Starting phenix.real_space_refine on Sat Apr 6 09:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8suw_40778/04_2024/8suw_40778_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 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 30 5.49 5 Mg 3 5.21 5 S 121 5.16 5 C 36162 2.51 5 N 9572 2.21 5 O 10689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 56577 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3175 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3192 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 2 Chain: "E" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "F" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3187 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3192 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 2 Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3145 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Chain: "J" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 Chain: "K" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3182 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Chain: "L" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3188 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 2 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4208 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 20, 'TRANS': 510} Chain breaks: 4 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.95, per 1000 atoms: 0.37 Number of scatterers: 56577 At special positions: 0 Unit cell: (187.59, 185.37, 218.67, 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 121 16.00 P 30 15.00 Mg 3 11.99 O 10689 8.00 N 9572 7.00 C 36162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 7.5 seconds 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 328 helices and 44 sheets defined 40.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.616A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.764A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 4.124A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.561A pdb=" N LYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR A 143 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A 144 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.506A pdb=" N PHE A 201 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.808A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.675A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.542A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.622A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.791A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.635A pdb=" N ASP B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.992A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.518A pdb=" N PHE B 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 142 through 153 Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.926A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 202 " --> pdb=" O GLN B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.644A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.538A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.815A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.752A pdb=" N VAL B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.570A pdb=" N SER C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.738A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 102 through 121 removed outlier: 3.860A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 153 removed outlier: 4.993A pdb=" N TYR C 143 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS C 144 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 153 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.706A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.916A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.645A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 257' Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.987A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.914A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 377 through 383 removed outlier: 4.041A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.555A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.596A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.601A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.762A pdb=" N PHE D 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 131' Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.755A pdb=" N LYS D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR D 143 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS D 144 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 153 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 3.699A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.637A pdb=" N PHE D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 283 through 296 removed outlier: 3.718A pdb=" N ILE D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 4.881A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 352 through 359 Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 397 through 403 removed outlier: 4.398A pdb=" N ALA D 402 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.515A pdb=" N CYS E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 removed outlier: 3.740A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.614A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.897A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 75 No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 82 through 99 removed outlier: 3.526A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.781A pdb=" N LYS E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.798A pdb=" N LYS E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS E 144 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS E 145 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 153 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN E 154 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 removed outlier: 3.879A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.572A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.618A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.771A pdb=" N LEU E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 345 removed outlier: 3.873A pdb=" N LYS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 359 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.625A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 383' Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'F' and resid 13 through 23 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 57 through 65 removed outlier: 4.157A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 82 through 98 removed outlier: 3.622A pdb=" N ILE F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 123 removed outlier: 3.703A pdb=" N GLU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.875A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 140 through 153 removed outlier: 4.510A pdb=" N TYR F 143 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS F 144 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS F 145 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER F 153 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 180 removed outlier: 3.633A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.956A pdb=" N PHE F 201 " --> pdb=" O PRO F 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 201' Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 283 through 296 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.671A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 321 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.571A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 360 removed outlier: 3.704A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 401 through 405 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 34 through 39 removed outlier: 3.774A pdb=" N SER G 37 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 34 through 39' Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 82 through 99 Processing helix chain 'G' and resid 102 through 122 removed outlier: 4.144A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 4.350A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 143 through 154 Processing helix chain 'G' and resid 173 through 180 Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.703A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP G 202 " --> pdb=" O GLN G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 253 through 257 removed outlier: 3.631A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 257' Processing helix chain 'G' and resid 278 through 295 removed outlier: 5.048A pdb=" N VAL G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 323 removed outlier: 3.706A pdb=" N LEU G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 344 Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.830A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN G 360 " --> pdb=" O VAL G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 375 No H-bonds generated for 'chain 'G' and resid 373 through 375' Processing helix chain 'G' and resid 377 through 383 removed outlier: 3.551A pdb=" N GLU G 382 " --> pdb=" O ASN G 378 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 404 Processing helix chain 'H' and resid 12 through 24 removed outlier: 4.223A pdb=" N GLN H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 72 through 76 removed outlier: 3.915A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 76' Processing helix chain 'H' and resid 83 through 98 Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.593A pdb=" N LEU H 115 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 130 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 142 through 153 Processing helix chain 'H' and resid 172 through 180 removed outlier: 3.718A pdb=" N ALA H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 245 through 251 Processing helix chain 'H' and resid 254 through 258 removed outlier: 3.529A pdb=" N ASN H 258 " --> pdb=" O ASN H 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 254 through 258' Processing helix chain 'H' and resid 283 through 294 removed outlier: 3.534A pdb=" N PHE H 288 " --> pdb=" O TYR H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 323 removed outlier: 3.866A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 345 removed outlier: 3.894A pdb=" N LYS H 345 " --> pdb=" O THR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 360 removed outlier: 3.590A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN H 360 " --> pdb=" O VAL H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 375 No H-bonds generated for 'chain 'H' and resid 373 through 375' Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.577A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 404 removed outlier: 4.275A pdb=" N ALA H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE H 403 " --> pdb=" O LEU H 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.992A pdb=" N GLN I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 40 removed outlier: 3.767A pdb=" N VAL I 38 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS I 40 " --> pdb=" O SER I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.608A pdb=" N GLN I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 removed outlier: 3.744A pdb=" N GLY I 61 " --> pdb=" O PRO I 57 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 82 through 99 removed outlier: 3.970A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 121 removed outlier: 3.882A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER I 114 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.787A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 139 through 153 removed outlier: 4.530A pdb=" N TYR I 143 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS I 144 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS I 145 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER I 153 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 180 removed outlier: 3.907A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP I 179 " --> pdb=" O TRP I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.672A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 245 through 251 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 281 through 296 removed outlier: 3.804A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER I 296 " --> pdb=" O GLY I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 323 removed outlier: 3.736A pdb=" N LEU I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 345 removed outlier: 4.122A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 357 Processing helix chain 'I' and resid 377 through 383 Processing helix chain 'I' and resid 395 through 397 No H-bonds generated for 'chain 'I' and resid 395 through 397' Processing helix chain 'I' and resid 399 through 405 Processing helix chain 'J' and resid 12 through 24 removed outlier: 3.618A pdb=" N CYS J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 57 through 65 removed outlier: 3.664A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 77 Processing helix chain 'J' and resid 84 through 99 Processing helix chain 'J' and resid 102 through 122 removed outlier: 3.627A pdb=" N GLU J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 131 removed outlier: 3.973A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 128 through 131' Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 139 through 154 removed outlier: 5.016A pdb=" N TYR J 143 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS J 144 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU J 147 " --> pdb=" O HIS J 144 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE J 152 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 153 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 180 removed outlier: 3.785A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 202 removed outlier: 3.573A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 251 removed outlier: 3.649A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 Processing helix chain 'J' and resid 282 through 296 removed outlier: 3.729A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER J 296 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 321 removed outlier: 3.568A pdb=" N ALA J 321 " --> pdb=" O ILE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 344 removed outlier: 3.703A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 Processing helix chain 'J' and resid 372 through 374 No H-bonds generated for 'chain 'J' and resid 372 through 374' Processing helix chain 'J' and resid 377 through 383 Processing helix chain 'J' and resid 396 through 401 Processing helix chain 'J' and resid 404 through 407 No H-bonds generated for 'chain 'J' and resid 404 through 407' Processing helix chain 'K' and resid 12 through 24 removed outlier: 3.556A pdb=" N CYS K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 40 removed outlier: 3.749A pdb=" N SER K 37 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 59 through 64 Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 82 through 99 removed outlier: 3.882A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 120 removed outlier: 3.516A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 removed outlier: 4.085A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.671A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 180 removed outlier: 3.566A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.860A pdb=" N PHE K 201 " --> pdb=" O PRO K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 251 Processing helix chain 'K' and resid 253 through 257 Processing helix chain 'K' and resid 281 through 296 removed outlier: 3.516A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER K 296 " --> pdb=" O GLY K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 323 removed outlier: 3.769A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU K 323 " --> pdb=" O LEU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 3.680A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.761A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 405 Processing helix chain 'L' and resid 12 through 22 Processing helix chain 'L' and resid 45 through 55 removed outlier: 3.759A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 82 through 98 removed outlier: 3.684A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 123 removed outlier: 4.053A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA L 123 " --> pdb=" O VAL L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 131 removed outlier: 4.427A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 128 through 131' Processing helix chain 'L' and resid 135 through 137 No H-bonds generated for 'chain 'L' and resid 135 through 137' Processing helix chain 'L' and resid 142 through 154 removed outlier: 3.559A pdb=" N GLU L 146 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN L 154 " --> pdb=" O LYS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 180 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.855A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 245 through 249 Processing helix chain 'L' and resid 253 through 258 Processing helix chain 'L' and resid 284 through 295 removed outlier: 3.704A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 323 removed outlier: 3.964A pdb=" N LEU L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU L 323 " --> pdb=" O LEU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 344 Processing helix chain 'L' and resid 350 through 360 Processing helix chain 'L' and resid 372 through 375 Processing helix chain 'L' and resid 377 through 383 Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'M' and resid 130 through 136 removed outlier: 3.724A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 146 Proline residue: M 145 - end of helix Processing helix chain 'M' and resid 165 through 168 No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 183 through 197 removed outlier: 3.603A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 260 No H-bonds generated for 'chain 'M' and resid 258 through 260' Processing helix chain 'M' and resid 263 through 270 removed outlier: 3.701A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 286 Processing helix chain 'M' and resid 288 through 290 No H-bonds generated for 'chain 'M' and