Starting phenix.real_space_refine on Sun Apr 7 04:27:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sub_40763/04_2024/8sub_40763_updated.pdb" } resolution = 2.89 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= 0.090 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 34 5.49 5 Mg 5 5.21 5 S 134 5.16 5 C 39110 2.51 5 N 10395 2.21 5 O 11548 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 "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 61226 Number of models: 1 Model: "" Number of chains: 34 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: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3186 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 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: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} 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: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 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: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} Chain breaks: 1 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: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} 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: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 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: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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} Chain: "P" 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: "Q" 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: 23.11, per 1000 atoms: 0.38 Number of scatterers: 61226 At special positions: 0 Unit cell: (187.59, 183.15, 220.89, 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 134 16.00 P 34 15.00 Mg 5 11.99 O 11548 8.00 N 10395 7.00 C 39110 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: 17.09 Conformation dependent library (CDL) restraints added in 9.0 seconds 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 46 sheets defined 40.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.05 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.538A pdb=" N ARG A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 removed outlier: 3.887A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.503A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 82 through 98 removed outlier: 3.535A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 123 removed outlier: 3.809A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 131 removed outlier: 4.420A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 131' 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 153 removed outlier: 3.668A pdb=" N LYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 143 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 144 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.591A 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: 3.690A pdb=" N MET A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.560A pdb=" N ALA A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.644A 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 360 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.749A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.514A 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 12 through 24 removed outlier: 3.909A pdb=" N ARG B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.620A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.534A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.878A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.752A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.975A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.950A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) 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 139 through 153 removed outlier: 3.790A pdb=" N LYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR B 143 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 144 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.004A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) 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 294 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.573A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.716A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.548A pdb=" N TYR C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 37 removed outlier: 3.515A pdb=" N SER C 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.552A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 102 through 121 removed outlier: 3.656A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.547A pdb=" N PHE C 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 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 152 removed outlier: 3.606A pdb=" N LYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR C 143 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS C 144 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.611A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.997A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 202 " --> pdb=" O GLN C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 202' Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.713A 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: 3.863A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.842A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 350 through 359 removed outlier: 3.605A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.598A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 383' Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.569A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.748A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.245A 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 57 through 65 removed outlier: 4.134A pdb=" N GLY D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.694A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 118 removed outlier: 3.695A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 4.242A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) 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: 3.971A pdb=" N LYS D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR D 143 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS D 144 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 179 removed outlier: 3.545A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.695A 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 251 removed outlier: 3.651A pdb=" N TYR D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 283 through 296 removed outlier: 3.521A pdb=" N GLU D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 295 " --> pdb=" O PHE D 291 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 5.109A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 350 through 360 removed outlier: 3.506A pdb=" N LYS D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 360 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.663A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 removed outlier: 4.453A pdb=" N GLN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.627A pdb=" N TRP E 49 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 65 removed outlier: 4.316A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'E' and resid 82 through 99 removed outlier: 3.617A pdb=" N ILE E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 123 removed outlier: 4.245A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 removed outlier: 3.878A pdb=" N PHE E 130 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 139 through 152 removed outlier: 4.925A pdb=" N TYR E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS E 144 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS E 145 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 removed outlier: 3.633A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.827A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 3.623A 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 294 removed outlier: 3.849A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 322 removed outlier: 3.779A pdb=" N LEU E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 345 removed outlier: 3.902A pdb=" N THR E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (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 382 removed outlier: 3.634A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 382' Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.665A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 40 removed outlier: 3.846A pdb=" N SER F 37 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY F 39 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS F 40 " --> pdb=" O SER F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.716A pdb=" N TRP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 65 removed outlier: 3.905A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 76 Processing helix chain 'F' and resid 83 through 98 removed outlier: 3.618A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 123 removed outlier: 4.066A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.882A 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 143 through 153 Processing helix chain 'F' and resid 172 through 180 Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.706A 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 257 Processing helix chain 'F' and resid 282 through 294 removed outlier: 3.771A pdb=" N GLU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 321 removed outlier: 3.839A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA F 321 " --> pdb=" O ILE F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.602A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 removed outlier: 3.610A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (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 removed outlier: 3.520A pdb=" N GLU F 382 " --> pdb=" O ASN F 378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 407 removed outlier: 4.249A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.704A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 45 through 53 Processing helix chain 'G' and resid 62 through 65 No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 102 through 122 removed outlier: 3.912A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 4.321A 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 140 through 154 removed outlier: 4.544A pdb=" N TYR G 143 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N HIS G 144 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS G 145 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER G 153 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN G 154 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 180 Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.912A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.584A 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 281 through 295 removed outlier: 3.517A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 323 removed outlier: 3.658A pdb=" N ARG G 316 " --> pdb=" O TYR G 312 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 344 removed outlier: 3.748A pdb=" N LYS G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 Processing helix chain 'G' and resid 377 through 383 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'H' and resid 12 through 24 removed outlier: 3.630A pdb=" N CYS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 53 Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 72 through 77 removed outlier: 4.069A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 99 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.614A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA H 123 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 3.718A pdb=" N PHE H 130 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 127 through 131' 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 139 through 154 removed outlier: 3.551A pdb=" N LYS H 142 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR H 143 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS H 144 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE H 152 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER H 153 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 154 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 180 removed outlier: 3.680A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.840A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 245 through 251 Processing helix chain 'H' and resid 282 through 294 Processing helix chain 'H' and resid 312 through 323 removed outlier: 4.096A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 344 Processing helix chain 'H' and resid 350 through 360 removed outlier: 3.930A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.694A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 407 removed outlier: 4.056A pdb=" N SER H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.562A pdb=" N CYS I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 40 removed outlier: 3.590A pdb=" N SER I 37 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY I 39 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.540A pdb=" N LYS I 50 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.565A pdb=" N LEU I 63 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE I 64 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP I 65 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 82 through 99 removed outlier: 3.923A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 123 removed outlier: 3.860A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.628A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 180 removed outlier: 3.967A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 202 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 292 Processing helix chain 'I' and resid 312 through 323 removed outlier: 3.679A pdb=" N ALA I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.816A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 359 Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.781A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 405 removed outlier: 4.246A pdb=" N GLU I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 22 removed outlier: 3.663A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 40 removed outlier: 3.674A pdb=" N SER J 37 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.507A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 removed outlier: 3.767A pdb=" N ILE J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 77 Processing helix chain 'J' and resid 82 through 98 removed outlier: 3.647A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 123 removed outlier: 3.822A pdb=" N LYS J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 131 removed outlier: 3.635A pdb=" N PHE J 130 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 127 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: 3.718A pdb=" N LYS J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR J 143 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS J 144 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS J 145 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER J 153 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.759A