Starting phenix.real_space_refine on Thu Feb 15 08:37:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uae_42061/02_2024/8uae_42061_neut_updated.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.046 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 39 5.49 5 Mg 5 5.21 5 S 150 5.16 5 C 41284 2.51 5 N 10985 2.21 5 O 12161 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 "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 382": "OE1" <-> "OE2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "N PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 455": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64624 Number of models: 1 Model: "" Number of chains: 35 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: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3054 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 11, 'TRANS': 369} 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: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3071 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 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: 3066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3066 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} 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: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3071 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 11, 'TRANS': 372} 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: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 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: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3067 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 11, 'TRANS': 371} 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: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 19, 'TRANS': 504} Chain breaks: 3 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.76, per 1000 atoms: 0.38 Number of scatterers: 64624 At special positions: 0 Unit cell: (188.7, 195.36, 223.11, 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 150 16.00 P 39 15.00 Mg 5 11.99 O 12161 8.00 N 10985 7.00 C 41284 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.75 Conformation dependent library (CDL) restraints added in 9.2 seconds 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 51 sheets defined 38.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.87 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.522A pdb=" N ARG A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 removed outlier: 3.759A 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 58 through 65 removed outlier: 4.080A pdb=" N ALA A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.558A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.557A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 131 removed outlier: 4.449A 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: 3.531A pdb=" N LYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR A 143 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 144 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.955A 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: 3.824A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.753A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.696A 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: 3.868A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.993A 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: 3.858A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.805A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.704A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.811A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 82 through 98 Processing helix chain 'B' and resid 102 through 123 removed outlier: 4.079A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 removed outlier: 4.033A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.099A pdb=" N LYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR B 143 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 144 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.517A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.574A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.535A pdb=" N ARG B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.644A pdb=" N CYS C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.166A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.731A 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 122 removed outlier: 3.719A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 142 through 153 removed outlier: 3.515A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.832A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.785A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.824A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.573A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.672A 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: 3.708A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.713A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.509A 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: 3.812A pdb=" N GLY D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.913A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 4.040A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.956A 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 142 through 153 Processing helix chain 'D' and resid 172 through 180 removed outlier: 3.738A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 283 through 294 removed outlier: 3.709A pdb=" N GLY D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 3.631A pdb=" N ILE D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 352 through 360 Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.913A pdb=" N GLN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.974A pdb=" N TRP E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 55 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 4.398A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 4.187A 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 83 through 99 removed outlier: 3.781A pdb=" N ASP E 87 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 4.079A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) 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: 3.500A pdb=" N LYS E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS E 144 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E 145 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.701A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 202 No H-bonds generated for 'chain 'E' and resid 200 through 202' Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.649A pdb=" N SER E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 321 Processing helix chain 'E' and resid 336 through 345 Processing helix chain 'E' and resid 350 through 359 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 383 removed outlier: 4.661A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.531A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.790A pdb=" N TRP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 