resid 288 through 290' Processing helix chain 'M' and resid 319 through 331 removed outlier: 3.805A pdb=" N LEU M 322 " --> pdb=" O GLN M 319 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA M 323 " --> pdb=" O SER M 320 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU M 324 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 355 removed outlier: 3.503A pdb=" N VAL M 350 " --> pdb=" O ALA M 347 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY M 354 " --> pdb=" O ALA M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 386 Proline residue: M 376 - end of helix Processing helix chain 'M' and resid 388 through 393 Processing helix chain 'M' and resid 408 through 420 removed outlier: 4.096A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 449 Proline residue: M 447 - end of helix No H-bonds generated for 'chain 'M' and resid 443 through 449' Processing helix chain 'M' and resid 451 through 464 removed outlier: 3.993A pdb=" N GLU M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 518 through 520 No H-bonds generated for 'chain 'M' and resid 518 through 520' Processing helix chain 'M' and resid 523 through 527 Processing helix chain 'M' and resid 540 through 542 No H-bonds generated for 'chain 'M' and resid 540 through 542' Processing helix chain 'M' and resid 544 through 549 Processing helix chain 'M' and resid 556 through 558 No H-bonds generated for 'chain 'M' and resid 556 through 558' Processing helix chain 'M' and resid 560 through 562 No H-bonds generated for 'chain 'M' and resid 560 through 562' Processing helix chain 'M' and resid 601 through 604 removed outlier: 4.093A pdb=" N ASN M 604 " --> pdb=" O GLU M 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 601 through 604' Processing helix chain 'N' and resid 130 through 136 removed outlier: 3.866A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE N 136 " --> pdb=" O PHE N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 146 No H-bonds generated for 'chain 'N' and resid 144 through 146' Processing helix chain 'N' and resid 165 through 168 No H-bonds generated for 'chain 'N' and resid 165 through 168' Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.887A pdb=" N GLN N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 264 through 270 removed outlier: 4.751A pdb=" N LYS N 268 " --> pdb=" O ALA N 264 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 286 removed outlier: 3.500A pdb=" N ARG N 282 " --> pdb=" O LEU N 278 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN N 283 " --> pdb=" O PRO N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 290 No H-bonds generated for 'chain 'N' and resid 288 through 290' Processing helix chain 'N' and resid 322 through 331 removed outlier: 3.951A pdb=" N ARG N 331 " --> pdb=" O ASP N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 355 removed outlier: 3.578A pdb=" N LEU N 346 " --> pdb=" O PHE N 343 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA N 347 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR N 348 " --> pdb=" O SER N 345 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU N 349 " --> pdb=" O LEU N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 371 No H-bonds generated for 'chain 'N' and resid 368 through 371' Processing helix chain 'N' and resid 375 through 386 removed outlier: 3.620A pdb=" N ILE N 380 " --> pdb=" O PRO N 376 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU N 386 " --> pdb=" O GLN N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 391 removed outlier: 3.965A pdb=" N LYS N 391 " --> pdb=" O ILE N 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 388 through 391' Processing helix chain 'N' and resid 410 through 420 removed outlier: 4.486A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 438 through 440 No H-bonds generated for 'chain 'N' and resid 438 through 440' Processing helix chain 'N' and resid 446 through 463 removed outlier: 3.625A pdb=" N GLU N 459 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 499 through 502 No H-bonds generated for 'chain 'N' and resid 499 through 502' Processing helix chain 'N' and resid 518 through 520 No H-bonds generated for 'chain 'N' and resid 518 through 520' Processing helix chain 'N' and resid 523 through 526 No H-bonds generated for 'chain 'N' and resid 523 through 526' Processing helix chain 'N' and resid 540 through 548 Processing helix chain 'N' and resid 557 through 559 No H-bonds generated for 'chain 'N' and resid 557 through 559' Processing helix chain 'O' and resid 130 through 136 removed outlier: 3.564A pdb=" N ILE O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 146 Proline residue: O 145 - end of helix Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 212 through 215 No H-bonds generated for 'chain 'O' and resid 212 through 215' Processing helix chain 'O' and resid 263 through 270 Processing helix chain 'O' and resid 278 through 290 removed outlier: 5.129A pdb=" N ASN O 289 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG O 290 " --> pdb=" O SER O 286 " (cutoff:3.500A) Processing helix chain 'O' and resid 322 through 331 Processing helix chain 'O' and resid 343 through 355 removed outlier: 4.024A pdb=" N ALA O 347 " --> pdb=" O PHE O 343 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR O 348 " --> pdb=" O LYS O 344 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS O 355 " --> pdb=" O ALA O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 385 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 390 through 393 No H-bonds generated for 'chain 'O' and resid 390 through 393' Processing helix chain 'O' and resid 408 through 421 removed outlier: 3.960A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU O 416 " --> pdb=" O ALA O 412 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL O 417 " --> pdb=" O MET O 413 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP O 418 " --> pdb=" O SER O 414 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR O 419 " --> pdb=" O ASP O 415 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 464 Proline residue: O 447 - end of helix removed outlier: 3.793A pdb=" N GLU O 459 " --> pdb=" O GLU O 455 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE O 460 " --> pdb=" O MET O 456 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 481 No H-bonds generated for 'chain 'O' and resid 479 through 481' Processing helix chain 'O' and resid 491 through 493 No H-bonds generated for 'chain 'O' and resid 491 through 493' Processing helix chain 'O' and resid 497 through 506 Processing helix chain 'O' and resid 518 through 520 No H-bonds generated for 'chain 'O' and resid 518 through 520' Processing helix chain 'O' and resid 523 through 526 No H-bonds generated for 'chain 'O' and resid 523 through 526' Processing helix chain 'O' and resid 541 through 548 removed outlier: 3.528A pdb=" N ALA O 545 " --> pdb=" O ASP O 542 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG O 547 " --> pdb=" O GLN O 544 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR O 548 " --> pdb=" O ALA O 545 " (cutoff:3.500A) Processing helix chain 'O' and resid 558 through 560 No H-bonds generated for 'chain 'O' and resid 558 through 560' Processing helix chain 'O' and resid 598 through 602 Processing helix chain 'P' and resid 130 through 136 Processing helix chain 'P' and resid 141 through 143 No H-bonds generated for 'chain 'P' and resid 141 through 143' Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 184 through 197 Processing helix chain 'P' and resid 212 through 215 Processing helix chain 'P' and resid 258 through 261 removed outlier: 3.541A pdb=" N LEU P 261 " --> pdb=" O TYR P 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 258 through 261' Processing helix chain 'P' and resid 265 through 269 Processing helix chain 'P' and resid 278 through 288 removed outlier: 3.869A pdb=" N ILE P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 353 removed outlier: 3.517A pdb=" N THR P 348 " --> pdb=" O SER P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.748A pdb=" N LYS P 379 " --> pdb=" O LEU P 375 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 390 through 392 No H-bonds generated for 'chain 'P' and resid 390 through 392' Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 446 through 464 removed outlier: 3.946A pdb=" N PHE P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG P 464 " --> pdb=" O ILE P 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 498 through 502 Processing helix chain 'P' and resid 518 through 520 No H-bonds generated for 'chain 'P' and resid 518 through 520' Processing helix chain 'P' and resid 523 through 528 removed outlier: 3.696A pdb=" N ALA P 527 " --> pdb=" O THR P 524 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 549 removed outlier: 3.754A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 556 through 563 removed outlier: 3.971A pdb=" N ILE P 561 " --> pdb=" O ILE P 557 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER P 562 " --> pdb=" O LEU P 558 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY P 563 " --> pdb=" O LYS P 559 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 8.728A pdb=" N THR A 367 