pdb=" N ALA J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 202 removed outlier: 3.752A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP J 202 " --> pdb=" O GLN J 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 202' Processing helix chain 'J' and resid 245 through 251 removed outlier: 3.745A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 258 Processing helix chain 'J' and resid 275 through 277 No H-bonds generated for 'chain 'J' and resid 275 through 277' Processing helix chain 'J' and resid 282 through 296 removed outlier: 3.717A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER J 296 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 323 removed outlier: 3.558A pdb=" N GLY J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 321 " --> pdb=" O ILE J 317 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU J 323 " --> pdb=" O LEU J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 344 removed outlier: 3.590A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 377 through 383 removed outlier: 3.529A pdb=" N HIS J 383 " --> pdb=" O SER J 379 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 407 removed outlier: 3.537A pdb=" N ALA J 402 " --> pdb=" O GLU J 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 removed outlier: 3.507A pdb=" N SER K 21 " --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 40 removed outlier: 3.632A pdb=" N SER K 37 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS K 40 " --> pdb=" O SER K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 55 removed outlier: 3.656A pdb=" N TRP K 49 " --> pdb=" O MET K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 82 through 99 removed outlier: 3.885A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 removed outlier: 3.583A pdb=" N GLU K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 123 removed outlier: 3.573A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 removed outlier: 4.332A 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 139 through 154 removed outlier: 4.972A pdb=" N TYR K 143 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS K 144 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS K 145 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE K 152 " --> pdb=" O SER K 149 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER K 153 " --> pdb=" O LYS K 150 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 178 Processing helix chain 'K' and resid 200 through 202 No H-bonds generated for 'chain 'K' and resid 200 through 202' Processing helix chain 'K' and resid 245 through 251 Processing helix chain 'K' and resid 253 through 257 removed outlier: 3.546A pdb=" N ILE K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 253 through 257' Processing helix chain 'K' and resid 280 through 296 removed outlier: 3.902A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU K 293 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER K 296 " --> pdb=" O GLY K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 323 removed outlier: 3.849A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU K 323 " --> pdb=" O LEU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 3.624A pdb=" N SER K 344 " --> pdb=" O ILE K 340 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 removed outlier: 3.531A pdb=" N THR K 357 " --> pdb=" O LYS K 353 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.781A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.644A 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 23 removed outlier: 3.584A pdb=" N CYS L 23 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 55 removed outlier: 4.052A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 4.026A 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 removed outlier: 3.852A pdb=" N ASP L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 76' Processing helix chain 'L' and resid 82 through 98 removed outlier: 3.621A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 123 removed outlier: 3.768A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA L 123 " --> pdb=" O VAL L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.963A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) 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 139 through 154 removed outlier: 4.982A pdb=" N TYR L 143 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS L 144 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS L 145 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE L 152 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER L 153 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN L 154 " --> pdb=" O LEU L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 180 removed outlier: 3.734A pdb=" N ALA L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.842A 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: 3.612A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 323 removed outlier: 4.011A pdb=" N LEU L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU L 323 " --> pdb=" O LEU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 344 Processing helix chain 'L' and resid 350 through 360 removed outlier: 3.545A pdb=" N LEU L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 375 removed outlier: 3.582A pdb=" N ALA L 375 " --> pdb=" O GLY L 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 372 through 375' Processing helix chain 'L' and resid 377 through 382 Processing helix chain 'L' and resid 394 through 406 Processing helix chain 'M' and resid 130 through 136 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: 3.583A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 270 removed outlier: 4.049A pdb=" N LEU M 261 " --> pdb=" O TYR M 258 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA M 264 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY M 265 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 266 " --> pdb=" O PHE M 263 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M 270 " --> pdb=" O ILE M 267 " (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 322 through 330 Processing helix chain 'M' and resid 343 through 355 removed outlier: 3.587A pdb=" N THR M 348 " --> pdb=" O SER M 345 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU M 349 " --> pdb=" O LEU M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 371 No H-bonds generated for 'chain 'M' and resid 368 through 371' Processing helix chain 'M' and resid 375 through 385 removed outlier: 3.703A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 392 No H-bonds generated for 'chain 'M' and resid 390 through 392' Processing helix chain 'M' and resid 408 through 421 removed outlier: 4.234A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 446 through 449 No H-bonds generated for 'chain 'M' and resid 446 through 449' Processing helix chain 'M' and resid 453 through 464 removed outlier: 4.070A pdb=" N ALA M 458 " --> pdb=" O LEU M 454 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG M 463 " --> pdb=" O GLU M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 468 No H-bonds generated for 'chain 'M' and resid 466 through 468' Processing helix chain 'M' and resid 479 through 482 No H-bonds generated for 'chain 'M' and resid 479 through 482' 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 528 Processing helix chain 'M' and resid 540 through 549 removed outlier: 3.855A pdb=" N GLN M 544 " --> pdb=" O GLU M 540 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA M 545 " --> pdb=" O ARG M 541 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU M 546 " --> pdb=" O ASP M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 558 through 563 removed outlier: 3.965A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 598 through 603 Processing helix chain 'N' and resid 30 through 33 Processing helix chain 'N' and resid 130 through 136 removed outlier: 3.687A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 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 195 Processing helix chain 'N' and resid 213 through 216 Processing helix chain 'N' and resid 258 through 267 removed outlier: 3.780A pdb=" N LEU N 261 " --> pdb=" O TYR N 258 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE N 263 " --> pdb=" O ALA N 260 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA N 264 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU N 266 " --> pdb=" O PHE N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 290 removed outlier: 3.550A pdb=" N ILE N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG N 290 " --> pdb=" O SER N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 330 Processing helix chain 'N' and resid 343 through 346 Processing helix chain 'N' and resid 348 through 355 Processing helix chain 'N' and resid 368 through 385 removed outlier: 3.904A pdb=" N SER N 372 " --> pdb=" O ALA N 368 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN N 373 " --> pdb=" O PHE N 369 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL N 374 " --> pdb=" O GLY N 370 " (cutoff:3.500A) Proline residue: N 376 - end of helix Processing helix chain 'N' and resid 408 through 421 removed outlier: 3.987A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 446 through 464 removed outlier: 3.580A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 504 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 525 through 527 No H-bonds generated for 'chain 'N' and resid 525 through 527' Processing helix chain 'N' and resid 540 through 549 removed outlier: 3.541A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 558 through 563 removed outlier: 4.405A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 136 removed outlier: 3.575A pdb=" N ILE O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 146 Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 213 through 216 Processing helix chain 'O' and resid 258 through 270 removed outlier: 3.543A pdb=" N LEU O 261 " --> pdb=" O TYR O 258 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY O 262 " --> pdb=" O GLN O 259 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE O 263 " --> pdb=" O ALA O 260 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA O 264 " --> pdb=" O LEU O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 287 Processing helix chain 'O' and resid 319 through 330 removed outlier: 3.650A pdb=" N LEU O 322 " --> pdb=" O GLN O 319 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA O 323 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU O 324 " --> pdb=" O LYS O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 353 removed outlier: 3.530A pdb=" N LEU O 346 " --> pdb=" O PHE O 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU O 349 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL O 350 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 384 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: 3.887A pdb=" N ALA O 412 " --> pdb=" O HIS O 408 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP O 418 " --> pdb=" O SER O 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 446 through 464 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 507 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 540 through 547 removed outlier: 3.530A pdb=" N LEU O 546 " --> pdb=" O ASP O 542 " (cutoff:3.500A) Processing helix chain 'O' and resid 560 through 563 Processing helix chain 'O' and resid 598 through 602 Processing helix chain 'P' and resid 30 through 33 removed outlier: 3.623A pdb=" N GLY P 33 " --> pdb=" O GLY P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 30 through 33' 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 168 No H-bonds generated for 'chain 'P' and resid 165 through 168' Processing helix chain 'P' and resid 183 through 197 Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'P' and resid 262 through 270 removed outlier: 3.753A pdb=" N LEU P 266 " --> pdb=" O GLY P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 286 Processing helix chain 'P' and resid 319 through 321 No H-bonds generated for 'chain 'P' and resid 319 through 321' Processing helix chain 'P' and resid 343 through 353 removed outlier: 3.758A pdb=" N LEU P 346 " --> pdb=" O PHE P 343 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA P 347 " --> pdb=" O LYS P 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR P 348 " --> pdb=" O SER P 345 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE P 353 " --> pdb=" O VAL P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.615A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 388 through 393 removed outlier: 3.683A pdb=" N SER P 392 " --> pdb=" O ILE P 388 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE P 393 " --> pdb=" O ARG P 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 388 through 393' Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 447 through 464 removed outlier: 3.966A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 507 removed outlier: 5.784A pdb=" N ARG P 505 " --> pdb=" O ALA P 501 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS P 506 " --> pdb=" O LYS P 502 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE P 507 " --> pdb=" O GLU P 503 " (cutoff:3.500A) 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 526 through 528 No H-bonds generated for 'chain 'P' and resid 526 through 528' Processing helix chain 'P' and resid 540 through 549 removed outlier: 3.803A pdb=" N ALA P 545 " --> pdb=" O ARG P 541 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 558 through 563 removed outlier: 3.669A pdb=" N ILE P 561 " --> pdb=" O LEU P 558 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER P 562 " --> pdb=" O LYS P 559 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY P 563 " --> pdb=" O GLN P 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 558 through 563' Processing helix chain 'P' and resid 599 through 602 Processing helix chain 'Q' and resid 130 through 137 removed outlier: 3.784A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 146 removed outlier: 3.641A pdb=" N LEU Q 144 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Proline residue: Q 145 - end of helix No H-bonds generated for 'chain 'Q' and resid 141 through 146' Processing helix chain 'Q' and resid 183 through 197 Processing helix chain 'Q' and resid 214 through 216 No H-bonds generated for 'chain 'Q' and resid 214 through 216' Processing helix chain 'Q' and resid 258 through 260 No H-bonds generated for 'chain 'Q' and resid 258 through 260' Processing helix chain 'Q' and resid 262 through 270 removed outlier: 3.810A pdb=" N LEU Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 285 Processing helix chain 'Q' and resid 322 through 331 Processing helix chain 'Q' and resid 343 through 354 Processing helix chain 'Q' and resid 370 through 385 removed outlier: 3.871A pdb=" N VAL Q 374 " --> pdb=" O GLY Q 370 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU Q 375 " --> pdb=" O PHE Q 371 " (cutoff:3.500A) Proline residue: Q 376 - end of helix Processing helix chain 'Q' and resid 388 through 393 removed outlier: 4.161A pdb=" N ILE Q 393 " --> pdb=" O ARG Q 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 420 removed outlier: 3.527A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 464 removed outlier: 4.006A pdb=" N ALA Q 452 " --> pdb=" O MET Q 448 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG Q 464 " --> pdb=" O ILE Q 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 479 through 481 No H-bonds generated for 'chain 'Q' and resid 479 through 481' Processing helix chain 'Q' and resid 523 through 528 removed outlier: 4.066A pdb=" N MET Q 528 " --> pdb=" O THR Q 524 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 through 549 removed outlier: 4.033A pdb=" N ALA Q 545 " --> pdb=" O ARG Q 541 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU Q 546 " --> pdb=" O ASP Q 542 " (cutoff:3.500A) Processing helix chain 'Q' and resid 558 through 560 No H-bonds generated for 'chain 'Q' and resid 558 through 560' Processing helix chain 'Q' and resid 598 through 601 No H-bonds generated for 'chain 'Q' and resid 598 through 601' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 8.835A pdb=" N THR A 367 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 329 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL A 369 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 163 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU A 32 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE A 165 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ILE A 164 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR A 166 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR A 224 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN A 183 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A 223 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.925A 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: 8.630A pdb=" N THR B 367 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 329 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N VAL B 369 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 331 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN B 27 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N PHE B 303 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 29 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN B 305 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 31 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 163 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU B 32 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 165 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ILE B 164 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR B 166 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR B 224 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.931A 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: 8.800A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 300 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N VAL C 330 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 302 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N TYR C 332 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 304 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN C 27 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N PHE C 303 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C 29 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ASN C 305 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 31 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA C 163 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU C 32 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE C 165 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ILE C 164 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR C 166 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR C 224 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN C 183 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU C 223 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 185 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.872A 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 8 through 10 removed outlier: 3.733A pdb=" N ASN D 8 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 5 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N PHE D 303 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY D 29 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN D 305 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 31 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA D 163 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU D 32 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE D 165 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N ILE D 164 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR D 222 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR D 166 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR D 224 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.874A 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 183 through 185 removed outlier: 3.602A pdb=" N ALA E 163 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 232 through 234 Processing sheet with id= K, first strand: chain 'F' and resid 3 through 5 removed outlier: 8.544A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA F 163 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N LEU F 32 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE F 165 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N ILE F 164 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR F 222 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR F 166 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR F 224 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 232 through 234 Processing sheet with id= M, first strand: chain 'G' and resid 29 through 31 removed outlier: 7.209A pdb=" N ALA G 163 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ILE G 164 " --> pdb=" O HIS G 220 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR G 222 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR G 166 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR G 224 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN G 183 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU G 223 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE G 185 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS G 225 " --> pdb=" O PHE G 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 232 through 234 Processing sheet with id= O, first strand: chain 'G' and resid 329 through 332 Processing sheet with id= P, first strand: chain 'H' and resid 3 through 5 removed outlier: 8.377A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN H 27 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N PHE H 303 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY H 29 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ASN H 305 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU H 31 " --> pdb=" O ASN H 305 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA H 163 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU H 32 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE H 165 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ILE H 164 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR H 222 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR H 166 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR H 224 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 3 through 5 removed outlier: 8.720A pdb=" N THR I 367 " --> pdb=" O PHE I 327 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL I 329 " --> pdb=" O THR I 367 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL I 369 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE I 331 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR I 300 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL I 330 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU I 302 " --> pdb=" O VAL I 330 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR I 332 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE I 304 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN I 305 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU I 31 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA I 163 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU I 32 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE I 165 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N ILE I 164 " --> pdb=" O HIS I 220 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR I 222 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR I 166 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR I 224 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN I 183 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU I 223 " --> pdb=" O GLN I 183 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE I 185 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS I 225 " --> pdb=" O PHE I 185 " (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 3 through 5 removed outlier: 8.611A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN J 27 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N PHE J 303 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY J 29 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ASN J 305 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU J 31 " --> pdb=" O ASN J 305 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA J 163 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU J 32 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE J 165 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ILE J 164 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR J 222 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR J 166 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR J 224 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.807A 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: 8.778A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA K 163 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU K 32 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE K 165 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ILE K 164 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR K 222 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR K 166 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR K 224 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 232 through 234 Processing sheet with id= W, first strand: chain 'L' and resid 3 through 5 removed outlier: 8.759A pdb=" N THR L 367 " --> pdb=" O PHE L 327 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR L 300 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL L 330 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU L 302 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR L 332 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE L 304 " --> pdb=" O TYR L 332 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA L 163 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU L 32 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE L 165 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE L 164 " --> pdb=" O HIS L 220 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR L 222 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR L 166 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR L 224 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 232 through 234 Processing sheet with id= Y, first strand: chain 'M' and resid 67 through 70 removed outlier: 3.697A pdb=" N ASP M 67 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 95 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU M 27 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG M 22 " --> pdb=" O GLU M 19 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU M 19 " --> pdb=" O ARG M 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'M' and resid 125 through 127 removed outlier: 3.887A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 252 through 254 removed outlier: 3.982A pdb=" N LYS M 254 " --> pdb=" O ILE M 226 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL M 433 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR M 225 " --> pdb=" O VAL M 433 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE M 435 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU M 227 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN M 437 " --> pdb=" O LEU M 227 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE M 203 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL M 436 " --> pdb=" O ILE M 203 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU M 477 " --> pdb=" O PHE M 206 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU M 173 " --> pdb=" O VAL M 513 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR M 515 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL M 175 " --> pdb=" O THR M 515 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN M 531 " --> pdb=" O ALA M 174 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU M 176 " --> pdb=" O ASN M 531 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE M 533 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE M 161 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 292 through 294 removed outlier: 3.778A pdb=" N HIS M 292 " --> pdb=" O TYR M 299 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR M 299 " --> pdb=" O HIS M 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE M 308 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.938A pdb=" N ASP N 67 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA N 69 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG N 92 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY N 17 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN N 26 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL N 15 " --> pdb=" O ASN N 26 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 35 through 38 removed outlier: 3.519A pdb=" N GLY N 41 " --> pdb=" O HIS N 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 125 through 127 removed outlier: 3.831A pdb=" N GLY N 100 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG N 64 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA N 98 " --> pdb=" O ARG N 64 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 222 through 226 removed outlier: 6.613A pdb=" N VAL N 433 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR N 225 " --> pdb=" O VAL N 433 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE N 435 " --> pdb=" O THR N 225 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE N 203 " --> pdb=" O HIS N 434 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL N 436 " --> pdb=" O ILE N 203 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE N 205 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL N 473 " --> pdb=" O VAL N 204 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE N 206 " --> pdb=" O VAL N 473 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU N 475 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU N 173 " --> pdb=" O VAL N 513 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR N 515 " --> pdb=" O LEU N 173 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL N 175 " --> pdb=" O THR N 515 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA N 174 " --> pdb=" O SER N 530 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP N 532 " --> pdb=" O ALA N 174 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU N 176 " --> pdb=" O TRP N 532 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER N 534 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 298 through 301 removed outlier: 4.677A pdb=" N ILE N 298 " --> pdb=" O LEU N 310 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 356 through 358 Processing sheet with id= AJ, first strand: chain 'O' and resid 67 through 70 removed outlier: 3.708A pdb=" N ASP O 67 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG O 92 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG O 22 " --> pdb=" O GLU O 19 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY O 17 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN O 26 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL O 15 " --> pdb=" O ASN O 26 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA O 125 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER O 124 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE O 52 " --> pdb=" O ALA O 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 61 " --> pdb=" O PHE O 54 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 35 through 38 Processing sheet with id= AL, first strand: chain 'O' and resid 222 through 226 removed outlier: 6.596A pdb=" N VAL O 433 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR O 225 " --> pdb=" O VAL O 433 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE O 435 " --> pdb=" O THR O 225 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL O 473 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE O 206 " --> pdb=" O VAL O 473 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU O 475 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU O 173 " --> pdb=" O VAL O 513 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR O 515 " --> pdb=" O LEU O 173 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL O 175 " --> pdb=" O THR O 515 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN O 531 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU O 176 " --> pdb=" O ASN O 531 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE O 533 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 67 through 70 removed outlier: 3.677A pdb=" N ASP P 67 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE P 95 " --> pdb=" O ASP P 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P 69 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG P 92 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG P 22 " --> pdb=" O GLU P 19 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY P 17 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN P 26 " --> pdb=" O VAL P 15 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL P 15 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 125 through 127 removed outlier: 3.698A pdb=" N GLY P 100 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 568 through 571 removed outlier: 7.057A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'P' and resid 222 through 225 removed outlier: 6.064A pdb=" N VAL P 433 " --> pdb=" O LYS P 223 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR P 225 " --> pdb=" O VAL P 433 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE P 435 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE P 203 " --> pdb=" O HIS P 434 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL P 436 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE P 205 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL P 473 " --> pdb=" O VAL P 204 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE P 206 " --> pdb=" O VAL P 473 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU P 475 " --> pdb=" O PHE P 206 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU P 173 " --> pdb=" O VAL P 513 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR P 515 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL P 175 " --> pdb=" O THR P 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER P 530 " --> pdb=" O HIS P 172 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA P 174 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP P 532 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU P 176 " --> pdb=" O TRP P 532 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 67 through 70 removed outlier: 3.502A pdb=" N ASP Q 67 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG Q 92 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY Q 17 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN Q 26 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL Q 15 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 125 through 127 removed outlier: 3.785A pdb=" N GLY Q 100 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA Q 98 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 151 through 153 removed outlier: 3.501A pdb=" N VAL Q 580 " --> pdb=" O ALA Q 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL Q 570 " --> pdb=" O SER Q 534 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER Q 534 " --> pdb=" O VAL Q 570 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 173 through 176 removed outlier: 3.532A pdb=" N VAL Q 513 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Q 474 " --> pdb=" O SER Q 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER Q 514 " --> pdb=" O LEU Q 476 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL Q 204 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) 1651 hydrogen bonds defined for protein. 4461 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: 20.77 Time building geometry restraints manager: 19.13 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: 19703 1.34 - 1.46: 10798 1.46 - 1.58: 31814 1.58 - 1.70: 63 1.70 - 1.82: 206 Bond restraints: 62584 Sorted by residual: bond pdb=" C ALA P 446 " pdb=" N PRO P 447 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 4.91e+00 bond pdb=" CB VAL J 243 " pdb=" CG1 VAL J 243 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CA GLY P 20 " pdb=" C GLY P 20 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.97e+00 bond pdb=" CB VAL A 243 " pdb=" CG1 VAL A 243 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" CG ARG J 194 " pdb=" CD ARG J 194 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.43e+00 ... (remaining 62579 not shown) Histogram of bond angle deviations from ideal: 91.92 - 100.82: 69 100.82 - 109.72: 7018 109.72 - 118.62: 41814 118.62 - 127.52: 35239 127.52 - 136.42: 527 Bond angle restraints: 84667 Sorted by residual: angle pdb=" C LEU L 323 " pdb=" N ASN L 324 " pdb=" CA ASN L 324 " ideal model delta sigma weight residual 121.61 129.81 -8.20 1.39e+00 5.18e-01 3.48e+01 angle pdb=" N ILE P 288 " pdb=" CA ILE P 288 " pdb=" C ILE P 288 " ideal model delta sigma weight residual 113.53 108.36 5.17 9.80e-01 1.04e+00 2.78e+01 angle pdb=" C HIS C 383 " pdb=" N LEU C 384 " pdb=" CA LEU C 384 " ideal model delta sigma weight residual 120.94 130.75 -9.81 1.90e+00 2.77e-01 2.67e+01 angle pdb=" C SER L 379 " pdb=" N PHE L 380 " pdb=" CA PHE L 380 " ideal model delta sigma weight residual 121.66 112.84 8.82 1.76e+00 3.23e-01 2.51e+01 angle pdb=" C ARG N 192 " pdb=" N LYS N 193 " pdb=" CA LYS N 193 " ideal model delta sigma weight residual 122.38 115.13 7.25 1.81e+00 3.05e-01 1.60e+01 ... (remaining 84662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 36492 33.88 - 67.76: 830 67.76 - 101.64: 105 101.64 - 135.51: 2 135.51 - 169.39: 5 Dihedral angle restraints: 37434 sinusoidal: 15422 harmonic: 22012 Sorted by residual: dihedral pdb=" C5' ADP P 701 " pdb=" O5' ADP P 701 " pdb=" PA ADP P 701 " pdb=" O2A ADP P 701 " ideal model delta sinusoidal sigma weight residual -60.00 107.76 -167.76 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA HIS D 218 " pdb=" C HIS D 218 " pdb=" N TYR D 219 " pdb=" CA TYR D 219 " ideal model delta harmonic sigma weight residual 180.00 149.72 30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA SER N 273 " pdb=" C SER N 273 " pdb=" N ASP N 274 " pdb=" CA ASP N 274 " ideal model delta harmonic sigma weight residual -180.00 -150.02 -29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 37431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 6348 0.044 - 0.087: 2248 0.087 - 0.131: 544 0.131 - 0.175: 59 0.175 - 0.218: 3 Chirality restraints: 9202 Sorted by residual: chirality pdb=" CB VAL O 16 " pdb=" CA VAL O 16 " pdb=" CG1 VAL O 16 " pdb=" CG2 VAL O 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE P 89 " pdb=" CA ILE P 89 " pdb=" CG1 ILE P 89 " pdb=" CG2 ILE P 89 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA TYR H 252 " pdb=" N TYR H 252 " pdb=" C TYR H 252 " pdb=" CB TYR H 252 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 9199 not shown) Planarity restraints: 10852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 270 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO H 271 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 271 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 271 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 333 " -0.053 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO E 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 219 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO P 220 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO P 220 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 220 " 0.031 5.00e-02 4.00e+02 ... (remaining 10849 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 195 2.54 - 3.13: 42852 3.13 - 3.72: 82449 3.72 - 4.31: 117430 4.31 - 4.90: 206857 Nonbonded interactions: 449783 Sorted by model distance: nonbonded pdb=" OG SER P 184 " pdb="MG MG P 702 " model vdw 1.948 2.170 nonbonded pdb=" O3B ADP O 701 " pdb="MG MG O 702 " model vdw 1.979 2.170 nonbonded pdb=" O3B ADP N 701 " pdb="MG MG N 702 " model vdw 2.004 2.170 nonbonded pdb=" O ASN M 134 " pdb=" OG SER M 138 " model vdw 2.033 2.440 nonbonded pdb=" OD2 ASP Q 153 " pdb=" OG1 THR Q 156 " model vdw 2.041 2.440 ... (remaining 449778 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 36 or resid 42 through 229 or resid 238 through \ 328 or resid 336 through 355 or resid 375 through 602 or resid 701 through 702)) \ selection = (chain 'N' and (resid 4 through 36 or resid 42 through 229 or resid 238 through \ 328 or resid 336 through 355 or resid 375 through 484 or resid 498 through 602 o \ r resid 701 through 702)) selection = (chain 'O' and (resid 4 through 36 or resid 42 through 71 or resid 89 through 22 \ 9 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 602 or resid 701 through 702)) selection = (chain 'P' and (resid 4 through 36 or resid 42 through 229 or resid 238 through \ 355 or resid 375 through 484 or resid 498 through 602 or resid 701 through 702)) \ selection = (chain 'Q' and (resid 4 through 328 or resid 336 through 355 or resid 375 throug \ h 484 or resid 498 through 602 or resid 701 through 702)) } 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.330 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 120.840 Find NCS groups from input model: 4.040 Set up NCS constraints: 0.220 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.005 0.069 62584 Z= 0.301 Angle : 0.701 12.034 84667 Z= 0.369 Chirality : 0.046 0.218 9202 Planarity : 0.005 0.083 10852 Dihedral : 15.078 169.393 23356 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.48 (0.09), residues: 7515 helix: -0.29 (0.09), residues: 3013 sheet: -0.21 (0.17), residues: 926 loop : -1.79 (0.09), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 431 HIS 0.012 0.002 HIS B 313 PHE 0.037 0.002 PHE L 380 TYR 0.030 0.002 TYR A 386 ARG 0.008 0.001 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 900 time to evaluate : 5.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.9093 (t) cc_final: 0.8789 (m) REVERT: A 73 ILE cc_start: 0.8061 (tt) cc_final: 0.7825 (tp) REVERT: A 266 GLN cc_start: 0.7849 (mt0) cc_final: 0.7629 (mt0) REVERT: A 312 TYR cc_start: 0.8823 (t80) cc_final: 0.8600 (t80) REVERT: B 12 GLU cc_start: 0.7749 (tt0) cc_final: 0.7383 (tp30) REVERT: B 74 ASP cc_start: 0.7582 (m-30) cc_final: 0.6990 (m-30) REVERT: B 107 GLU cc_start: 0.8255 (tp30) cc_final: 0.7764 (tp30) REVERT: B 110 LYS cc_start: 0.7864 (mttp) cc_final: 0.7543 (mtmt) REVERT: B 342 LYS cc_start: 0.8168 (mttm) cc_final: 0.7687 (tttp) REVERT: C 106 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6939 (tp30) REVERT: C 352 GLU cc_start: 0.7436 (mp0) cc_final: 0.7001 (mp0) REVERT: E 102 GLU cc_start: 0.7163 (pm20) cc_final: 0.6945 (tm-30) REVERT: F 76 ASP cc_start: 0.6606 (m-30) cc_final: 0.6349 (m-30) REVERT: F 117 LYS cc_start: 0.8122 (tttt) cc_final: 0.7712 (ttmm) REVERT: F 337 LYS cc_start: 0.7282 (pttt) cc_final: 0.6737 (mmpt) REVERT: G 9 LYS cc_start: 0.6122 (ttmt) cc_final: 0.5577 (pptt) REVERT: G 101 CYS cc_start: 0.7136 (t) cc_final: 0.6933 (t) REVERT: G 143 TYR cc_start: 0.6860 (m-80) cc_final: 0.6141 (m-80) REVERT: G 260 ASP cc_start: 0.5946 (p0) cc_final: 0.5493 (t0) REVERT: G 345 LYS cc_start: 0.4864 (mptt) cc_final: 0.4262 (tmtm) REVERT: G 361 MET cc_start: 0.5665 (mmm) cc_final: 0.5259 (pmt) REVERT: H 110 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7012 (ttpt) REVERT: H 316 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7191 (mmm160) REVERT: I 259 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6855 (ttmt) REVERT: J 74 ASP cc_start: 0.7752 (m-30) cc_final: 0.7509 (m-30) REVERT: J 337 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7291 (mptp) REVERT: K 74 ASP cc_start: 0.7873 (m-30) cc_final: 0.7668 (m-30) REVERT: K 79 LEU cc_start: 0.9045 (mt) cc_final: 0.8756 (mt) REVERT: K 106 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7086 (OUTLIER) REVERT: K 287 MET cc_start: 0.9072 (mmt) cc_final: 0.8765 (mmp) REVERT: L 235 ASN cc_start: 0.6203 (m-40) cc_final: 0.5784 (p0) REVERT: L 342 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7565 (tttm) REVERT: M 18 LEU cc_start: 0.8338 (mt) cc_final: 0.7911 (mm) REVERT: M 153 ASP cc_start: 0.7943 (t0) cc_final: 0.7706 (t0) REVERT: M 413 MET cc_start: 0.5946 (ttt) cc_final: 0.5394 (ppp) REVERT: M 498 GLU cc_start: 0.3601 (pt0) cc_final: 0.2949 (mp0) REVERT: M 550 MET cc_start: 0.7442 (ptt) cc_final: 0.7239 (ptm) REVERT: M 592 LYS cc_start: 0.7332 (tttt) cc_final: 0.6830 (ttpt) REVERT: N 67 ASP cc_start: 0.8989 (m-30) cc_final: 0.8759 (m-30) REVERT: N 131 ASP cc_start: 0.8595 (m-30) cc_final: 0.8358 (m-30) REVERT: N 242 LYS cc_start: 0.7160 (tttp) cc_final: 0.6899 (tptt) REVERT: N 327 ASP cc_start: 0.6656 (t0) cc_final: 0.6168 (m-30) REVERT: N 508 LYS cc_start: 0.8242 (mttp) cc_final: 0.7895 (mtpm) REVERT: N 592 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7405 (tppt) REVERT: O 382 GLN cc_start: 0.6000 (mt0) cc_final: 0.5209 (mm110) REVERT: O 383 GLN cc_start: 0.5210 (tm-30) cc_final: 0.4957 (pt0) REVERT: O 550 MET cc_start: 0.8996 (ptm) cc_final: 0.8761 (ptp) REVERT: O 559 LYS cc_start: 0.8871 (mttt) cc_final: 0.8554 (mtpm) REVERT: P 55 ASP cc_start: 0.7796 (t0) cc_final: 0.7555 (p0) REVERT: P 413 MET cc_start: 0.3248 (ttp) cc_final: 0.2561 (mpt) REVERT: P 478 GLU cc_start: 0.7808 (mp0) cc_final: 0.7280 (mm-30) REVERT: P 540 GLU cc_start: 0.7178 (tp30) cc_final: 0.6671 (tp30) REVERT: Q 413 MET cc_start: 0.5253 (ttm) cc_final: 0.4856 (ttt) REVERT: Q 536 ARG cc_start: 0.5284 (ttt180) cc_final: 0.4849 (tmm-80) outliers start: 0 outliers final: 3 residues processed: 900 average time/residue: 1.5225 time to fit residues: 