72 through 76 Processing helix chain 'F' and resid 82 through 98 removed outlier: 3.525A pdb=" N ILE F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 123 removed outlier: 4.223A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 131 removed outlier: 4.201A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 128 through 131' 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 173 through 180 removed outlier: 3.532A pdb=" N ASP F 179 " --> pdb=" O TRP F 175 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 201 removed outlier: 3.969A 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 283 through 296 removed outlier: 3.572A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.624A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 344 removed outlier: 3.622A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 removed outlier: 3.606A pdb=" N LYS F 353 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA F 354 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE F 355 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'G' and resid 13 through 24 removed outlier: 4.004A pdb=" N GLN G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 removed outlier: 4.157A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 55 removed outlier: 3.559A pdb=" N GLN G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) 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 82 through 99 removed outlier: 3.554A pdb=" N ASP G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 121 removed outlier: 3.635A pdb=" N GLU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.674A pdb=" N PHE G 130 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 131' 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 143 through 153 Processing helix chain 'G' and resid 172 through 180 removed outlier: 3.852A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 4.020A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 278 through 295 removed outlier: 4.530A pdb=" N VAL G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 323 removed outlier: 3.633A pdb=" N ILE G 317 " --> pdb=" O HIS G 313 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 344 Processing helix chain 'G' and resid 350 through 357 Processing helix chain 'G' and resid 377 through 383 Processing helix chain 'G' and resid 397 through 405 Processing helix chain 'H' and resid 12 through 24 removed outlier: 3.942A pdb=" N GLN H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 53 removed outlier: 3.758A pdb=" N TRP H 49 " --> pdb=" O MET H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 82 through 99 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.618A pdb=" N LEU H 115 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR H 120 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 153 Processing helix chain 'H' and resid 172 through 180 removed outlier: 3.676A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.949A 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 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.657A pdb=" N PHE H 288 " --> pdb=" O TYR H 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG H 289 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER H 296 " --> pdb=" O GLY H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 322 removed outlier: 3.742A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 343 Processing helix chain 'H' and resid 350 through 359 removed outlier: 3.738A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 377 through 383 removed outlier: 4.088A pdb=" N GLU H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS H 383 " --> pdb=" O SER H 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.610A pdb=" N SER I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 45 through 50 Processing helix chain 'I' and resid 52 through 55 No H-bonds generated for 'chain 'I' and resid 52 through 55' Processing helix chain 'I' and resid 60 through 65 Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 82 through 99 Processing helix chain 'I' and resid 102 through 123 removed outlier: 4.213A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 131 removed outlier: 4.341A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.993A pdb=" N GLU I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU I 147 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE I 148 " --> pdb=" O HIS I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 180 removed outlier: 3.652A pdb=" N GLU I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP I 179 " --> pdb=" O TRP I 175 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.783A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 251 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 281 through 296 removed outlier: 3.852A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER I 296 " --> pdb=" O GLY I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 321 Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.570A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 357 Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.706A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 405 removed outlier: 4.162A pdb=" N GLU I 401 " --> pdb=" O ASP I 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 removed outlier: 4.136A pdb=" N GLN J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.508A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 removed outlier: 3.519A pdb=" N GLY J 61 " --> pdb=" O PRO J 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 77 Processing helix chain 'J' and resid 82 through 99 removed outlier: 3.767A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 123 removed outlier: 3.519A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 154 removed outlier: 3.516A pdb=" N LYS J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR J 143 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS J 144 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS J 145 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER J 153 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 180 removed outlier: 3.585A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'J' and resid 245 through 251 removed outlier: 3.726A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 Processing helix chain 'J' and resid 282 through 296 removed outlier: 3.523A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET J 287 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER J 296 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 321 Processing helix chain 'J' and resid 337 through 344 removed outlier: 3.579A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.690A pdb=" N ALA J 354 " --> pdb=" O GLU J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 377 through 383 Processing helix chain 'K' and resid 12 through 22 Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 57 through 65 removed outlier: 3.609A pdb=" N LEU K 60 " --> pdb=" O PRO K 57 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA K 62 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 63 