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 329 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL A 369 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 163 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LEU A 32 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE A 165 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ILE A 164 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N THR A 166 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 224 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 183 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 223 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS A 225 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 232 through 234 Processing sheet with id= C, first strand: chain 'B' and resid 3 through 5 removed outlier: 8.747A pdb=" N THR B 367 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 329 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL B 369 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 331 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN B 27 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE B 303 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 29 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN B 305 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 31 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA B 163 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU B 32 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 165 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ILE B 164 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR B 166 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 224 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LYS B 225 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 232 through 234 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 5 removed outlier: 8.693A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 300 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL C 330 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 302 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR C 332 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE C 304 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 163 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU C 32 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 165 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N ILE C 164 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N THR C 166 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR C 224 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN C 183 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 223 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE C 185 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LYS C 225 " --> pdb=" O PHE C 185 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 232 through 234 Processing sheet with id= G, first strand: chain 'D' and resid 3 through 5 removed outlier: 8.417A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N PHE D 303 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY D 29 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA D 163 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ILE D 164 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR D 222 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR D 166 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR D 224 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 232 through 234 Processing sheet with id= I, first strand: chain 'E' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'E' and resid 183 through 185 removed outlier: 3.754A pdb=" N ALA E 163 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 328 " --> pdb=" O THR E 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 232 through 234 Processing sheet with id= L, first strand: chain 'F' and resid 3 through 5 removed outlier: 8.488A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA F 163 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LEU F 32 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE F 165 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N ILE F 164 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR F 222 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR F 166 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR F 224 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 232 through 234 Processing sheet with id= N, first strand: chain 'G' and resid 183 through 185 removed outlier: 3.665A pdb=" N ALA G 221 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 223 " --> pdb=" O PHE G 185 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA G 163 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 367 " --> pdb=" O VAL G 329 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 3 through 5 removed outlier: 8.235A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN H 27 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N PHE H 303 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY H 29 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 163 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ILE H 164 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR H 222 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR H 166 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR H 224 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 232 through 234 Processing sheet with id= Q, first strand: chain 'I' and resid 183 through 185 removed outlier: 3.687A pdb=" N LEU I 223 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL I 30 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN I 305 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR I 367 " --> pdb=" O VAL I 329 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 232 through 234 Processing sheet with id= S, first strand: chain 'J' and resid 8 through 10 removed outlier: 4.283A pdb=" N ILE J 3 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN J 27 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N PHE J 303 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY J 29 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASN J 305 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU J 31 " --> pdb=" O ASN J 305 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA J 163 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N LEU J 32 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE J 165 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N ILE J 164 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR J 222 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR J 166 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR J 224 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 232 through 234 Processing sheet with id= U, first strand: chain 'K' and resid 3 through 5 removed outlier: 8.766A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA K 163 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEU K 32 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE K 165 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ILE K 164 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR K 222 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N THR K 166 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR K 224 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.659A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN L 5 " --> pdb=" O ASN L 8 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N THR L 367 " --> pdb=" O PHE L 327 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR L 300 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL L 330 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU L 302 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR L 332 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE L 304 " --> pdb=" O TYR L 332 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA L 163 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU L 32 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE L 165 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ILE L 164 " --> pdb=" O HIS L 220 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR L 222 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR L 166 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR L 224 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 232 through 234 Processing sheet with id= X, first strand: chain 'M' and resid 67 through 70 removed outlier: 5.541A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 51 through 56 removed outlier: 3.692A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE M 101 " --> pdb=" O ILE M 112 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 532 through 534 removed outlier: 3.604A pdb=" N PHE M 572 " --> pdb=" O TRP M 532 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE M 161 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 204 through 207 removed outlier: 7.322A pdb=" N HIS M 434 " --> pdb=" O ILE M 205 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP M 207 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL M 436 " --> pdb=" O ASP M 207 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS M 223 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASN M 437 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR M 225 " --> pdb=" O ASN M 437 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'M' and resid 298 through 300 removed outlier: 4.076A pdb=" N LEU M 300 " --> pdb=" O PHE M 308 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE M 308 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.583A pdb=" N ALA N 69 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG N 92 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU N 27 " --> pdb=" O ARG N 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA N 96 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY N 17 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN N 26 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL N 15 " --> pdb=" O ASN N 26 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 35 through 37 removed outlier: 3.588A pdb=" N SER N 43 " --> pdb=" O ALA N 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 125 through 127 removed outlier: 3.824A pdb=" N GLY N 100 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG N 64 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA N 98 " --> pdb=" O ARG N 64 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE N 101 " --> pdb=" O ILE N 112 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 147 through 149 Processing sheet with id= AG, first strand: chain 'N' and resid 151 through 153 removed outlier: 3.875A pdb=" N PHE N 572 " --> pdb=" O TRP N 532 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 204 through 206 removed outlier: 3.594A pdb=" N PHE N 206 " --> pdb=" O LEU N 475 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 222 through 226 removed outlier: 6.281A pdb=" N VAL N 433 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR N 225 " --> pdb=" O VAL N 433 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE N 435 " --> pdb=" O THR N 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'O' and resid 67 through 70 removed outlier: 3.650A pdb=" N ASP O 67 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARG O 92 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU O 27 " --> pdb=" O ARG O 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA O 96 " --> pdb=" O ILE O 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY O 17 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN O 26 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL O 15 " --> pdb=" O ASN O 26 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA O 125 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER O 124 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP O 55 " --> pdb=" O SER O 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 151 through 153 removed outlier: 3.540A pdb=" N PHE O 572 " --> pdb=" O TRP O 532 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 203 through 205 removed outlier: 3.521A pdb=" N ILE O 205 " --> pdb=" O HIS O 434 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 291 through 293 Processing sheet with id= AN, first strand: chain 'P' and resid 124 through 126 removed outlier: 3.650A pdb=" N GLY P 13 " --> pdb=" O ALA P 125 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG P 24 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU P 18 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL P 62 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE P 101 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU P 60 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 36 through 38 Processing sheet with id= AP, first strand: chain 'P' and resid 173 through 175 removed outlier: 3.658A pdb=" N VAL P 513 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE P 512 " --> pdb=" O LEU P 474 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU P 476 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER P 514 " --> pdb=" O LEU P 476 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL P 204 " --> pdb=" O LEU P 475 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU P 477 " --> pdb=" O VAL P 204 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE P 206 " --> pdb=" O GLU P 477 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 531 through 534 removed outlier: 3.670A pdb=" N PHE P 572 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER P 534 " --> pdb=" O VAL P 570 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL P 570 " --> pdb=" O SER P 534 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'P' and resid 147 through 152 removed outlier: 6.943A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) 1530 hydrogen bonds defined for protein. 4215 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: 16.60 Time building geometry restraints manager: 16.60 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: 18357 1.34 - 1.46: 11721 1.46 - 1.58: 27520 1.58 - 1.69: 57 1.69 - 1.81: 185 Bond restraints: 57840 Sorted by residual: bond pdb=" C PRO A 385 " pdb=" N TYR A 386 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.86e-02 2.89e+03 2.96e+00 bond pdb=" C TYR I 197 " pdb=" O TYR I 197 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 2.09e+00 bond pdb=" CA GLY J 127 " pdb=" C GLY J 127 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.37e+00 bond pdb=" N GLY J 127 " pdb=" CA GLY J 127 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.10e+00 bond pdb=" C4 ADP O 701 " pdb=" C5 ADP O 701 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.97e-01 ... (remaining 57835 not shown) Histogram of bond angle deviations from ideal: 93.03 - 101.67: 121 101.67 - 110.31: 11242 110.31 - 118.94: 35212 118.94 - 127.58: 31208 127.58 - 136.22: 470 Bond angle restraints: 78253 Sorted by residual: angle pdb=" N VAL K 208 " pdb=" CA VAL K 208 " pdb=" C VAL K 208 " ideal model delta sigma weight residual 113.10 107.54 5.56 9.70e-01 1.06e+00 3.29e+01 angle pdb=" N ILE P 288 " pdb=" CA ILE P 288 " pdb=" C ILE P 288 " ideal model delta sigma weight residual 113.42 107.60 5.82 1.17e+00 7.31e-01 2.47e+01 angle pdb=" N ILE L 280 " pdb=" CA ILE L 280 " pdb=" C ILE L 280 " ideal model delta sigma weight residual 112.83 108.99 3.84 9.90e-01 1.02e+00 1.50e+01 angle pdb=" CA LEU D 238 " pdb=" CB LEU D 238 " pdb=" CG LEU D 238 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 angle pdb=" N ILE M 208 " pdb=" CA ILE M 208 " pdb=" C ILE M 208 " ideal model delta sigma weight residual 113.53 110.08 3.45 9.80e-01 1.04e+00 1.24e+01 ... (remaining 78248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 33464 32.04 - 64.08: 978 64.08 - 96.13: 127 96.13 - 128.17: 2 128.17 - 160.21: 1 Dihedral angle restraints: 34572 sinusoidal: 14227 harmonic: 20345 Sorted by residual: dihedral pdb=" O1B ADP O 701 " pdb=" O3A ADP O 701 " pdb=" PB ADP O 701 " pdb=" PA ADP O 701 " ideal model delta sinusoidal sigma weight residual -60.00 -165.39 105.39 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" O1B ADP N 701 " pdb=" O3A ADP N 701 " pdb=" PB ADP N 701 " pdb=" PA ADP N 701 " ideal model delta sinusoidal sigma weight residual -60.00 -162.84 102.83 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" O1A AR6 L 501 " pdb=" O3A AR6 L 501 " pdb=" PA AR6 L 501 " pdb=" PB AR6 L 501 " ideal model delta sinusoidal sigma weight residual -82.51 77.70 -160.21 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 34569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 6947 0.049 - 0.098: 1231 0.098 - 0.147: 318 0.147 - 0.196: 2 0.196 - 0.245: 2 Chirality restraints: 8500 Sorted by residual: chirality pdb=" CG LEU N 521 " pdb=" CB LEU N 521 " pdb=" CD1 LEU N 521 " pdb=" CD2 LEU N 521 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB THR M 538 " pdb=" CA THR M 538 " pdb=" OG1 THR M 538 " pdb=" CG2 THR M 538 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR P 317 " pdb=" CA THR P 317 " pdb=" OG1 THR P 317 " pdb=" CG2 THR P 317 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 8497 not shown) Planarity restraints: 10034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 270 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO H 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 271 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 271 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 390 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO H 391 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 391 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 391 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 333 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO E 334 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.028 5.00e-02 4.00e+02 ... (remaining 10031 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 441 2.64 - 3.20: 47865 3.20 - 3.77: 76241 3.77 - 4.33: 105252 4.33 - 4.90: 179636 Nonbonded interactions: 409435 Sorted by model distance: nonbonded pdb=" OE1 GLU O 477 " pdb="MG MG O 702 " model vdw 2.072 2.170 nonbonded pdb=" OE2 GLU J 83 " pdb=" O2D AR6 J 501 " model vdw 2.196 2.440 nonbonded pdb=" OE1 GLN C 266 " pdb=" OH TYR C 276 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR O 258 " pdb=" O PRO O 341 " model vdw 2.202 2.440 nonbonded pdb=" OE2 GLU K 106 " pdb=" NZ LYS