1714.0263 Evaluate side-chains 437 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain N residue 107 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 637 optimal weight: 7.9990 chunk 572 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 386 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 591 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 440 optimal weight: 0.0020 chunk 685 optimal weight: 0.9980 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN C 405 ASN F 55 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 HIS J 207 ASN J 274 ASN M 172 HIS M 187 ASN M 289 ASN M 297 ASN M 382 GLN M 432 ASN M 544 GLN N 224 HIS N 289 ASN N 382 GLN N 383 GLN O 544 GLN P 429 ASN Q 481 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 62584 Z= 0.259 Angle : 0.618 11.198 84667 Z= 0.316 Chirality : 0.045 0.200 9202 Planarity : 0.005 0.077 10852 Dihedral : 10.071 165.930 8929 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.91 % Allowed : 8.84 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -1.38 (0.09), residues: 7515 helix: -0.20 (0.10), residues: 2975 sheet: 0.07 (0.17), residues: 908 loop : -1.80 (0.09), residues: 3632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 116 HIS 0.011 0.001 HIS B 313 PHE 0.021 0.002 PHE O 206 TYR 0.019 0.002 TYR A 386 ARG 0.008 0.001 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 457 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8068 (tt) cc_final: 0.7835 (tp) REVERT: B 12 GLU cc_start: 0.7702 (tt0) cc_final: 0.7383 (tp30) REVERT: B 74 ASP cc_start: 0.7635 (m-30) cc_final: 0.7039 (m-30) REVERT: B 110 LYS cc_start: 0.7751 (mttp) cc_final: 0.7478 (mtmt) REVERT: B 342 LYS cc_start: 0.8109 (mttm) cc_final: 0.7655 (tttm) REVERT: C 8 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7567 (m-40) REVERT: C 106 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7127 (tp30) REVERT: C 352 GLU cc_start: 0.7463 (mp0) cc_final: 0.7164 (mp0) REVERT: E 386 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7454 (t80) REVERT: F 76 ASP cc_start: 0.6608 (m-30) cc_final: 0.6351 (m-30) REVERT: F 97 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7428 (tttt) REVERT: F 117 LYS cc_start: 0.8261 (tttt) cc_final: 0.7972 (ttmt) REVERT: F 337 LYS cc_start: 0.7254 (pttt) cc_final: 0.6571 (mmtm) REVERT: G 143 TYR cc_start: 0.6739 (m-80) cc_final: 0.6445 (m-80) REVERT: G 260 ASP cc_start: 0.5733 (p0) cc_final: 0.5120 (t0) REVERT: G 264 ARG cc_start: 0.6216 (mmm-85) cc_final: 0.5954 (mmm-85) REVERT: G 313 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7480 (m90) REVERT: G 345 LYS cc_start: 0.4949 (mptt) cc_final: 0.4273 (tmtm) REVERT: G 361 MET cc_start: 0.5531 (mmm) cc_final: 0.5309 (pmt) REVERT: H 110 LYS cc_start: 0.7314 (mtmm) cc_final: 0.7039 (ttpt) REVERT: H 316 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7174 (mmm160) REVERT: I 259 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6762 (tttt) REVERT: I 361 MET cc_start: 0.7993 (mtp) cc_final: 0.7743 (mtp) REVERT: I 363 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: J 207 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7194 (t0) REVERT: J 264 ARG cc_start: 0.6070 (mpp-170) cc_final: 0.5658 (mtm180) REVERT: J 337 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7369 (mptp) REVERT: J 345 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.6259 (tppp) REVERT: J 378 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8151 (m110) REVERT: K 79 LEU cc_start: 0.9042 (mt) cc_final: 0.8783 (mt) REVERT: K 106 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7220 (tp30) REVERT: K 287 MET cc_start: 0.9059 (mmt) cc_final: 0.8685 (mmp) REVERT: K 352 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: L 235 ASN cc_start: 0.6279 (m-40) cc_final: 0.5820 (p0) REVERT: L 342 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7551 (tttm) REVERT: M 34 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6313 (ptm160) REVERT: M 153 ASP cc_start: 0.7906 (t0) cc_final: 0.7668 (t0) REVERT: M 413 MET cc_start: 0.5864 (ttt) cc_final: 0.5389 (ppp) REVERT: M 498 GLU cc_start: 0.3984 (pt0) cc_final: 0.2954 (mp0) REVERT: M 548 TYR cc_start: 0.7260 (t80) cc_final: 0.7017 (t80) REVERT: M 592 LYS cc_start: 0.7437 (tttt) cc_final: 0.6932 (tttt) REVERT: N 67 ASP cc_start: 0.8716 (m-30) cc_final: 0.8485 (m-30) REVERT: N 131 ASP cc_start: 0.8591 (m-30) cc_final: 0.8346 (m-30) REVERT: N 229 GLU cc_start: 0.7234 (pp20) cc_final: 0.6965 (pm20) REVERT: N 242 LYS cc_start: 0.7131 (tttp) cc_final: 0.6904 (tptt) REVERT: N 478 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: N 506 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7774 (mtmt) REVERT: N 508 LYS cc_start: 0.8251 (mttp) cc_final: 0.7810 (mtpm) REVERT: N 592 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7382 (tppt) REVERT: O 382 GLN cc_start: 0.5839 (mt0) cc_final: 0.4980 (mm-40) REVERT: O 383 GLN cc_start: 0.4924 (tm-30) cc_final: 0.4659 (pt0) REVERT: O 427 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6552 (mt0) REVERT: O 559 LYS cc_start: 0.8803 (mttt) cc_final: 0.8495 (mtpp) REVERT: P 413 MET cc_start: 0.3772 (ttp) cc_final: 0.2412 (mpm) REVERT: P 478 GLU cc_start: 0.7777 (mp0) cc_final: 0.7321 (mm-30) REVERT: P 551 GLU cc_start: 0.3483 (OUTLIER) cc_final: 0.2949 (mm-30) REVERT: P 559 LYS cc_start: 0.8304 (mtpm) cc_final: 0.7583 (mmmt) REVERT: Q 1 MET cc_start: 0.6568 (mmp) cc_final: 0.5079 (mmt) REVERT: Q 528 MET cc_start: 0.6160 (mpp) cc_final: 0.5786 (mtt) REVERT: Q 536 ARG cc_start: 0.5430 (ttt180) cc_final: 0.4984 (tmm-80) outliers start: 124 outliers final: 52 residues processed: 543 average time/residue: 1.3876 time to fit residues: 966.6372 Evaluate side-chains 453 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 389 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 313 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 338 ASN Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 478 GLU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 539 ASN Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 251 TYR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 162 PHE Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 570 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 381 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 570 optimal weight: 9.9990 chunk 466 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 686 optimal weight: 10.0000 chunk 742 optimal weight: 5.9990 chunk 611 optimal weight: 7.9990 chunk 681 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 551 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 HIS ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 313 HIS J 207 ASN J 274 ASN M 289 ASN M 432 ASN M 556 GLN O 241 GLN P 429 ASN P 432 ASN Q 224 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 62584 Z= 0.227 Angle : 0.584 14.597 84667 Z= 0.297 Chirality : 0.043 0.172 9202 Planarity : 0.004 0.060 10852 Dihedral : 9.588 166.204 8927 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.28 % Allowed : 10.97 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -1.24 (0.09), residues: 7515 helix: -0.05 (0.10), residues: 2969 sheet: 0.13 (0.17), residues: 931 loop : -1.75 (0.09), residues: 3615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.008 0.001 HIS D 227 PHE 0.025 0.002 PHE J 205 TYR 0.022 0.001 TYR O 258 ARG 0.013 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 414 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8057 (tt) cc_final: 0.7837 (tp) REVERT: A 259 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7820 (ttpt) REVERT: A 266 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: B 12 GLU cc_start: 0.7743 (tt0) cc_final: 0.7361 (tp30) REVERT: B 74 ASP cc_start: 0.7719 (m-30) cc_final: 0.7055 (m-30) REVERT: B 110 LYS cc_start: 0.7657 (mttp) cc_final: 0.7394 (mtmt) REVERT: B 342 LYS cc_start: 0.8092 (mttm) cc_final: 0.7637 (tttm) REVERT: C 8 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7613 (m-40) REVERT: C 106 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6969 (tp30) REVERT: C 335 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: C 352 GLU cc_start: 0.7522 (mp0) cc_final: 0.7159 (mp0) REVERT: E 288 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8143 (t80) REVERT: E 386 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7559 (t80) REVERT: F 76 ASP cc_start: 0.6554 (m-30) cc_final: 0.6288 (m-30) REVERT: F 97 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7417 (tttt) REVERT: F 117 LYS cc_start: 0.8291 (tttt) cc_final: 0.7993 (ttmt) REVERT: F 337 LYS cc_start: 0.7261 (pttt) cc_final: 0.6566 (mmtm) REVERT: G 9 LYS cc_start: 0.5891 (ttpp) cc_final: 0.5062 (pptt) REVERT: G 143 TYR cc_start: 0.6688 (m-80) cc_final: 0.6447 (m-80) REVERT: G 313 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7447 (m90) REVERT: G 345 LYS cc_start: 0.5154 (mptt) cc_final: 0.4446 (tmtm) REVERT: G 361 MET cc_start: 0.5447 (mmm) cc_final: 0.5145 (pmt) REVERT: H 110 LYS cc_start: 0.7204 (mtmm) cc_final: 0.6979 (ttpt) REVERT: H 316 ARG cc_start: 0.7635 (mmm160) cc_final: 0.7083 (mmm160) REVERT: I 259 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6751 (tttt) REVERT: I 363 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: J 264 ARG cc_start: 0.5869 (mpp-170) cc_final: 0.5461 (mtm180) REVERT: J 337 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7324 (mptp) REVERT: J 342 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7571 (mtpp) REVERT: J 378 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8172 (m110) REVERT: K 106 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7226 (tp30) REVERT: K 287 MET cc_start: 0.9039 (mmt) cc_final: 0.8657 (mmp) REVERT: K 352 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: L 69 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8481 (mp) REVERT: L 235 ASN cc_start: 0.6360 (m-40) cc_final: 0.5877 (p0) REVERT: L 342 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7541 (mtpt) REVERT: M 34 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6259 (ptm160) REVERT: M 153 ASP cc_start: 0.7831 (t0) cc_final: 0.7621 (m-30) REVERT: M 410 ASP cc_start: 0.6286 (m-30) cc_final: 0.5682 (p0) REVERT: M 413 MET cc_start: 0.5958 (ttt) cc_final: 0.5476 (ppp) REVERT: M 478 GLU cc_start: 0.8124 (mp0) cc_final: 0.7617 (mp0) REVERT: M 498 GLU cc_start: 0.4050 (pt0) cc_final: 0.2983 (mp0) REVERT: M 592 LYS cc_start: 0.7413 (tttt) cc_final: 0.6860 (tttt) REVERT: M 600 GLU cc_start: 0.7019 (mp0) cc_final: 0.6763 (mm-30) REVERT: N 67 ASP cc_start: 0.8747 (m-30) cc_final: 0.8500 (m-30) REVERT: N 131 ASP cc_start: 0.8597 (m-30) cc_final: 0.8352 (m-30) REVERT: N 508 LYS cc_start: 0.8167 (mttp) cc_final: 0.7848 (mtpm) REVERT: N 528 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (mmm) REVERT: N 592 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7405 (tppt) REVERT: O 107 ASN cc_start: 0.6986 (OUTLIER) cc_final: 0.6638 (t0) REVERT: O 382 GLN cc_start: 0.6048 (mt0) cc_final: 0.5133 (mm-40) REVERT: O 427 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6522 (mt0) REVERT: O 430 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5717 (m-30) REVERT: P 241 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5540 (mm-40) REVERT: P 413 MET cc_start: 0.3991 (ttp) cc_final: 0.2777 (mpm) REVERT: P 478 GLU cc_start: 0.7820 (mp0) cc_final: 0.7409 (mm-30) REVERT: P 499 ARG cc_start: 0.6240 (ttm170) cc_final: 0.5776 (ttt180) REVERT: P 551 GLU cc_start: 0.3527 (OUTLIER) cc_final: 0.2863 (mm-30) REVERT: P 559 LYS cc_start: 0.8386 (mtpm) cc_final: 0.7806 (mmmt) REVERT: Q 35 LEU cc_start: 0.1971 (OUTLIER) cc_final: 0.1300 (tt) REVERT: Q 438 MET cc_start: -0.0128 (OUTLIER) cc_final: -0.0665 (mpt) REVERT: Q 528 MET cc_start: 0.6448 (mpp) cc_final: 0.6097 (mtt) REVERT: Q 536 ARG cc_start: 0.5466 (ttt180) cc_final: 0.5198 (tmm-80) outliers start: 148 outliers final: 63 residues processed: 518 average time/residue: 1.3684 time to fit residues: 913.7027 Evaluate side-chains 464 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 380 time to evaluate : 5.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 MET Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 313 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 342 LYS Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 268 LYS Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 539 ASN Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 558 LEU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 678 optimal weight: 10.0000 chunk 516 optimal weight: 0.5980 chunk 356 optimal weight: 0.9990 chunk 76 optimal weight: 0.0040 chunk 327 optimal weight: 5.9990 chunk 461 optimal weight: 8.9990 chunk 689 optimal weight: 9.9990 chunk 729 optimal weight: 0.7980 chunk 360 optimal weight: 9.9990 chunk 653 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN D 154 ASN D 247 GLN F 324 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 HIS M 289 ASN P 429 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 62584 Z= 0.162 Angle : 0.523 12.958 84667 Z= 0.265 Chirality : 0.041 0.165 9202 Planarity : 0.004 0.052 10852 Dihedral : 9.181 168.288 8925 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.19 % Allowed : 12.68 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 7515 helix: 0.15 (0.10), residues: 2953 sheet: 0.26 (0.17), residues: 922 loop : -1.63 (0.09), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 602 HIS 0.008 0.001 HIS G 267 PHE 0.014 0.001 PHE L 130 TYR 0.014 0.001 TYR D 284 ARG 0.011 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 431 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8017 (tt) cc_final: 0.7802 (tp) REVERT: A 266 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: B 12 GLU cc_start: 0.7675 (tt0) cc_final: 0.7382 (tp30) REVERT: B 68 LEU cc_start: 0.8991 (mp) cc_final: 0.8772 (mt) REVERT: B 74 ASP cc_start: 0.7703 (m-30) cc_final: 0.7026 (m-30) REVERT: B 107 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: B 110 LYS cc_start: 0.7586 (mttp) cc_final: 0.7349 (mtmt) REVERT: B 342 LYS cc_start: 0.8053 (mttm) cc_final: 0.7601 (tttm) REVERT: C 8 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7742 (m-40) REVERT: C 54 GLN cc_start: 0.8066 (tt0) cc_final: 0.7820 (tt0) REVERT: C 106 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6884 (tp30) REVERT: C 352 GLU cc_start: 0.7557 (mp0) cc_final: 0.7204 (mp0) REVERT: D 83 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6235 (mm-30) REVERT: E 102 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6407 (tm-30) REVERT: E 106 GLU cc_start: 0.6800 (mp0) cc_final: 0.6507 (mp0) REVERT: E 288 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8088 (t80) REVERT: E 386 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7484 (t80) REVERT: F 76 ASP cc_start: 0.6570 (m-30) cc_final: 0.6316 (m-30) REVERT: F 117 LYS cc_start: 0.8277 (tttt) cc_final: 0.7820 (ttmm) REVERT: F 156 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6854 (mp10) REVERT: F 337 LYS cc_start: 0.7266 (pttt) cc_final: 0.6490 (mmpt) REVERT: G 9 LYS cc_start: 0.5824 (ttpp) cc_final: 0.4982 (pptt) REVERT: G 313 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7396 (m90) REVERT: G 345 LYS cc_start: 0.5179 (mptt) cc_final: 0.4484 (tmtm) REVERT: G 361 MET cc_start: 0.5256 (mmm) cc_final: 0.5054 (pmt) REVERT: H 110 LYS cc_start: 