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP K 65 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 removed outlier: 3.540A pdb=" N ASP K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 99 removed outlier: 3.774A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 123 removed outlier: 3.527A pdb=" N GLU K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 131 removed outlier: 4.053A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 128 through 131' Processing helix chain 'K' and resid 139 through 154 removed outlier: 4.970A pdb=" N TYR K 143 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS K 144 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS K 145 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER K 153 " --> pdb=" O LYS K 150 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 180 removed outlier: 3.823A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.989A pdb=" N PHE K 201 " --> pdb=" O PRO K 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP K 202 " --> pdb=" O GLN K 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 198 through 202' Processing helix chain 'K' and resid 245 through 251 Processing helix chain 'K' and resid 253 through 257 Processing helix chain 'K' and resid 280 through 296 removed outlier: 3.789A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 323 removed outlier: 3.658A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU K 323 " --> pdb=" O LEU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 3.804A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.906A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'L' and resid 12 through 24 removed outlier: 3.559A pdb=" N SER L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN L 24 " --> pdb=" O TYR L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 37 removed outlier: 3.948A pdb=" N SER L 37 " --> pdb=" O ALA L 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 34 through 37' Processing helix chain 'L' and resid 45 through 55 Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 82 through 98 removed outlier: 3.521A pdb=" N ILE L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 123 removed outlier: 3.965A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA L 123 " --> pdb=" O VAL L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 131 removed outlier: 4.233A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 128 through 131' Processing helix chain 'L' and resid 135 through 137 No H-bonds generated for 'chain 'L' and resid 135 through 137' Processing helix chain 'L' and resid 139 through 154 removed outlier: 5.211A pdb=" N TYR L 143 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS L 144 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS L 145 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 153 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN L 154 " --> pdb=" O LEU L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 180 Processing helix chain 'L' and resid 198 through 202 removed outlier: 3.667A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 251 Processing helix chain 'L' and resid 253 through 257 Processing helix chain 'L' and resid 283 through 295 removed outlier: 3.696A pdb=" N MET L 287 " --> pdb=" O VAL L 283 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 323 removed outlier: 3.742A pdb=" N LEU L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU L 323 " --> pdb=" O LEU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 344 Processing helix chain 'L' and resid 350 through 359 Processing helix chain 'L' and resid 372 through 375 Processing helix chain 'L' and resid 377 through 383 Processing helix chain 'M' and resid 130 through 136 removed outlier: 3.698A pdb=" N ASN M 134 " --> pdb=" O SER M 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE M 136 " --> pdb=" O PHE M 132 " (cutoff:3.500A) No H-bonds generated for '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: 3.526A pdb=" N LYS M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'M' and resid 258 through 270 removed outlier: 3.520A pdb=" N LEU M 261 " --> pdb=" O TYR M 258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY M 262 " --> pdb=" O GLN M 259 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA M 264 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY M 265 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU M 266 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 285 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 354 Processing helix chain 'M' and resid 372 through 385 Proline residue: M 376 - end of helix removed outlier: 3.551A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 421 removed outlier: 4.450A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 449 Proline residue: M 447 - end of helix Processing helix chain 'M' and resid 453 through 464 Processing helix chain 'M' and resid 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 523 through 528 removed outlier: 3.518A pdb=" N MET M 528 " --> pdb=" O THR M 524 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 549 removed outlier: 4.001A pdb=" N GLN M 544 " --> pdb=" O GLU M 540 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA M 545 " --> pdb=" O ARG M 541 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU M 546 " --> pdb=" O ASP M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 558 through 563 removed outlier: 3.994A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY M 563 " --> pdb=" O GLN M 560 " (cutoff:3.500A) Processing helix chain 'M' and resid 598 through 602 removed outlier: 3.531A pdb=" N TRP M 602 " --> pdb=" O PHE M 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 598 through 602' Processing helix chain 'N' and resid 31 through 33 No H-bonds generated for 'chain 'N' and resid 31 through 33' Processing helix chain 'N' and resid 130 through 136 removed outlier: 4.053A pdb=" N ASN N 134 " --> pdb=" O SER N 130 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 146 No H-bonds generated for 'chain 'N' and resid 144 through 146' Processing helix chain 'N' and resid 165 through 168 No H-bonds generated for 'chain 'N' and resid 165 through 168' Processing helix chain 'N' and resid 183 through 197 removed outlier: 4.000A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 216 No H-bonds generated for 'chain 'N' and resid 214 through 216' Processing helix chain 'N' and resid 258 through 261 Processing helix chain 'N' and resid 263 through 269 removed outlier: 3.716A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS N 268 " --> pdb=" O ALA N 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 263 through 269' Processing helix chain 'N' and resid 277 through 290 removed outlier: 4.906A pdb=" N ASN N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 5.580A 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 354 removed outlier: 3.684A pdb=" N THR N 348 " --> pdb=" O SER N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 384 removed outlier: 4.051A pdb=" N SER N 372 " --> pdb=" O ALA N 368 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN N 373 " --> pdb=" O PHE N 369 