K 110 " model vdw 2.222 2.520 ... (remaining 409430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'B' and (resid 2 through 387 or resid 395 through 406 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 406 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 4 through 328 or resid 336 through 356 or resid 375 throug \ h 585)) selection = (chain 'N' and (resid 4 through 328 or resid 336 through 356 or resid 375 throug \ h 484 or resid 498 through 585)) selection = (chain 'O' and (resid 4 through 71 or resid 89 through 328 or resid 336 through \ 356 or resid 375 through 484 or resid 498 through 585)) selection = (chain 'P' and (resid 4 through 484 or resid 498 through 585)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.770 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 105.550 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.002 0.034 57840 Z= 0.137 Angle : 0.502 13.263 78253 Z= 0.275 Chirality : 0.040 0.245 8500 Planarity : 0.003 0.066 10034 Dihedral : 15.083 160.211 21568 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 6943 helix: 0.50 (0.10), residues: 2788 sheet: 0.03 (0.19), residues: 721 loop : -1.47 (0.10), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 116 HIS 0.004 0.001 HIS N 292 PHE 0.032 0.001 PHE N 457 TYR 0.014 0.001 TYR D 284 ARG 0.004 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASN cc_start: 0.8382 (t0) cc_final: 0.8154 (t0) REVERT: E 4 TYR cc_start: 0.8434 (m-80) cc_final: 0.8084 (m-10) REVERT: G 48 VAL cc_start: 0.7084 (m) cc_final: 0.6849 (p) REVERT: G 313 HIS cc_start: 0.7154 (m90) cc_final: 0.6802 (m90) REVERT: J 287 MET cc_start: 0.8790 (mmt) cc_final: 0.8444 (mmt) REVERT: K 179 ASP cc_start: 0.7914 (t0) cc_final: 0.7666 (t0) REVERT: O 22 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7592 (mtt90) REVERT: P 150 LEU cc_start: 0.3735 (mm) cc_final: 0.3481 (tp) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.5549 time to fit residues: 536.8929 Evaluate side-chains 298 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 292 optimal weight: 0.1980 chunk 180 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 545 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 406 optimal weight: 0.3980 chunk 632 optimal weight: 30.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 278 HIS C 266 GLN E 129 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS G 383 HIS K 247 GLN L 154 ASN ** M 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 585 ASN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 373 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 57840 Z= 0.284 Angle : 0.572 9.638 78253 Z= 0.293 Chirality : 0.043 0.213 8500 Planarity : 0.004 0.051 10034 Dihedral : 9.004 157.471 8267 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.78 % Allowed : 6.64 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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 (0.10), residues: 6943 helix: 0.22 (0.10), residues: 2805 sheet: -0.03 (0.19), residues: 747 loop : -1.62 (0.10), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 532 HIS 0.007 0.001 HIS P 434 PHE 0.024 0.002 PHE N 457 TYR 0.028 0.002 TYR M 246 ARG 0.008 0.000 ARG G 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 311 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.8672 (t80) cc_final: 0.8464 (t80) REVERT: C 266 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7771 (mm110) REVERT: G 48 VAL cc_start: 0.7193 (m) cc_final: 0.6963 (p) REVERT: J 287 MET cc_start: 0.8767 (mmt) cc_final: 0.8544 (mmt) REVERT: K 105 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7494 (tm-30) REVERT: K 179 ASP cc_start: 0.7948 (t0) cc_final: 0.7701 (t0) REVERT: N 448 MET cc_start: 0.1877 (OUTLIER) cc_final: 0.1038 (mmm) REVERT: O 438 MET cc_start: 0.0112 (mmt) cc_final: -0.0342 (mmt) REVERT: P 32 GLN cc_start: 0.6291 (pp30) cc_final: 0.5086 (mm110) REVERT: P 456 MET cc_start: 0.1772 (mmt) cc_final: 0.1306 (mmm) REVERT: P 463 ARG cc_start: 0.2421 (mmm160) cc_final: -0.0891 (mpt180) outliers start: 47 outliers final: 36 residues processed: 344 average time/residue: 0.5504 time to fit residues: 317.6209 Evaluate side-chains 300 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 396 LEU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 92 ARG Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 181 TYR Chi-restraints excluded: chain O residue 256 ILE Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain P residue 209 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 351 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 526 optimal weight: 0.0040 chunk 430 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 633 optimal weight: 20.0000 chunk 684 optimal weight: 7.9990 chunk 563 optimal weight: 20.0000 chunk 627 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 507 optimal weight: 3.9990 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS I 218 HIS L 8 ASN ** M 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 57840 Z= 0.236 Angle : 0.527 9.466 78253 Z= 0.270 Chirality : 0.042 0.175 8500 Planarity : 0.003 0.051 10034 Dihedral : 8.577 159.336 8267 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.00 % Allowed : 9.32 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -1.03 (0.10), residues: 6943 helix: 0.21 (0.10), residues: 2795 sheet: -0.05 (0.19), residues: 738 loop : -1.61 (0.10), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 602 HIS 0.007 0.001 HIS P 434 PHE 0.017 0.001 PHE N 54 TYR 0.026 0.001 TYR I 386 ARG 0.014 0.000 ARG P 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 280 time to evaluate : 4.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.8735 (t80) cc_final: 0.8521 (t80) REVERT: C 266 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7991 (mm110) REVERT: G 48 VAL cc_start: 0.7204 (m) cc_final: 0.6954 (p) REVERT: I 150 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7489 (mtmt) REVERT: I 386 TYR cc_start: 0.5242 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: K 179 ASP cc_start: 0.7939 (t0) cc_final: 0.7689 (t0) REVERT: N 448 MET cc_start: 0.2199 (OUTLIER) cc_final: 0.1031 (mmt) REVERT: N 460 ILE cc_start: 0.0888 (OUTLIER) cc_final: 0.0515 (mp) REVERT: O 22 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7496 (mtt90) REVERT: O 410 ASP cc_start: 0.3678 (m-30) cc_final: 0.3196 (t0) REVERT: O 438 MET cc_start: 0.0304 (mmt) cc_final: -0.0120 (mmt) REVERT: P 32 GLN cc_start: 0.6409 (pp30) cc_final: 0.5132 (mm110) REVERT: P 463 ARG cc_start: 0.2785 (mmm160) cc_final: -0.0607 (mpt180) outliers start: 60 outliers final: 43 residues processed: 326 average time/residue: 0.5498 time to fit residues: 303.1113 Evaluate side-chains 304 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 257 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 181 TYR Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain P residue 207 ASP Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 625 optimal weight: 7.9990 chunk 476 optimal weight: 10.0000 chunk 328 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 302 optimal weight: 0.0370 chunk 425 optimal weight: 2.9990 chunk 635 optimal weight: 20.0000 chunk 672 optimal weight: 0.0670 chunk 331 optimal weight: 10.0000 chunk 602 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS M 481 HIS M 556 GLN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 57840 Z= 0.170 Angle : 0.486 10.252 78253 Z= 0.248 Chirality : 0.040 0.164 8500 Planarity : 0.003 0.040 10034 Dihedral : 8.268 161.251 8267 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.23 % Allowed : 10.56 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.92 (0.10), residues: 6943 helix: 0.32 (0.10), residues: 2791 sheet: 0.01 (0.19), residues: 747 loop : -1.55 (0.10), residues: 3405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP M 602 HIS 0.008 0.001 HIS P 434 PHE 0.014 0.001 PHE N 420 TYR 0.016 0.001 TYR F 284 ARG 0.011 0.000 ARG P 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 271 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 266 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7705 (mm110) REVERT: E 84 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7558 (tt) REVERT: G 48 VAL cc_start: 0.7159 (m) cc_final: 0.6932 (p) REVERT: J 205 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: K 179 ASP cc_start: 0.7925 (t0) cc_final: 0.7679 (t0) REVERT: N 206 PHE cc_start: 0.0843 (OUTLIER) cc_final: 0.0059 (m-80) REVERT: N 448 MET cc_start: 0.1783 (OUTLIER) cc_final: 0.0786 (mmt) REVERT: N 460 ILE cc_start: 0.0842 (OUTLIER) cc_final: 0.0439 (mp) REVERT: O 438 MET cc_start: 0.0020 (mmt) cc_final: -0.0284 (mmt) REVERT: P 32 GLN cc_start: 0.6481 (pp30) cc_final: 0.5116 (mm110) REVERT: P 463 ARG cc_start: 0.2738 (mmm160) cc_final: -0.0438 (mpt180) outliers start: 74 outliers final: 48 residues processed: 334 average time/residue: 0.5271 time to fit residues: 299.2389 Evaluate side-chains 303 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 249 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain J residue 205 PHE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 396 LEU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 92 ARG Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 