0.7075 (mtmm) cc_final: 0.6822 (ttpt) REVERT: H 316 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7126 (mmm160) REVERT: I 259 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6791 (tttt) REVERT: J 264 ARG cc_start: 0.6029 (mpp-170) cc_final: 0.5578 (mtm180) REVERT: J 337 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7282 (mptp) REVERT: J 378 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8173 (m110) REVERT: K 106 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7176 (tp30) REVERT: K 287 MET cc_start: 0.9017 (mmt) cc_final: 0.8622 (mmp) REVERT: L 132 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: L 235 ASN cc_start: 0.6282 (m-40) cc_final: 0.5874 (p0) REVERT: L 342 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7513 (mtpt) REVERT: M 8 GLU cc_start: 0.6301 (tp30) cc_final: 0.6091 (tp30) REVERT: M 34 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6036 (ptm160) REVERT: M 338 ASN cc_start: 0.2213 (OUTLIER) cc_final: 0.1998 (m-40) REVERT: M 410 ASP cc_start: 0.6313 (m-30) cc_final: 0.5863 (p0) REVERT: M 413 MET cc_start: 0.6038 (ttt) cc_final: 0.5519 (ppp) REVERT: M 438 MET cc_start: 0.7967 (mtp) cc_final: 0.7738 (mtp) REVERT: M 478 GLU cc_start: 0.8102 (mp0) cc_final: 0.7617 (mp0) REVERT: M 498 GLU cc_start: 0.3716 (pt0) cc_final: 0.2635 (mp0) REVERT: M 555 GLU cc_start: 0.6947 (tp30) cc_final: 0.6555 (mt-10) REVERT: M 592 LYS cc_start: 0.7518 (tttt) cc_final: 0.7021 (tttt) REVERT: N 67 ASP cc_start: 0.8599 (m-30) cc_final: 0.8366 (m-30) REVERT: N 131 ASP cc_start: 0.8580 (m-30) cc_final: 0.8339 (m-30) REVERT: N 325 TRP cc_start: 0.6589 (m100) cc_final: 0.6326 (m100) REVERT: N 508 LYS cc_start: 0.8277 (mttp) cc_final: 0.7818 (mtpm) REVERT: N 592 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7385 (tppt) REVERT: O 105 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: O 340 TRP cc_start: 0.6724 (m100) cc_final: 0.6419 (m100) REVERT: O 382 GLN cc_start: 0.5900 (mt0) cc_final: 0.5108 (mm-40) REVERT: O 427 GLN cc_start: 0.7017 (mm-40) cc_final: 0.6531 (mt0) REVERT: O 430 ASP cc_start: 0.6320 (OUTLIER) cc_final: 0.5826 (m-30) REVERT: P 9 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8082 (mm) REVERT: P 241 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.5640 (mm-40) REVERT: P 289 ASN cc_start: -0.1107 (OUTLIER) cc_final: -0.1569 (p0) REVERT: P 413 MET cc_start: 0.4240 (ttp) cc_final: 0.2962 (mpm) REVERT: P 478 GLU cc_start: 0.7771 (mp0) cc_final: 0.7396 (mm-30) REVERT: P 528 MET cc_start: 0.8438 (mtp) cc_final: 0.8184 (mtp) REVERT: P 551 GLU cc_start: 0.3612 (OUTLIER) cc_final: 0.2932 (mm-30) REVERT: Q 149 GLU cc_start: 0.6457 (pt0) cc_final: 0.6197 (mt-10) REVERT: Q 438 MET cc_start: -0.0321 (OUTLIER) cc_final: -0.0711 (mpt) REVERT: Q 528 MET cc_start: 0.6317 (mpp) cc_final: 0.6107 (mtt) outliers start: 142 outliers final: 70 residues processed: 535 average time/residue: 1.3745 time to fit residues: 958.6362 Evaluate side-chains 480 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 392 time to evaluate : 5.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 313 HIS Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 338 ASN Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 595 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 592 LYS Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain Q residue 438 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 607 optimal weight: 10.0000 chunk 414 optimal weight: 0.0770 chunk 10 optimal weight: 10.0000 chunk 543 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 622 optimal weight: 5.9990 chunk 504 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 655 optimal weight: 0.4980 chunk 184 optimal weight: 7.9990 overall best weight: 2.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 HIS I 227 HIS J 54 GLN J 207 ASN M 28 HIS P 429 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 62584 Z= 0.247 Angle : 0.588 14.430 84667 Z= 0.298 Chirality : 0.043 0.176 9202 Planarity : 0.004 0.052 10852 Dihedral : 9.336 169.904 8925 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.70 % Allowed : 13.61 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -1.14 (0.09), residues: 7515 helix: 0.00 (0.10), residues: 3005 sheet: 0.27 (0.17), residues: 892 loop : -1.69 (0.09), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 116 HIS 0.009 0.001 HIS D 227 PHE 0.018 0.002 PHE K 130 TYR 0.016 0.002 TYR C 116 ARG 0.018 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 400 time to evaluate : 5.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8080 (tt) cc_final: 0.7855 (tp) REVERT: A 259 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7898 (ttpt) REVERT: A 266 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: B 12 GLU cc_start: 0.7844 (tt0) cc_final: 0.7461 (tp30) REVERT: B 68 LEU cc_start: 0.9012 (mp) cc_final: 0.8775 (mt) REVERT: B 74 ASP cc_start: 0.7722 (m-30) cc_final: 0.7054 (m-30) REVERT: B 88 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 110 LYS cc_start: 0.7722 (mttp) cc_final: 0.7480 (mtmt) REVERT: B 342 LYS cc_start: 0.8073 (mttm) cc_final: 0.7594 (tttp) REVERT: C 8 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7792 (m-40) REVERT: C 54 GLN cc_start: 0.8121 (tt0) cc_final: 0.7850 (tt0) REVERT: C 106 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6920 (tp30) REVERT: C 352 GLU cc_start: 0.7606 (mp0) cc_final: 0.7197 (mp0) REVERT: D 83 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: E 102 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6385 (tm-30) REVERT: E 106 GLU cc_start: 0.6835 (mp0) cc_final: 0.6468 (mp0) REVERT: E 288 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8158 (t80) REVERT: E 386 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7552 (t80) REVERT: F 10 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7602 (mp) REVERT: F 76 ASP cc_start: 0.6577 (m-30) cc_final: 0.6304 (m-30) REVERT: F 117 LYS cc_start: 0.8286 (tttt) cc_final: 0.7845 (ttmm) REVERT: F 337 LYS cc_start: 0.7247 (pttt) cc_final: 0.6592 (mmpt) REVERT: G 9 LYS cc_start: 0.5874 (ttpp) cc_final: 0.5032 (pptt) REVERT: G 143 TYR cc_start: 0.6165 (m-80) cc_final: 0.5780 (m-80) REVERT: G 345 LYS cc_start: 0.5172 (mptt) cc_final: 0.4443 (tmtm) REVERT: G 361 MET cc_start: 0.5124 (mmm) cc_final: 0.4863 (pmt) REVERT: H 316 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7096 (mmm160) REVERT: I 259 LYS cc_start: 0.7140 (mmmt) cc_final: 0.6875 (ttmt) REVERT: I 361 MET cc_start: 0.8304 (mtp) cc_final: 0.8063 (mtp) REVERT: J 207 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.7105 (t0) REVERT: J 259 LYS cc_start: 0.7149 (ttmm) cc_final: 0.6823 (ttpt) REVERT: J 264 ARG cc_start: 0.6028 (mpp-170) cc_final: 0.5685 (mtm180) REVERT: J 337 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7286 (mptp) REVERT: J 342 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7880 (tttp) REVERT: J 378 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (m110) REVERT: K 83 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: K 106 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7152 (tp30) REVERT: K 287 MET cc_start: 0.9016 (mmt) cc_final: 0.8689 (mmp) REVERT: K 352 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: L 69 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8479 (mp) REVERT: L 132 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: L 235 ASN cc_start: 0.6462 (m-40) cc_final: 0.5989 (p0) REVERT: L 342 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7594 (mtpt) REVERT: M 34 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6108 (ptm160) REVERT: M 410 ASP cc_start: 0.6295 (m-30) cc_final: 0.5749 (p0) REVERT: M 413 MET cc_start: 0.5856 (ttt) cc_final: 0.5293 (ppp) REVERT: M 438 MET cc_start: 0.8115 (mtp) cc_final: 0.7868 (mtp) REVERT: M 478 GLU cc_start: 0.8136 (mp0) cc_final: 0.7617 (mp0) REVERT: M 498 GLU cc_start: 0.3782 (pt0) cc_final: 0.2815 (mp0) REVERT: M 555 GLU cc_start: 0.6896 (tp30) cc_final: 0.6651 (mt-10) REVERT: M 592 LYS cc_start: 0.7659 (tttt) cc_final: 0.7148 (tttt) REVERT: M 600 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6728 (mp0) REVERT: N 67 ASP cc_start: 0.8751 (m-30) cc_final: 0.8507 (m-30) REVERT: N 131 ASP cc_start: 0.8612 (m-30) cc_final: 0.8350 (m-30) REVERT: N 229 GLU cc_start: 0.7191 (pp20) cc_final: 0.6877 (pm20) REVERT: N 508 LYS cc_start: 0.8292 (mttp) cc_final: 0.7911 (mtpm) REVERT: N 528 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8424 (mmm) REVERT: N 592 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7396 (tppt) REVERT: O 105 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: O 340 TRP cc_start: 0.6771 (m100) cc_final: 0.6446 (m100) REVERT: O 382 GLN cc_start: 0.5733 (mt0) cc_final: 0.5009 (mm-40) REVERT: O 427 GLN cc_start: 0.7100 (mm-40) cc_final: 0.6669 (mt0) REVERT: O 430 ASP cc_start: 0.6397 (OUTLIER) cc_final: 0.5897 (m-30) REVERT: P 9 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8132 (mm) REVERT: P 241 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5860 (mm-40) REVERT: P 289 ASN cc_start: -0.0931 (OUTLIER) cc_final: -0.1401 (p0) REVERT: P 413 MET cc_start: 0.4189 (ttp) cc_final: 0.2830 (mpm) REVERT: P 478 GLU cc_start: 0.7726 (mp0) cc_final: 0.7367 (mm-30) REVERT: P 499 ARG cc_start: 0.6449 (ttm170) cc_final: 0.6116 (ttm170) REVERT: P 551 GLU cc_start: 0.3709 (OUTLIER) cc_final: 0.3031 (mm-30) REVERT: Q 35 LEU cc_start: 0.2081 (OUTLIER) cc_final: 0.1286 (tt) REVERT: Q 289 ASN cc_start: -0.2085 (OUTLIER) cc_final: -0.2318 (p0) REVERT: Q 438 MET cc_start: -0.0172 (OUTLIER) cc_final: -0.0805 (mpt) REVERT: Q 519 SER cc_start: 0.6306 (t) cc_final: 0.5978 (p) REVERT: Q 550 MET cc_start: 0.1781 (tmm) cc_final: 0.1502 (tmm) outliers start: 175 outliers final: 91 residues processed: 533 average time/residue: 1.3252 time to fit residues: 922.9558 Evaluate side-chains 484 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 368 time to evaluate : 5.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 341 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 407 THR Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 595 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 592 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 289 ASN Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 245 optimal weight: 10.0000 chunk 657 optimal weight: 0.0670 chunk 144 optimal weight: 10.0000 chunk 428 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 730 optimal weight: 10.0000 chunk 606 optimal weight: 7.9990 chunk 338 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 383 optimal weight: 5.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 HIS I 227 HIS P 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 62584 Z= 0.222 Angle : 0.567 14.066 84667 Z= 0.287 Chirality : 0.043 0.173 9202 Planarity : 0.004 0.049 10852 Dihedral : 9.255 169.358 8925 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.87 % Allowed : 14.42 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -1.09 (0.09), residues: 7515 helix: 0.05 (0.10), residues: 2983 sheet: 0.27 (0.17), residues: 914 loop : -1.66 (0.09), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.008 0.001 HIS D 227 PHE 0.024 0.001 PHE J 205 TYR 0.015 0.001 TYR Q 548 ARG 0.010 0.000 ARG Q 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 388 time to evaluate : 5.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8064 (tt) cc_final: 0.7832 (tp) REVERT: A 259 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7772 (ttpt) REVERT: A 266 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: B 12 GLU cc_start: 0.7836 (tt0) cc_final: 0.7471 (tp30) REVERT: B 68 LEU cc_start: 0.8998 (mp) cc_final: 0.8752 (mt) REVERT: B 74 ASP cc_start: 0.7695 (m-30) cc_final: 0.7014 (m-30) REVERT: B 77 ASN cc_start: 0.6361 (m-40) cc_final: 0.5718 (t0) REVERT: B 88 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 107 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: B 110 LYS cc_start: 0.7666 (mttp) cc_final: 0.7428 (mtmt) REVERT: B 121 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8210 (tttt) REVERT: B 342 LYS cc_start: 0.8087 (mttm) cc_final: 0.7617 (tttp) REVERT: C 8 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7788 (m-40) REVERT: C 54 GLN cc_start: 0.8127 (tt0) cc_final: 0.7803 (tt0) REVERT: C 106 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6880 (tp30) REVERT: C 352 GLU cc_start: 0.7597 (mp0) cc_final: 0.7176 (mp0) REVERT: D 83 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6241 (mm-30) REVERT: E 8 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: E 102 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6321 (tm-30) REVERT: E 106 GLU cc_start: 0.6849 (mp0) cc_final: 0.6461 (mp0) REVERT: E 288 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7968 (t80) REVERT: E 386 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7592 (t80) REVERT: F 10 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (mp) REVERT: F 76 ASP cc_start: 0.6580 (m-30) cc_final: 0.6306 (m-30) REVERT: F 156 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6838 (mp10) REVERT: F 337 LYS cc_start: 0.7267 (pttt) cc_final: 0.6604 (mmpt) REVERT: G 9 LYS cc_start: 0.5830 (ttpp) cc_final: 0.4987 (pptt) REVERT: G 143 TYR cc_start: 0.6180 (m-80) cc_final: 0.5830 (m-80) REVERT: G 345 LYS cc_start: 0.5333 (mptt) cc_final: 0.4618 (tmtm) REVERT: G 361 MET cc_start: 0.5078 (mmm) cc_final: 0.4827 (pmt) REVERT: H 316 ARG cc_start: 0.7618 (mmm160) cc_final: 0.7107 (mmm160) REVERT: I 30 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8664 (t) REVERT: I 106 GLU cc_start: 0.7922 (tp30) cc_final: 0.7543 (pt0) REVERT: I 259 LYS cc_start: 0.7106 (mmmt) cc_final: 0.6822 (tttt) REVERT: I 361 MET cc_start: 0.8332 (mtp) cc_final: 0.8069 (mtp) REVERT: J 259 LYS cc_start: 0.7154 (ttmm) cc_final: 0.6804 (ttpt) REVERT: J 264 ARG cc_start: 0.6146 (mpp-170) cc_final: 0.5766 (mtm180) REVERT: J 337 LYS cc_start: 0.8008 (ttpp) cc_final: 0.7329 (mptp) REVERT: J 342 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7855 (tttp) REVERT: J 345 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6142 (tppp) REVERT: J 378 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8180 (m110) REVERT: K 106 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7152 (tp30) REVERT: K 287 MET cc_start: 0.9003 (mmt) cc_final: 0.8619 (mmp) REVERT: K 352 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: L 9 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8124 (ttpp) REVERT: L 69 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8452 (mp) REVERT: L 132 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: L 235 ASN cc_start: 0.6553 (m-40) cc_final: 0.6061 (p0) REVERT: L 342 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7596 (mtpt) REVERT: L 352 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: M 34 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.5914 (ptm160) REVERT: M 373 ASN cc_start: 0.7135 (m-40) cc_final: 0.6904 (m110) REVERT: M 410 ASP cc_start: 0.5785 (m-30) cc_final: 0.5562 (p0) REVERT: M 413 MET cc_start: 0.5505 (ttt) cc_final: 0.4997 (ppp) REVERT: M 478 GLU cc_start: 0.8096 (mp0) cc_final: 0.7563 (mp0) REVERT: M 498 GLU cc_start: 0.4022 (pt0) cc_final: 0.2990 (mp0) REVERT: M 592 LYS cc_start: 0.7761 (tttt) cc_final: 0.7262 (tttt) REVERT: N 67 ASP cc_start: 0.8715 (m-30) cc_final: 0.8476 (m-30) REVERT: N 131 ASP cc_start: 0.8610 (m-30) cc_final: 0.8350 (m-30) REVERT: N 229 GLU cc_start: 0.7224 (pp20) cc_final: 0.6961 (pm20) REVERT: N 325 TRP cc_start: 0.6748 (m100) cc_final: 0.6495 (m100) REVERT: N 508 LYS cc_start: 0.8179 (mttp) cc_final: 0.7795 (mtpm) REVERT: N 528 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (mmm) REVERT: O 105 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: O 340 TRP cc_start: 0.6832 (m100) cc_final: 0.6494 (m100) REVERT: O 382 GLN cc_start: 0.5724 (mt0) cc_final: 0.4997 (mm-40) REVERT: O 427 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6699 (mt0) REVERT: O 430 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: P 9 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8104 (mm) REVERT: P 241 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.5945 (mm-40) REVERT: P 289 ASN cc_start: -0.0905 (OUTLIER) cc_final: -0.1260 (p0) REVERT: P 413 MET cc_start: 0.4124 (ttp) cc_final: 0.2744 (mpm) REVERT: P 478 GLU cc_start: 0.7741 (mp0) cc_final: 0.7392 (mm-30) REVERT: P 551 GLU cc_start: 0.3864 (OUTLIER) cc_final: 0.3231 (mm-30) REVERT: P 592 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5476 (ptmm) REVERT: Q 35 LEU cc_start: 0.2286 (OUTLIER) cc_final: 0.1437 (tp) REVERT: Q 438 MET cc_start: 0.0117 (OUTLIER) cc_final: -0.0353 (mpt) REVERT: Q 472 THR cc_start: 0.7042 (m) cc_final: 0.6459 (p) REVERT: Q 519 SER cc_start: 0.6682 (t) cc_final: 0.6386 (p) outliers start: 186 outliers final: 103 residues processed: 529 average time/residue: 1.2817 time to fit residues: 887.0327 Evaluate side-chains 501 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 368 time to evaluate : 5.