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL N 374 " --> pdb=" O GLY N 370 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU N 375 " --> pdb=" O PHE N 371 " (cutoff:3.500A) Proline residue: N 376 - end of helix Processing helix chain 'N' and resid 388 through 391 No H-bonds generated for 'chain 'N' and resid 388 through 391' Processing helix chain 'N' and resid 408 through 421 removed outlier: 3.829A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 446 through 464 Processing helix chain 'N' and resid 499 through 502 No H-bonds generated for 'chain 'N' and resid 499 through 502' Processing helix chain 'N' and resid 505 through 507 No H-bonds generated for 'chain 'N' and resid 505 through 507' Processing helix chain 'N' and resid 518 through 520 No H-bonds generated for 'chain 'N' and resid 518 through 520' Processing helix chain 'N' and resid 523 through 528 removed outlier: 3.838A pdb=" N MET N 528 " --> pdb=" O THR N 524 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 549 removed outlier: 3.666A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 558 through 563 removed outlier: 3.834A pdb=" N ILE N 561 " --> pdb=" O LEU N 558 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY N 563 " --> pdb=" O GLN N 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 558 through 563' Processing helix chain 'O' and resid 130 through 136 Processing helix chain 'O' and resid 144 through 146 No H-bonds generated for 'chain 'O' and resid 144 through 146' Processing helix chain 'O' and resid 166 through 170 Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 214 through 216 No H-bonds generated for 'chain 'O' and resid 214 through 216' Processing helix chain 'O' and resid 263 through 270 Processing helix chain 'O' and resid 277 through 286 Processing helix chain 'O' and resid 319 through 330 removed outlier: 3.733A pdb=" N LEU O 322 " --> pdb=" O GLN O 319 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA O 323 " --> pdb=" O SER O 320 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU O 324 " --> pdb=" O LYS O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 353 removed outlier: 3.619A pdb=" N ALA O 347 " --> pdb=" O LYS O 344 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR O 348 " --> pdb=" O SER O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 385 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 408 through 421 removed outlier: 3.592A pdb=" N ALA O 412 " --> pdb=" O HIS O 408 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP O 418 " --> pdb=" O SER O 414 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR O 419 " --> pdb=" O ASP O 415 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 464 Proline residue: O 447 - end of helix 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 496 through 506 Processing helix chain 'O' and resid 518 through 520 No H-bonds generated for 'chain 'O' and resid 518 through 520' Processing helix chain 'O' and resid 523 through 528 removed outlier: 4.104A pdb=" N MET O 528 " --> pdb=" O THR O 524 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 549 removed outlier: 3.617A pdb=" N GLN O 544 " --> pdb=" O GLU O 540 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA O 545 " --> pdb=" O ARG O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 561 through 563 No H-bonds generated for 'chain 'O' and resid 561 through 563' Processing helix chain 'O' and resid 598 through 603 Processing helix chain 'P' and resid 31 through 33 No H-bonds generated for 'chain 'P' and resid 31 through 33' Processing helix chain 'P' and resid 130 through 136 Processing helix chain 'P' and resid 141 through 146 removed outlier: 3.961A pdb=" N LEU P 144 " --> pdb=" O LYS P 141 " (cutoff:3.500A) Proline residue: P 145 - end of helix No H-bonds generated for 'chain 'P' and resid 141 through 146' Processing helix chain 'P' and resid 166 through 169 No H-bonds generated for 'chain 'P' and resid 166 through 169' 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 263 through 269 removed outlier: 3.618A pdb=" N ILE P 267 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 288 removed outlier: 4.066A pdb=" N ILE P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) 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 354 removed outlier: 3.554A pdb=" N GLU P 352 " --> pdb=" O LEU P 349 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE P 353 " --> pdb=" O VAL P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 377 through 385 removed outlier: 4.014A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 390 through 392 No H-bonds generated for 'chain 'P' and resid 390 through 392' Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 443 through 464 Proline residue: P 447 - end of helix Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 498 through 502 Processing helix chain 'P' and resid 504 through 507 Processing helix chain 'P' and resid 518 through 520 No H-bonds generated for 'chain 'P' and resid 518 through 520' Processing helix chain 'P' and resid 523 through 527 Processing helix chain 'P' and resid 540 through 549 removed outlier: 4.108A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 558 through 563 removed outlier: 4.142A pdb=" N SER P 562 " --> pdb=" O LYS P 559 " (cutoff:3.500A) Processing helix chain 'P' and resid 598 through 600 No H-bonds generated for 'chain 'P' and resid 598 through 600' Processing helix chain 'Q' and resid 130 through 137 removed outlier: 3.592A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 146 removed outlier: 3.889A 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 166 through 169 No H-bonds generated for 'chain 'Q' and resid 166 through 169' 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 269 removed outlier: 3.544A pdb=" N GLY Q 262 " --> pdb=" O GLN Q 259 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE Q 263 " --> pdb=" O ALA Q 260 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA Q 264 " --> pdb=" O LEU Q 261 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY Q 265 " --> pdb=" O GLY Q 262 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Q 269 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 286 Processing helix chain 'Q' and resid 322 through 331 Processing helix chain 'Q' and resid 343 through 353 removed outlier: 3.563A pdb=" N LEU Q 346 " --> pdb=" O PHE Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 371 through 383 removed outlier: 3.697A pdb=" N LEU Q 375 " --> pdb=" O SER Q 372 " (cutoff:3.500A) Proline residue: Q 376 - end of helix Processing helix chain 'Q' and resid 388 through 392 Processing helix chain 'Q' and resid 408 through 420 removed outlier: 4.146A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 464 removed outlier: 3.756A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 499 through 503 Processing helix chain 'Q' and resid 540 through 549 removed outlier: 3.845A pdb=" N ALA Q 549 " --> pdb=" O ALA Q 545 " (cutoff:3.500A) Processing helix chain 'Q' and resid 558 through 563 removed outlier: 3.573A pdb=" N ILE Q 561 " --> pdb=" O LEU Q 558 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 