181 TYR Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain P residue 207 ASP Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 317 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 560 optimal weight: 0.0970 chunk 381 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 500 optimal weight: 0.0970 chunk 277 optimal weight: 3.9990 chunk 574 optimal weight: 20.0000 chunk 465 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 343 optimal weight: 0.0030 chunk 603 optimal weight: 2.9990 chunk 169 optimal weight: 0.0570 overall best weight: 0.6506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 383 HIS ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS H 364 ASN I 183 GLN K 156 GLN L 18 HIS ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 200 ASN N 481 HIS ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 57840 Z= 0.112 Angle : 0.446 10.905 78253 Z= 0.227 Chirality : 0.039 0.167 8500 Planarity : 0.003 0.037 10034 Dihedral : 7.942 164.290 8267 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 0.83 % Allowed : 11.47 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.69 (0.10), residues: 6943 helix: 0.52 (0.10), residues: 2773 sheet: 0.20 (0.19), residues: 752 loop : -1.46 (0.10), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP M 602 HIS 0.007 0.000 HIS P 434 PHE 0.014 0.001 PHE E 15 TYR 0.016 0.001 TYR I 386 ARG 0.006 0.000 ARG H 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 283 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 287 MET cc_start: 0.8153 (mmm) cc_final: 0.7907 (mmt) REVERT: G 48 VAL cc_start: 0.7106 (m) cc_final: 0.6882 (p) REVERT: K 179 ASP cc_start: 0.7913 (t0) cc_final: 0.7667 (t0) REVERT: N 206 PHE cc_start: 0.0780 (OUTLIER) cc_final: 0.0011 (m-80) REVERT: N 448 MET cc_start: 0.1972 (mmt) cc_final: 0.0921 (mtp) REVERT: N 460 ILE cc_start: 0.0598 (OUTLIER) cc_final: 0.0195 (mp) REVERT: O 438 MET cc_start: -0.0292 (mmt) cc_final: -0.0584 (mmt) REVERT: P 32 GLN cc_start: 0.6657 (pp30) cc_final: 0.4986 (mm110) REVERT: P 420 PHE cc_start: 0.0843 (OUTLIER) cc_final: 0.0556 (m-10) REVERT: P 463 ARG cc_start: 0.2726 (mmm160) cc_final: -0.0241 (mpt180) outliers start: 50 outliers final: 32 residues processed: 323 average time/residue: 0.5445 time to fit residues: 298.6254 Evaluate side-chains 285 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 250 time to evaluate : 4.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 92 ARG Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 207 ASP Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 226 optimal weight: 6.9990 chunk 605 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 394 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 673 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 chunk 311 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS C 81 ASN C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS H 278 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN M 556 GLN M 585 ASN ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 57840 Z= 0.244 Angle : 0.524 10.390 78253 Z= 0.267 Chirality : 0.042 0.210 8500 Planarity : 0.003 0.052 10034 Dihedral : 8.172 157.689 8267 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.66 % Favored : 94.33 % Rotamer: Outliers : 1.35 % Allowed : 11.97 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.87 (0.10), residues: 6943 helix: 0.34 (0.10), residues: 2793 sheet: 0.10 (0.19), residues: 751 loop : -1.54 (0.10), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP M 602 HIS 0.006 0.001 HIS B 313 PHE 0.018 0.002 PHE C 130 TYR 0.023 0.001 TYR I 386 ARG 0.010 0.000 ARG O 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 255 time to evaluate : 4.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: C 266 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7976 (mm110) REVERT: E 84 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7680 (tt) REVERT: G 48 VAL cc_start: 0.7092 (m) cc_final: 0.6870 (p) REVERT: I 146 GLU cc_start: 0.6655 (tt0) cc_final: 0.6298 (tt0) REVERT: I 183 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6189 (mm110) REVERT: I 386 TYR cc_start: 0.4445 (OUTLIER) cc_final: 0.3950 (m-80) REVERT: N 206 PHE cc_start: 0.0779 (OUTLIER) cc_final: 0.0142 (m-80) REVERT: N 448 MET cc_start: 0.2063 (OUTLIER) cc_final: 0.0978 (mmt) REVERT: N 456 MET cc_start: 0.3979 (mtt) cc_final: 0.3548 (mtp) REVERT: N 460 ILE cc_start: 0.0814 (OUTLIER) cc_final: 0.0375 (mp) REVERT: N 528 MET cc_start: 0.5090 (tmm) cc_final: 0.3824 (ptt) REVERT: O 176 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7348 (tt) REVERT: O 410 ASP cc_start: 0.3754 (m-30) cc_final: 0.3183 (t0) REVERT: O 438 MET cc_start: -0.0127 (mmt) cc_final: -0.0395 (mmt) REVERT: P 32 GLN cc_start: 0.6615 (pp30) cc_final: 0.4907 (mm110) REVERT: P 181 TYR cc_start: 0.4514 (OUTLIER) cc_final: 0.3002 (m-10) REVERT: P 420 PHE cc_start: 0.1017 (OUTLIER) cc_final: 0.0669 (m-10) REVERT: P 463 ARG cc_start: 0.2889 (mmm160) cc_final: 0.0114 (mpt180) outliers start: 81 outliers final: 56 residues processed: 323 average time/residue: 0.5303 time to fit residues: 292.6598 Evaluate side-chains 307 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 276 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 181 TYR Chi-restraints excluded: chain P residue 207 ASP Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 472 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 649 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 383 optimal weight: 2.9990 chunk 491 optimal weight: 1.9990 chunk 381 optimal weight: 4.9990 chunk 566 optimal weight: 40.0000 chunk 376 optimal weight: 0.9990 chunk 670 optimal weight: 4.9990 chunk 419 optimal weight: 0.0000 chunk 408 optimal weight: 5.9990 chunk 309 optimal weight: 0.0970 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 57840 Z= 0.115 Angle : 0.455 12.252 78253 Z= 0.230 Chirality : 0.039 0.227 8500 Planarity : 0.003 0.038 10034 Dihedral : 7.815 163.455 8267 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.18 % Favored : 95.81 % Rotamer: Outliers : 1.17 % Allowed : 12.56 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.10), residues: 6943 helix: 0.59 (0.11), residues: 2762 sheet: 0.27 (0.19), residues: 751 loop : -1.42 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP M 602 HIS 0.016 0.001 HIS C 267 PHE 0.012 0.001 PHE P 462 TYR 0.018 0.001 TYR I 386 ARG 0.009 0.000 ARG O 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 269 time to evaluate : 4.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: B 174 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: C 266 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: F 287 MET cc_start: 0.8132 (mmm) cc_final: 0.7898 (mmt) REVERT: G 48 VAL cc_start: 0.7038 (m) cc_final: 0.6802 (p) REVERT: I 146 GLU cc_start: 0.6522 (tt0) cc_final: 0.6152 (tt0) REVERT: I 183 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6058 (mm110) REVERT: I 386 TYR cc_start: 0.4308 (OUTLIER) cc_final: 0.3829 (m-80) REVERT: N 206 PHE cc_start: 0.0868 (OUTLIER) cc_final: 0.0054 (m-80) REVERT: N 448 MET cc_start: 0.1754 (OUTLIER) cc_final: 0.0749 (mmt) REVERT: N 456 MET cc_start: 0.3968 (mtt) cc_final: 0.3535 (mtp) REVERT: N 460 ILE cc_start: 0.0609 (OUTLIER) cc_final: 0.0176 (mp) REVERT: N 528 MET cc_start: 0.4672 (tmm) cc_final: 0.3421 (ptt) REVERT: O 176 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7177 (tt) REVERT: O 410 ASP cc_start: 0.3693 (m-30) cc_final: 0.3152 (t0) REVERT: O 438 MET cc_start: 0.0073 (mmt) cc_final: -0.0147 (mmt) REVERT: P 32 GLN cc_start: 0.6673 (pp30) cc_final: 0.4835 (mm110) REVERT: P 420 PHE cc_start: 0.1203 (OUTLIER) cc_final: 0.0852 (m-10) REVERT: P 461 LEU cc_start: 0.1947 (OUTLIER) cc_final: 0.1547 (pp) REVERT: P 463 ARG cc_start: 0.2889 (mmm160) cc_final: -0.0064 (mpt180) outliers start: 70 outliers final: 44 residues processed: 329 average time/residue: 0.5369 time to fit residues: 298.1332 Evaluate side-chains 300 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 245 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 374 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 415 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 426 optimal weight: 0.3980 chunk 457 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 527 optimal weight: 0.0570 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 57840 Z= 0.128 Angle : 0.455 9.671 78253 Z= 0.230 Chirality : 0.039 0.214 8500 Planarity : 0.003 0.038 10034 Dihedral : 7.698 161.814 8267 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.70 % Favored : 95.29 % Rotamer: Outliers : 1.15 % Allowed : 13.01 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.58 (0.10), residues: 6943 helix: 0.61 (0.11), residues: 2773 sheet: 0.31 (0.19), residues: 752 loop : -1.41 (0.10), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP M 602 HIS 0.010 0.001 HIS C 267 PHE 0.011 0.001 PHE C 130 TYR 0.016 0.001 TYR I 386 ARG 0.006 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 267 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: B 174 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: C 266 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7274 (mm110) REVERT: F 