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 289 ARG Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain K residue 341 THR Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 232 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 407 THR Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 538 THR Chi-restraints excluded: chain O residue 595 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 222 VAL Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 592 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain Q residue 438 MET Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 704 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 416 optimal weight: 6.9990 chunk 533 optimal weight: 6.9990 chunk 413 optimal weight: 0.5980 chunk 614 optimal weight: 2.9990 chunk 407 optimal weight: 0.0470 chunk 727 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 335 optimal weight: 0.8980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN D 247 GLN F 394 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN H 313 HIS K 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 62584 Z= 0.131 Angle : 0.495 13.312 84667 Z= 0.249 Chirality : 0.040 0.187 9202 Planarity : 0.003 0.045 10852 Dihedral : 8.889 174.855 8925 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.08 % Allowed : 15.30 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -0.80 (0.10), residues: 7515 helix: 0.29 (0.10), residues: 2966 sheet: 0.41 (0.17), residues: 937 loop : -1.50 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.007 0.001 HIS G 267 PHE 0.030 0.001 PHE M 371 TYR 0.020 0.001 TYR H 284 ARG 0.007 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 402 time to evaluate : 5.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.7998 (tt) cc_final: 0.7771 (tp) REVERT: A 266 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: B 12 GLU cc_start: 0.7796 (tt0) cc_final: 0.7408 (tp30) REVERT: B 68 LEU cc_start: 0.8980 (mp) cc_final: 0.8746 (mt) REVERT: B 74 ASP cc_start: 0.7692 (m-30) cc_final: 0.7029 (m-30) REVERT: B 77 ASN cc_start: 0.6282 (m-40) cc_final: 0.5692 (t0) REVERT: B 88 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 107 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: B 121 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8108 (tttt) REVERT: B 342 LYS cc_start: 0.8035 (mttm) cc_final: 0.7578 (tttp) REVERT: C 54 GLN cc_start: 0.8089 (tt0) cc_final: 0.7734 (tt0) REVERT: C 106 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7266 (mm-30) REVERT: C 352 GLU cc_start: 0.7570 (mp0) cc_final: 0.7149 (mp0) REVERT: D 83 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6277 (mm-30) REVERT: E 102 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6322 (tm-30) REVERT: E 106 GLU cc_start: 0.6847 (mp0) cc_final: 0.6521 (mp0) REVERT: E 288 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7941 (t80) REVERT: E 386 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7535 (t80) REVERT: F 76 ASP cc_start: 0.6517 (m-30) cc_final: 0.6257 (m-30) REVERT: F 117 LYS cc_start: 0.8274 (tttt) cc_final: 0.7809 (ttmm) REVERT: F 156 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6906 (mp10) REVERT: F 337 LYS cc_start: 0.7230 (pttt) cc_final: 0.6574 (mmpt) REVERT: G 9 LYS cc_start: 0.5532 (ttpp) cc_final: 0.4805 (pptt) REVERT: G 143 TYR cc_start: 0.6334 (m-80) cc_final: 0.5941 (m-80) REVERT: G 345 LYS cc_start: 0.5380 (mptt) cc_final: 0.4696 (tmtm) REVERT: H 316 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7064 (mmm160) REVERT: I 106 GLU cc_start: 0.8080 (tp30) cc_final: 0.7658 (pt0) REVERT: I 251 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6726 (mt-10) REVERT: I 259 LYS cc_start: 0.6997 (mmmt) cc_final: 0.6736 (tttt) REVERT: J 14 ASP cc_start: 0.8473 (m-30) cc_final: 0.8033 (m-30) REVERT: J 259 LYS cc_start: 0.7175 (ttmm) cc_final: 0.6834 (ttpt) REVERT: J 264 ARG cc_start: 0.6017 (mpp-170) cc_final: 0.5666 (mtm180) REVERT: J 337 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7313 (mptp) REVERT: J 342 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7792 (tttp) REVERT: J 378 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8183 (m110) REVERT: K 83 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: K 106 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7209 (tp30) REVERT: K 287 MET cc_start: 0.8997 (mmt) cc_final: 0.8614 (mmp) REVERT: K 352 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: L 69 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8395 (mp) REVERT: L 132 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: L 235 ASN cc_start: 0.6409 (m-40) cc_final: 0.5969 (p0) REVERT: L 342 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7594 (mtpt) REVERT: M 34 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.5862 (ptm160) REVERT: M 410 ASP cc_start: 0.5713 (m-30) cc_final: 0.5510 (p0) REVERT: M 413 MET cc_start: 0.5440 (ttt) cc_final: 0.4977 (ppp) REVERT: M 478 GLU cc_start: 0.8083 (mp0) cc_final: 0.7569 (mp0) REVERT: M 498 GLU cc_start: 0.4054 (pt0) cc_final: 0.2978 (mp0) REVERT: M 592 LYS cc_start: 0.7757 (tttt) cc_final: 0.7310 (tttt) REVERT: N 67 ASP cc_start: 0.8557 (m-30) cc_final: 0.8322 (m-30) REVERT: N 131 ASP cc_start: 0.8548 (m-30) cc_final: 0.8286 (m-30) REVERT: N 194 VAL cc_start: 0.7287 (t) cc_final: 0.7025 (t) REVERT: N 508 LYS cc_start: 0.8148 (mttp) cc_final: 0.7733 (mtpm) REVERT: O 105 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: O 340 TRP cc_start: 0.6823 (m100) cc_final: 0.6488 (m100) REVERT: O 382 GLN cc_start: 0.5754 (mt0) cc_final: 0.4980 (mm-40) REVERT: O 427 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6679 (mt0) REVERT: O 430 ASP cc_start: 0.6265 (OUTLIER) cc_final: 0.5748 (m-30) REVERT: P 9 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8014 (mm) REVERT: P 241 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.5932 (mm-40) REVERT: P 289 ASN cc_start: -0.1050 (OUTLIER) cc_final: -0.1440 (p0) REVERT: P 413 MET cc_start: 0.4088 (ttp) cc_final: 0.2718 (mpm) REVERT: P 478 GLU cc_start: 0.7576 (mp0) cc_final: 0.7245 (mm-30) REVERT: P 550 MET cc_start: 0.6471 (ttp) cc_final: 0.6221 (ttp) REVERT: Q 35 LEU cc_start: 0.2258 (OUTLIER) cc_final: 0.1520 (tp) REVERT: Q 463 ARG cc_start: 0.2483 (tpm170) cc_final: 0.0510 (mmp-170) REVERT: Q 472 THR cc_start: 0.7137 (m) cc_final: 0.6684 (p) REVERT: Q 516 GLN cc_start: 0.6509 (pt0) cc_final: 0.6256 (pm20) REVERT: Q 519 SER cc_start: 0.6344 (t) cc_final: 0.6106 (p) outliers start: 135 outliers final: 75 residues processed: 503 average time/residue: 1.3032 time to fit residues: 854.3036 Evaluate side-chains 465 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 371 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 232 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 595 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 438 MET Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 450 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 434 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 462 optimal weight: 0.9990 chunk 495 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 571 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 GLN F 324 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 313 HIS I 227 HIS J 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 62584 Z= 0.156 Angle : 0.514 13.865 84667 Z= 0.259 Chirality : 0.041 0.162 9202 Planarity : 0.003 0.050 10852 Dihedral : 8.882 176.676 8925 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.03 % Allowed : 15.84 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 7515 helix: 0.33 (0.10), residues: 2963 sheet: 0.43 (0.17), residues: 935 loop : -1.47 (0.10), residues: 3617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Q 325 HIS 0.007 0.001 HIS G 267 PHE 0.047 0.001 PHE Q 462 TYR 0.015 0.001 TYR G 233 ARG 0.007 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 389 time to evaluate : 5.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8018 (tt) cc_final: 0.7784 (tp) REVERT: A 266 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: B 12 GLU cc_start: 0.7816 (tt0) cc_final: 0.7415 (tp30) REVERT: B 68 LEU cc_start: 0.8984 (mp) cc_final: 0.8747 (mt) REVERT: B 74 ASP cc_start: 0.7703 (m-30) cc_final: 0.7030 (m-30) REVERT: B 77 ASN cc_start: 0.6306 (m-40) cc_final: 0.5722 (t0) REVERT: B 88 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: B 107 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: B 121 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (tttt) REVERT: B 342 LYS cc_start: 0.8044 (mttm) cc_final: 0.7583 (tttp) REVERT: C 106 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7268 (mm-30) REVERT: C 352 GLU cc_start: 0.7588 (mp0) cc_final: 0.7169 (mp0) REVERT: D 83 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: E 102 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6310 (tm-30) REVERT: E 106 GLU cc_start: 0.6831 (mp0) cc_final: 0.6487 (mp0) REVERT: E 288 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7931 (t80) REVERT: E 386 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7620 (t80) REVERT: F 76 ASP cc_start: 0.6522 (m-30) cc_final: 0.6258 (m-30) REVERT: F 117 LYS cc_start: 0.8274 (tttt) cc_final: 0.7819 (ttmm) REVERT: F 156 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6906 (mp10) REVERT: F 337 LYS cc_start: 0.7213 (pttt) cc_final: 0.6548 (mmpt) REVERT: G 9 LYS cc_start: 0.5508 (ttpp) cc_final: 0.4778 (pptt) REVERT: G 143 TYR cc_start: 0.6344 (m-80) cc_final: 0.5986 (m-80) REVERT: G 345 LYS cc_start: 0.5385 (mptt) cc_final: 0.4711 (tmtm) REVERT: H 316 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7078 (mmm160) REVERT: I 259 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6745 (tttt) REVERT: J 14 ASP cc_start: 0.8471 (m-30) cc_final: 0.8015 (m-30) REVERT: J 207 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.7088 (t0) REVERT: J 264 ARG cc_start: 0.6022 (mpp-170) cc_final: 0.5669 (mtm180) REVERT: J 337 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7325 (mptp) REVERT: J 342 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7799 (tttp) REVERT: J 345 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6074 (tppp) REVERT: J 378 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8198 (m110) REVERT: K 83 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: K 106 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7208 (tp30) REVERT: K 287 MET cc_start: 0.8990 (mmt) cc_final: 0.8614 (mmp) REVERT: K 352 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: L 69 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8398 (mp) REVERT: L 132 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: L 235 ASN cc_start: 0.6430 (m-40) cc_final: 0.5977 (p0) REVERT: L 342 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7607 (mtpt) REVERT: M 34 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.5877 (ptm160) REVERT: M 373 ASN cc_start: 0.7235 (m-40) cc_final: 0.6940 (m110) REVERT: M 413 MET cc_start: 0.5099 (ttt) cc_final: 0.4680 (tmm) REVERT: M 478 GLU cc_start: 0.8073 (mp0) cc_final: 0.7557 (mp0) REVERT: M 498 GLU cc_start: 0.4099 (pt0) cc_final: 0.3192 (mm-30) REVERT: M 592 LYS cc_start: 0.7767 (tttt) cc_final: 0.7322 (tttt) REVERT: N 67 ASP cc_start: 0.8611 (m-30) cc_final: 0.8368 (m-30) REVERT: N 131 ASP cc_start: 0.8550 (m-30) cc_final: 0.8288 (m-30) REVERT: N 229 GLU cc_start: 0.7143 (pp20) cc_final: 0.6856 (pm20) REVERT: N 508 LYS cc_start: 0.8143 (mttp) cc_final: 0.7760 (mtpm) REVERT: O 105 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: O 340 TRP cc_start: 0.6818 (m100) cc_final: 0.6465 (m100) REVERT: O 382 GLN cc_start: 0.5717 (mt0) cc_final: 0.4981 (mm-40) REVERT: O 427 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6687 (mt0) REVERT: O 430 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5753 (m-30) REVERT: P 9 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8025 (mm) REVERT: P 241 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5979 (mm-40) REVERT: P 289 ASN cc_start: -0.1035 (OUTLIER) cc_final: -0.1420 (p0) REVERT: P 413 MET cc_start: 0.3905 (ttp) cc_final: 0.2647 (mpm) REVERT: P 478 GLU cc_start: 0.7524 (mp0) cc_final: 0.7206 (mm-30) REVERT: P 592 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.5540 (ptmm) REVERT: Q 35 LEU cc_start: 0.2223 (OUTLIER) cc_final: 0.1485 (tp) REVERT: Q 144 LEU cc_start: 0.6510 (mt) cc_final: 0.6189 (mm) REVERT: Q 300 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2284 (pp) REVERT: Q 337 THR cc_start: 0.3179 (t) cc_final: 0.2969 (p) REVERT: Q 448 MET cc_start: 0.3303 (tpp) cc_final: 0.1801 (pmt) REVERT: Q 463 ARG cc_start: 0.2578 (tpm170) cc_final: 0.0797 (mmp-170) REVERT: Q 472 THR cc_start: 0.7148 (m) cc_final: 0.6658 (p) REVERT: Q 516 GLN cc_start: 0.6535 (pt0) cc_final: 0.5995 (pm20) outliers start: 132 outliers final: 87 residues processed: 490 average time/residue: 1.3193 time to fit residues: 845.4169 Evaluate side-chains 479 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 369 time to evaluate : 5.