 465 MET cc_start: 0.8138 (mpt) cc_final: 0.7813 (mpt) REVERT: E 474 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7592 (tm-30) REVERT: F 286 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4451 (pp-130) REVERT: F 474 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 734 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7743 (tm-30) REVERT: G 286 MET cc_start: 0.4793 (OUTLIER) cc_final: 0.4452 (pp-130) REVERT: G 474 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7547 (tm-30) REVERT: G 734 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7757 (tm-30) REVERT: H 474 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7685 (tm-30) REVERT: H 502 MET cc_start: 0.8602 (mtm) cc_final: 0.8401 (mtt) REVERT: I 86 ILE cc_start: 0.8274 (mm) cc_final: 0.7738 (tt) REVERT: I 205 LEU cc_start: 0.9151 (tp) cc_final: 0.8696 (mp) REVERT: I 290 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6996 (mmt-90) REVERT: I 516 GLU cc_start: 0.7961 (mp0) cc_final: 0.7505 (mm-30) REVERT: I 683 ASP cc_start: 0.8100 (m-30) cc_final: 0.7844 (m-30) REVERT: I 689 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8671 (p) REVERT: J 86 ILE cc_start: 0.8257 (mm) cc_final: 0.7671 (tt) REVERT: J 205 LEU cc_start: 0.9128 (tp) cc_final: 0.8671 (mp) REVERT: J 290 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6900 (mmt180) REVERT: J 474 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7477 (tm-30) REVERT: J 502 MET cc_start: 0.8268 (mtp) cc_final: 0.7957 (mtt) REVERT: J 734 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7713 (tm-30) REVERT: K 86 ILE cc_start: 0.8406 (mm) cc_final: 0.7864 (tt) REVERT: K 87 TYR cc_start: 0.8253 (t80) cc_final: 0.7997 (t80) REVERT: K 465 MET cc_start: 0.8099 (mpt) cc_final: 0.7774 (mpt) REVERT: K 474 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7536 (tm-30) REVERT: L 286 MET cc_start: 0.4909 (OUTLIER) cc_final: 0.4555 (pp-130) REVERT: L 465 MET cc_start: 0.9005 (mpt) cc_final: 0.8104 (mpt) REVERT: L 474 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7482 (tm-30) REVERT: L 734 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7726 (tm-30) outliers start: 85 outliers final: 56 residues processed: 364 average time/residue: 1.2369 time to fit residues: 650.0444 Evaluate side-chains 323 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 256 time to evaluate : 6.423 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 534 VAL 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 774 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 186 LEU 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 774 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 613 ILE 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 534 VAL 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 266 ILE Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 534 VAL 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 381 LEU Chi-restraints excluded: chain H residue 534 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 689 THR Chi-restraints excluded: chain I residue 774 ASP 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 726 VAL Chi-restraints excluded: chain J residue 774 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 534 VAL 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 286 MET Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 6.9990 chunk 888 optimal weight: 7.9990 chunk 542 optimal weight: 3.9990 chunk 421 optimal weight: 0.0270 chunk 617 optimal weight: 0.9980 chunk 932 optimal weight: 0.9990 chunk 858 optimal weight: 30.0000 chunk 742 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 573 optimal weight: 0.8980 chunk 455 optimal weight: 6.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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** H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 77574 Z= 0.147 Angle : 0.543 15.625 105908 Z= 0.265 Chirality : 0.041 0.169 11324 Planarity : 0.004 0.051 13940 Dihedral : 5.202 87.057 10472 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.85 % Allowed : 11.13 % Favored : 88.02 % 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: 1.00 (0.09), residues: 9450 helix: 1.99 (0.08), residues: 4092 sheet: -0.24 (0.16), residues: 1165 loop : -0.37 (0.09), residues: 4193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 295 HIS 0.010 0.001 HIS J 775 PHE 0.036 0.001 PHE B 233 TYR 0.014 0.001 TYR F 71 ARG 0.008 0.000 ARG K 515 ********************** 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 350 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 282 time to evaluate : 6.385 Fit side-chains REVERT: A 286 MET cc_start: 0.4977 (OUTLIER) cc_final: 0.4674 (pp-130) REVERT: A 734 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 86 ILE cc_start: 0.8414 (mm) cc_final: 0.7852 (tt) REVERT: B 87 TYR cc_start: 0.8248 (t80) cc_final: 0.7947 (t80) REVERT: B 290 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6786 (mmt-90) REVERT: B 474 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 502 MET cc_start: 0.8545 (mtt) cc_final: 0.8297 (mtp) REVERT: C 86 ILE cc_start: 0.8349 (mm) cc_final: 0.7861 (tt) REVERT: C 290 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6964 (mmt180) REVERT: C 474 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 683 ASP cc_start: 0.8114 (m-30) cc_final: 0.7864 (m-30) REVERT: C 734 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7702 (tm-30) REVERT: D 86 ILE cc_start: 0.8347 (mm) cc_final: 0.7876 (tt) REVERT: D 87 TYR cc_start: 0.8280 (t80) cc_final: 0.8076 (t80) REVERT: D 186 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8427 (tm) REVERT: D 290 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7080 (mmt180) REVERT: D 474 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 516 GLU cc_start: 0.8025 (mp0) cc_final: 0.7575 (mm-30) REVERT: D 683 ASP cc_start: 0.8071 (m-30) cc_final: 0.7797 (m-30) REVERT: D 734 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7595 (tm-30) REVERT: E 465 MET cc_start: 0.8149 (mpt) cc_final: 0.7816 (mpt) REVERT: E 474 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7546 (tm-30) REVERT: F 286 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.4429 (pp-130) REVERT: F 474 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 734 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7720 (tm-30) REVERT: G 286 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.4447 (pp-130) REVERT: G 474 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7564 (tm-30) REVERT: G 734 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7747 (tm-30) REVERT: H 255 MET cc_start: 0.7984 (tmt) cc_final: 0.7747 (tmm) REVERT: H 474 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7697 (tm-30) REVERT: H 502 MET cc_start: 0.8607 (mtm) cc_final: 0.8404 (mtt) REVERT: I 86 ILE cc_start: 0.8286 (mm) cc_final: 0.7740 (tt) REVERT: I 205 LEU cc_start: 0.9150 (tp) cc_final: 0.8691 (mp) REVERT: I 290 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7012 (mmt-90) REVERT: I 516 GLU cc_start: 0.7997 (mp0) cc_final: 0.7597 (mm-30) REVERT: I 683 ASP cc_start: 0.8099 (m-30) cc_final: 0.7844 (m-30) REVERT: I 689 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (p) REVERT: J 205 LEU cc_start: 0.9147 (tp) cc_final: 0.8706 (mp) REVERT: J 290 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6897 (mmt180) REVERT: J 474 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7505 (tm-30) REVERT: J 502 MET cc_start: 0.8287 (mtp) cc_final: 0.8002 (mtt) REVERT: J 734 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7628 (tm-30) REVERT: K 86 ILE cc_start: 0.8397 (mm) cc_final: 0.7905 (tt) REVERT: K 465 MET cc_start: 0.8121 (mpt) cc_final: 0.7796 (mpt) REVERT: K 474 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7627 (tm-30) REVERT: L 286 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4585 (pp-130) REVERT: L 474 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7497 (tm-30) REVERT: L 734 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 68 outliers final: 50 residues processed: 325 average time/residue: 1.3805 time to fit residues: 651.7997 Evaluate side-chains 322 residues out of total 7930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 261 time to evaluate : 6.389 ------------------------------------------------------------------------------- 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 499 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 534 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 D residue 186 LEU 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 E residue 251 LEU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 613 ILE 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 534 VAL 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 266 ILE Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 774 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 381 LEU Chi-restraints excluded: chain H residue 534 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 689 THR 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 726 VAL 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 534 VAL 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 286 MET Chi-restraints excluded: chain L residue 534 VAL Chi-restraints excluded: chain L residue 613 ILE Chi-restraints excluded: chain L residue 726 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 4.9990 chunk 790 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 684 optimal weight: 0.0970 chunk 109 optimal weight: 9.9990 chunk 206 optimal weight: 0.1980 chunk 743 optimal weight: 10.0000 chunk 311 optimal weight: 0.0040 chunk 763 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** I 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.108998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076161 restraints weight = 383522.368| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.28 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 77574 Z= 0.142 Angle : 0.539 14.648 105908 Z= 0.263 Chirality : 0.041 0.169 11324 Planarity : 0.004 0.051 13940 Dihedral : 5.157 86.845 10472 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.89 % Allowed : 11.39 % Favored : 87.72 % 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: 1.02 (0.09), residues: 9450 helix: 2.01 (0.08), residues: 4092 sheet: -0.20 (0.15), residues: 1165 loop : -0.36 (0.09), residues: 4193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 295 HIS 0.013 0.000 HIS G 775 PHE 0.034 0.001 PHE B 233 TYR 0.019 0.001 TYR A 87 ARG 0.007 0.000 ARG K 515 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14860.70 seconds wall clock time: 260 minutes 11.23 seconds (15611.23 seconds total)