45 MET cc_start: 0.7587 (mpp) cc_final: 0.7105 (mpp) REVERT: F 287 MET cc_start: 0.8183 (mmm) cc_final: 0.7956 (mmt) REVERT: G 48 VAL cc_start: 0.7061 (m) cc_final: 0.6831 (p) REVERT: I 183 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6052 (mm110) REVERT: I 386 TYR cc_start: 0.4211 (OUTLIER) cc_final: 0.3755 (m-80) REVERT: N 206 PHE cc_start: 0.0918 (OUTLIER) cc_final: 0.0107 (m-80) REVERT: N 413 MET cc_start: 0.1726 (mmt) cc_final: 0.1335 (mmt) REVERT: N 448 MET cc_start: 0.2036 (OUTLIER) cc_final: 0.0976 (mmt) REVERT: N 456 MET cc_start: 0.3893 (mtt) cc_final: 0.3454 (mtp) REVERT: N 460 ILE cc_start: 0.0650 (OUTLIER) cc_final: 0.0224 (mp) REVERT: N 528 MET cc_start: 0.4942 (tmm) cc_final: 0.3584 (ptt) REVERT: O 176 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7166 (tt) REVERT: O 187 ASN cc_start: 0.5568 (m110) cc_final: 0.5329 (t0) REVERT: O 410 ASP cc_start: 0.3727 (m-30) cc_final: 0.3166 (t0) REVERT: P 32 GLN cc_start: 0.6675 (pp30) cc_final: 0.4820 (mm110) REVERT: P 420 PHE cc_start: 0.1339 (OUTLIER) cc_final: 0.1043 (m-10) REVERT: P 461 LEU cc_start: 0.2016 (OUTLIER) cc_final: 0.1742 (pp) REVERT: P 463 ARG cc_start: 0.2741 (mmm160) cc_final: 0.0053 (mpt180) outliers start: 69 outliers final: 51 residues processed: 324 average time/residue: 0.5378 time to fit residues: 295.3138 Evaluate side-chains 314 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 252 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 610 optimal weight: 0.2980 chunk 642 optimal weight: 5.9990 chunk 586 optimal weight: 7.9990 chunk 625 optimal weight: 20.0000 chunk 376 optimal weight: 3.9990 chunk 272 optimal weight: 0.2980 chunk 490 optimal weight: 20.0000 chunk 191 optimal weight: 0.9990 chunk 564 optimal weight: 5.9990 chunk 591 optimal weight: 2.9990 chunk 622 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS C 81 ASN C 266 GLN E 227 HIS ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 57840 Z= 0.128 Angle : 0.454 9.572 78253 Z= 0.229 Chirality : 0.039 0.193 8500 Planarity : 0.003 0.039 10034 Dihedral : 7.604 160.644 8267 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.34 % Favored : 95.65 % Rotamer: Outliers : 1.18 % Allowed : 13.12 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.10), residues: 6943 helix: 0.67 (0.11), residues: 2754 sheet: 0.35 (0.19), residues: 744 loop : -1.38 (0.10), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 602 HIS 0.005 0.001 HIS P 434 PHE 0.010 0.001 PHE C 130 TYR 0.017 0.001 TYR H 263 ARG 0.006 0.000 ARG K 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 264 time to evaluate : 4.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 174 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: C 266 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7228 (mm110) REVERT: F 45 MET cc_start: 0.7627 (mpp) cc_final: 0.7159 (mpp) REVERT: G 48 VAL cc_start: 0.7066 (m) cc_final: 0.6829 (p) REVERT: I 183 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6041 (mm110) REVERT: I 386 TYR cc_start: 0.4287 (OUTLIER) cc_final: 0.3638 (m-80) REVERT: N 206 PHE cc_start: 0.0925 (OUTLIER) cc_final: 0.0115 (m-80) REVERT: N 413 MET cc_start: 0.1368 (mmt) cc_final: 0.0976 (mmt) REVERT: N 448 MET cc_start: 0.2044 (OUTLIER) cc_final: 0.0975 (mmt) REVERT: N 456 MET cc_start: 0.3884 (mtt) cc_final: 0.3430 (mtp) REVERT: N 460 ILE cc_start: 0.0651 (OUTLIER) cc_final: 0.0224 (mp) REVERT: N 528 MET cc_start: 0.4709 (tmm) cc_final: 0.3368 (ptt) REVERT: O 176 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7150 (tt) REVERT: O 410 ASP cc_start: 0.3733 (m-30) cc_final: 0.3173 (t0) REVERT: P 32 GLN cc_start: 0.6677 (pp30) cc_final: 0.4817 (mm110) REVERT: P 420 PHE cc_start: 0.1311 (OUTLIER) cc_final: 0.1009 (m-10) REVERT: P 461 LEU cc_start: 0.2007 (OUTLIER) cc_final: 0.1782 (pp) REVERT: P 463 ARG cc_start: 0.2818 (mmm160) cc_final: 0.0142 (mpt180) outliers start: 71 outliers final: 55 residues processed: 322 average time/residue: 0.5314 time to fit residues: 291.7156 Evaluate side-chains 313 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 247 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 480 HIS Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 562 SER Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 181 TYR Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Chi-restraints excluded: chain P residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 410 optimal weight: 0.7980 chunk 661 optimal weight: 8.9990 chunk 403 optimal weight: 0.0970 chunk 313 optimal weight: 6.9990 chunk 459 optimal weight: 0.0000 chunk 693 optimal weight: 5.9990 chunk 638 optimal weight: 5.9990 chunk 552 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 426 optimal weight: 0.3980 chunk 338 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 57840 Z= 0.118 Angle : 0.452 14.539 78253 Z= 0.227 Chirality : 0.039 0.196 8500 Planarity : 0.003 0.040 10034 Dihedral : 7.489 159.855 8267 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 1.12 % Allowed : 13.29 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.46 (0.10), residues: 6943 helix: 0.73 (0.11), residues: 2746 sheet: 0.43 (0.20), residues: 742 loop : -1.34 (0.10), residues: 3455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP M 602 HIS 0.005 0.000 HIS P 434 PHE 0.012 0.001 PHE P 462 TYR 0.015 0.001 TYR I 386 ARG 0.007 0.000 ARG K 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13886 Ramachandran restraints generated. 6943 Oldfield, 0 Emsley, 6943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 257 time to evaluate : 4.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 174 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: C 266 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7238 (mm110) REVERT: F 45 MET cc_start: 0.7603 (mpp) cc_final: 0.7134 (mpp) REVERT: G 48 VAL cc_start: 0.7061 (m) cc_final: 0.6827 (p) REVERT: I 183 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6032 (mm110) REVERT: I 386 TYR cc_start: 0.4331 (OUTLIER) cc_final: 0.3959 (m-80) REVERT: N 206 PHE cc_start: 0.0912 (OUTLIER) cc_final: 0.0111 (m-80) REVERT: N 413 MET cc_start: 0.1282 (mmt) cc_final: 0.0851 (mmt) REVERT: N 448 MET cc_start: 0.2045 (OUTLIER) cc_final: 0.0967 (mmt) REVERT: N 456 MET cc_start: 0.3870 (mtt) cc_final: 0.3410 (mtp) REVERT: N 460 ILE cc_start: 0.0593 (OUTLIER) cc_final: 0.0174 (mp) REVERT: N 528 MET cc_start: 0.4634 (tmm) cc_final: 0.3267 (ptt) REVERT: O 176 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7093 (tt) REVERT: O 410 ASP cc_start: 0.3716 (m-30) cc_final: 0.3167 (t0) REVERT: P 32 GLN cc_start: 0.6702 (pp30) cc_final: 0.4806 (mm110) REVERT: P 420 PHE cc_start: 0.1338 (OUTLIER) cc_final: 0.1021 (m-10) outliers start: 67 outliers final: 54 residues processed: 311 average time/residue: 0.5258 time to fit residues: 279.1375 Evaluate side-chains 315 residues out of total 5997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 251 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 267 HIS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 275 LYS Chi-restraints excluded: chain H residue 400 VAL Chi-restraints excluded: chain I residue 183 GLN Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain L residue 139 ASP Chi-restraints excluded: chain L residue 400 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 474 LEU Chi-restraints excluded: chain M residue 480 HIS Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 139 ILE Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 256 ILE Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain O residue 444 ASP Chi-restraints excluded: chain O residue 500 LEU Chi-restraints excluded: chain O residue 550 MET Chi-restraints excluded: chain O residue 593 SER Chi-restraints excluded: chain O residue 597 VAL Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 420 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 438 optimal weight: 0.0470 chunk 588 optimal weight: 0.1980 chunk 169 optimal weight: 0.9990 chunk 509 optimal weight: 50.0000 chunk 81 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 553 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 567 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 HIS C 266 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.181516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144718 restraints weight = 87079.664| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.64 r_work: 0.3340 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 57840 Z= 0.147 Angle : 0.464 14.355 78253 Z= 0.234 Chirality : 0.039 0.189 8500 Planarity : 0.003 0.039 10034 Dihedral : 7.491 156.774 8267 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 1.13 % Allowed : 13.31 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.15 % 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: -0.51 (0.10), residues: 6943 helix: 0.65 (0.11), residues: 2768 sheet: 0.44 (0.19), residues: 739 loop : -1.37 (0.10), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 602 HIS 0.005 0.001 HIS I 144 PHE 0.027 0.001 PHE P 462 TYR 0.019 0.001 TYR H 263 ARG 0.007 0.000 ARG K 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8778.64 seconds wall clock time: 156 minutes 41.44 seconds (9401.44 seconds total)