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 205 PHE Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 383 HIS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 345 LYS Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 GLU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 318 ASN Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 232 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 522 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 219 ILE Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 595 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 461 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain P residue 592 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 661 optimal weight: 9.9990 chunk 697 optimal weight: 0.9990 chunk 636 optimal weight: 4.9990 chunk 678 optimal weight: 0.0670 chunk 696 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 295 optimal weight: 0.0980 chunk 532 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 612 optimal weight: 7.9990 chunk 641 optimal weight: 0.5980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 GLN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 HIS I 227 HIS K 266 GLN P 445 HIS Q 560 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 62584 Z= 0.108 Angle : 0.473 13.333 84667 Z= 0.238 Chirality : 0.039 0.148 9202 Planarity : 0.003 0.043 10852 Dihedral : 8.594 178.415 8925 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.56 % Allowed : 16.33 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: -0.57 (0.10), residues: 7515 helix: 0.48 (0.10), residues: 2966 sheet: 0.56 (0.17), residues: 943 loop : -1.38 (0.10), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 325 HIS 0.019 0.001 HIS P 445 PHE 0.024 0.001 PHE M 371 TYR 0.020 0.001 TYR H 284 ARG 0.008 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 398 time to evaluate : 5.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.7969 (tt) cc_final: 0.7736 (tp) REVERT: A 266 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: B 12 GLU cc_start: 0.7743 (tt0) cc_final: 0.7462 (tp30) REVERT: B 68 LEU cc_start: 0.8950 (mp) cc_final: 0.8721 (mt) REVERT: B 74 ASP cc_start: 0.7662 (m-30) cc_final: 0.7003 (m-30) REVERT: B 77 ASN cc_start: 0.6210 (m-40) cc_final: 0.5673 (t0) REVERT: B 88 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 107 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: B 121 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (tttt) REVERT: B 268 LEU cc_start: 0.8499 (pt) cc_final: 0.8269 (pp) REVERT: B 342 LYS cc_start: 0.8020 (mttm) cc_final: 0.7587 (tttp) REVERT: C 352 GLU cc_start: 0.7555 (mp0) cc_final: 0.7144 (mp0) REVERT: D 83 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6280 (mm-30) REVERT: D 230 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8249 (mp) REVERT: E 8 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7789 (m-40) REVERT: E 102 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6280 (tm-30) REVERT: E 106 GLU cc_start: 0.6823 (mp0) cc_final: 0.6498 (mp0) REVERT: E 288 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7936 (t80) REVERT: E 386 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7640 (t80) REVERT: F 117 LYS cc_start: 0.8212 (tttt) cc_final: 0.7769 (ttmm) REVERT: F 156 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6803 (mp10) REVERT: F 337 LYS cc_start: 0.7204 (pttt) cc_final: 0.6548 (mmpt) REVERT: F 374 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7605 (mmmm) REVERT: G 143 TYR cc_start: 0.6336 (m-80) cc_final: 0.6010 (m-80) REVERT: G 345 LYS cc_start: 0.5555 (mptt) cc_final: 0.4875 (tmtm) REVERT: H 102 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5739 (mm-30) REVERT: H 316 ARG cc_start: 0.7622 (mmm160) cc_final: 0.7099 (mmm160) REVERT: I 146 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7364 (tp30) REVERT: I 251 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6691 (mt-10) REVERT: I 259 LYS cc_start: 0.6938 (mmmt) cc_final: 0.6714 (tttt) REVERT: J 14 ASP cc_start: 0.8447 (m-30) cc_final: 0.8005 (m-30) REVERT: J 259 LYS cc_start: 0.7300 (ttmm) cc_final: 0.7022 (ttpt) REVERT: J 264 ARG cc_start: 0.5938 (mpp-170) cc_final: 0.5593 (mtm180) REVERT: J 337 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7302 (mptp) REVERT: J 342 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7812 (tttp) REVERT: K 83 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: K 106 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7219 (tp30) REVERT: K 287 MET cc_start: 0.8988 (mmt) cc_final: 0.8594 (mmp) REVERT: L 69 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (mp) REVERT: L 235 ASN cc_start: 0.6340 (m-40) cc_final: 0.5911 (p0) REVERT: L 342 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7539 (mtpt) REVERT: M 34 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.5738 (ptm160) REVERT: M 413 MET cc_start: 0.5392 (ttt) cc_final: 0.4985 (ppp) REVERT: M 478 GLU cc_start: 0.8078 (mp0) cc_final: 0.7572 (mp0) REVERT: M 498 GLU cc_start: 0.4090 (pt0) cc_final: 0.3187 (mm-30) REVERT: N 67 ASP cc_start: 0.8491 (m-30) cc_final: 0.8277 (m-30) REVERT: N 131 ASP cc_start: 0.8475 (m-30) cc_final: 0.8237 (m-30) REVERT: N 229 GLU cc_start: 0.7276 (pp20) cc_final: 0.6868 (pm20) REVERT: N 505 ARG cc_start: 0.7066 (tpm-80) cc_final: 0.6721 (mmm160) REVERT: N 508 LYS cc_start: 0.8113 (mttp) cc_final: 0.7765 (mtpm) REVERT: O 105 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: O 340 TRP cc_start: 0.6758 (m100) cc_final: 0.6476 (m100) REVERT: O 382 GLN cc_start: 0.5751 (mt0) cc_final: 0.4971 (mm-40) REVERT: O 427 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6570 (mt0) REVERT: O 430 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5778 (m-30) REVERT: O 466 GLN cc_start: 0.6177 (mm110) cc_final: 0.5829 (tm-30) REVERT: O 507 PHE cc_start: 0.6967 (m-80) cc_final: 0.6656 (m-80) REVERT: P 9 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7976 (mm) REVERT: P 241 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5980 (tm-30) REVERT: P 289 ASN cc_start: -0.0921 (OUTLIER) cc_final: -0.1196 (p0) REVERT: P 413 MET cc_start: 0.4216 (ttp) cc_final: 0.2945 (mpm) REVERT: P 445 HIS cc_start: 0.5654 (OUTLIER) cc_final: 0.5110 (t-90) REVERT: P 478 GLU cc_start: 0.7537 (mp0) cc_final: 0.7203 (mm-30) REVERT: Q 35 LEU cc_start: 0.2184 (OUTLIER) cc_final: 0.1562 (tp) REVERT: Q 70 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6160 (t80) REVERT: Q 300 LEU cc_start: 0.2728 (OUTLIER) cc_final: 0.2252 (pp) REVERT: Q 413 MET cc_start: 0.5201 (mtt) cc_final: 0.3827 (mtt) REVERT: Q 448 MET cc_start: 0.3167 (tpp) cc_final: 0.1700 (pmm) REVERT: Q 456 MET cc_start: 0.1903 (mpm) cc_final: 0.0250 (mmm) REVERT: Q 463 ARG cc_start: 0.2633 (tpm170) cc_final: 0.0916 (mmp-170) REVERT: Q 472 THR cc_start: 0.7149 (m) cc_final: 0.6730 (p) outliers start: 101 outliers final: 56 residues processed: 475 average time/residue: 1.3194 time to fit residues: 816.7929 Evaluate side-chains 441 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 364 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 141 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 232 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 445 HIS Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 675 optimal weight: 0.3980 chunk 445 optimal weight: 0.9990 chunk 717 optimal weight: 6.9990 chunk 437 optimal weight: 7.9990 chunk 340 optimal weight: 6.9990 chunk 498 optimal weight: 1.9990 chunk 752 optimal weight: 6.9990 chunk 692 optimal weight: 0.0970 chunk 598 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 HIS ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 313 HIS I 227 HIS ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 ASN N 319 GLN ** P 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 62584 Z= 0.117 Angle : 0.478 13.551 84667 Z= 0.239 Chirality : 0.040 0.152 9202 Planarity : 0.003 0.042 10852 Dihedral : 8.528 175.699 8925 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.43 % Allowed : 16.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 7515 helix: 0.52 (0.10), residues: 2975 sheet: 0.64 (0.17), residues: 947 loop : -1.34 (0.10), residues: 3593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 325 HIS 0.033 0.001 HIS P 445 PHE 0.024 0.001 PHE M 371 TYR 0.016 0.001 TYR G 233 ARG 0.008 0.000 ARG A 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15030 Ramachandran restraints generated. 7515 Oldfield, 0 Emsley, 7515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 371 time to evaluate : 5.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.7986 (tt) cc_final: 0.7756 (tp) REVERT: A 266 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: B 12 GLU cc_start: 0.7747 (tt0) cc_final: 0.7467 (tp30) REVERT: B 68 LEU cc_start: 0.8962 (mp) cc_final: 0.8736 (mt) REVERT: B 74 ASP cc_start: 0.7652 (m-30) cc_final: 0.6989 (m-30) REVERT: B 77 ASN cc_start: 0.6208 (m-40) cc_final: 0.5678 (t0) REVERT: B 88 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: B 121 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8036 (tttt) REVERT: B 268 LEU cc_start: 0.8522 (pt) cc_final: 0.8297 (pp) REVERT: B 342 LYS cc_start: 0.7921 (mttm) cc_final: 0.7439 (tttp) REVERT: C 352 GLU cc_start: 0.7575 (mp0) cc_final: 0.7165 (mp0) REVERT: D 83 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6196 (mm-30) REVERT: D 230 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8202 (mp) REVERT: E 8 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: E 102 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6283 (tm-30) REVERT: E 106 GLU cc_start: 0.6786 (mp0) cc_final: 0.6486 (mp0) REVERT: E 288 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7927 (t80) REVERT: E 386 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7632 (t80) REVERT: F 117 LYS cc_start: 0.8212 (tttt) cc_final: 0.7767 (ttmm) REVERT: F 156 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6809 (mp10) REVERT: F 337 LYS cc_start: 0.7221 (pttt) cc_final: 0.6571 (mmpt) REVERT: F 374 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7617 (mmmm) REVERT: G 143 TYR cc_start: 0.6337 (m-80) cc_final: 0.6018 (m-80) REVERT: G 345 LYS cc_start: 0.5546 (mptt) cc_final: 0.4891 (tmtt) REVERT: H 102 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5807 (mm-30) REVERT: H 316 ARG cc_start: 0.7601 (mmm160) cc_final: 0.7079 (mmm160) REVERT: I 146 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7395 (tp30) REVERT: I 259 LYS cc_start: 0.6919 (mmmt) cc_final: 0.6696 (tttt) REVERT: J 14 ASP cc_start: 0.8482 (m-30) cc_final: 0.8020 (m-30) REVERT: J 259 LYS cc_start: 0.7332 (ttmm) cc_final: 0.7019 (ttpt) REVERT: J 264 ARG cc_start: 0.5983 (mpp-170) cc_final: 0.5642 (mtm180) REVERT: J 337 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7314 (mptp) REVERT: J 342 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7817 (tttp) REVERT: K 83 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: K 106 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7219 (tp30) REVERT: K 287 MET cc_start: 0.8987 (mmt) cc_final: 0.8644 (mmp) REVERT: L 235 ASN cc_start: 0.6344 (m-40) cc_final: 0.5909 (p0) REVERT: L 342 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7496 (mtpt) REVERT: M 34 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.5704 (ptm160) REVERT: M 413 MET cc_start: 0.4980 (ttt) cc_final: 0.4609 (tmm) REVERT: M 478 GLU cc_start: 0.8075 (mp0) cc_final: 0.7569 (mp0) REVERT: M 498 GLU cc_start: 0.3921 (pt0) cc_final: 0.2858 (mp0) REVERT: M 592 LYS cc_start: 0.7761 (tttt) cc_final: 0.7426 (tmmt) REVERT: N 31 LEU cc_start: 0.7316 (tp) cc_final: 0.7102 (tp) REVERT: N 67 ASP cc_start: 0.8502 (m-30) cc_final: 0.8302 (m-30) REVERT: N 131 ASP cc_start: 0.8476 (m-30) cc_final: 0.8249 (m-30) REVERT: N 229 GLU cc_start: 0.7271 (pp20) cc_final: 0.6846 (pm20) REVERT: N 319 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: N 508 LYS cc_start: 0.8144 (mttp) cc_final: 0.7762 (mtpm) REVERT: O 105 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: O 107 ASN cc_start: 0.7034 (m110) cc_final: 0.6350 (t0) REVERT: O 340 TRP cc_start: 0.6759 (m100) cc_final: 0.6470 (m100) REVERT: O 382 GLN cc_start: 0.5760 (mt0) cc_final: 0.4971 (mm-40) REVERT: O 427 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6561 (mt0) REVERT: O 430 ASP cc_start: 0.6287 (OUTLIER) cc_final: 0.5772 (m-30) REVERT: O 466 GLN cc_start: 0.6429 (mm110) cc_final: 0.6101 (tm-30) REVERT: O 507 PHE cc_start: 0.6983 (m-80) cc_final: 0.6651 (m-80) REVERT: P 9 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7971 (mm) REVERT: P 241 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: P 289 ASN cc_start: -0.0918 (OUTLIER) cc_final: -0.1198 (p0) REVERT: P 413 MET cc_start: 0.4245 (ttp) cc_final: 0.3054 (mpm) REVERT: P 478 GLU cc_start: 0.7516 (mp0) cc_final: 0.7184 (mm-30) REVERT: Q 35 LEU cc_start: 0.2229 (OUTLIER) cc_final: 0.1597 (tp) REVERT: Q 70 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6159 (t80) REVERT: Q 300 LEU cc_start: 0.2532 (OUTLIER) cc_final: 0.2086 (pp) REVERT: Q 413 MET cc_start: 0.5007 (mtt) cc_final: 0.4671 (mtt) REVERT: Q 448 MET cc_start: 0.3219 (tpp) cc_final: 0.1961 (pmm) REVERT: Q 463 ARG cc_start: 0.2800 (tpm170) cc_final: 0.1254 (mmp-170) REVERT: Q 472 THR cc_start: 0.7244 (m) cc_final: 0.6880 (p) outliers start: 93 outliers final: 59 residues processed: 444 average time/residue: 1.3414 time to fit residues: 776.6506 Evaluate side-chains 442 residues out of total 6490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 364 time to evaluate : 5.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 8 ASN Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 288 PHE Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain L residue 380 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 580 VAL Chi-restraints excluded: chain N residue 107 ASN Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 232 ASN Chi-restraints excluded: chain N residue 286 SER Chi-restraints excluded: chain N residue 319 GLN Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain N residue 597 VAL Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 144 LEU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 374 VAL Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 107 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain P residue 241 GLN Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 317 THR Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 580 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 583 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 755 random chunks: chunk 367 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 638 optimal weight: 4.9990 chunk 183 optimal weight: 0.0870 chunk 552 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 599 optimal weight: 0.7980 chunk 251 optimal weight: 8.9990 chunk 616 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 HIS F 324 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 313 HIS I 227 HIS ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** P 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121853 restraints weight = 78283.021| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.90 r_work: 0.3195 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.223 62584 Z= 0.158 Angle : 0.543 59.194 84667 Z= 0.288 Chirality : 0.042 1.180 9202 Planarity : 0.003 0.080 10852 Dihedral : 8.529 175.690 8925 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.43 % Allowed : 16.96 % Favored : 81.60 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 7515 helix: 0.52 (0.10), residues: 2975 sheet: 0.65 (0.17), residues: 947 loop : -1.34 (0.10), residues: 3593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 325 HIS 0.026 0.001 HIS P 445 PHE 0.023 0.001 PHE M 371 TYR 0.015 0.001 TYR G 233 ARG 0.006 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16660.89 seconds wall clock time: 289 minutes 52.37 seconds (17392.37 seconds total)