137 Processing helix chain 'R' and resid 141 through 143 No H-bonds generated for 'chain 'R' and resid 141 through 143' Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 183 through 197 removed outlier: 3.811A pdb=" N LYS R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 270 Processing helix chain 'R' and resid 277 through 287 removed outlier: 3.543A pdb=" N ALA R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 331 Processing helix chain 'R' and resid 343 through 352 removed outlier: 3.575A pdb=" N LEU R 346 " --> pdb=" O PHE R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 385 Proline residue: R 376 - end of helix Processing helix chain 'R' and resid 404 through 406 No H-bonds generated for 'chain 'R' and resid 404 through 406' Processing helix chain 'R' and resid 409 through 421 removed outlier: 3.587A pdb=" N MET R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU R 416 " --> pdb=" O ALA R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 464 removed outlier: 3.603A pdb=" N SER R 451 " --> pdb=" O PRO R 447 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA R 452 " --> pdb=" O MET R 448 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU R 453 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU R 454 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET R 456 " --> pdb=" O ALA R 452 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 457 " --> pdb=" O LEU R 453 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 482 No H-bonds generated for 'chain 'R' and resid 479 through 482' Processing helix chain 'R' and resid 492 through 506 removed outlier: 3.565A pdb=" N ARG R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS R 506 " --> pdb=" O LYS R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 525 through 527 No H-bonds generated for 'chain 'R' and resid 525 through 527' Processing helix chain 'R' and resid 541 through 548 Processing helix chain 'R' and resid 555 through 563 removed outlier: 4.183A pdb=" N SER R 562 " --> pdb=" O LEU R 558 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY R 563 " --> pdb=" O LYS R 559 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 8.762A pdb=" N THR A 367 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 329 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N VAL A 369 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA A 163 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LEU A 32 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 165 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 185 Processing sheet with id= C, first strand: chain 'B' and resid 8 through 10 removed outlier: 4.400A pdb=" N ILE B 3 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR B 367 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 329 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL B 369 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 331 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 27 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N PHE B 303 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 29 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASN B 305 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 31 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 163 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU B 32 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE B 165 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N ILE B 164 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR B 166 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 224 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.701A 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: 4.422A pdb=" N ILE C 3 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 8 " --> pdb=" O GLN C 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 185 removed outlier: 3.522A pdb=" N ALA C 163 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 232 through 234 Processing sheet with id= H, first strand: chain 'D' and resid 8 through 10 removed outlier: 4.174A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N PHE D 303 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY D 29 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 163 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ILE D 164 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR D 222 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR D 166 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR D 224 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 232 through 234 Processing sheet with id= J, first strand: chain 'E' and resid 183 through 185 removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 163 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 30 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS E 328 " --> pdb=" O THR E 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 232 through 234 Processing sheet with id= L, first strand: chain 'F' and resid 3 through 5 removed outlier: 8.550A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA F 163 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU F 32 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE F 165 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ILE F 164 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR F 222 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR F 166 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR F 224 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 232 through 234 Processing sheet with id= N, first strand: chain 'G' and resid 183 through 185 removed outlier: 3.552A pdb=" N ALA G 163 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS G 328 " --> pdb=" O THR G 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 3 through 5 removed outlier: 8.339A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN H 27 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE H 303 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY H 29 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASN H 305 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU H 31 " --> pdb=" O ASN H 305 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA H 163 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU H 32 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE H 165 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ILE H 164 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR H 222 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR H 166 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR H 224 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 3 through 5 removed outlier: 8.843A pdb=" N THR I 367 " --> pdb=" O PHE I 327 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL I 329 " --> pdb=" O THR I 367 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL I 369 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE I 331 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR I 300 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL I 330 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU I 302 " --> pdb=" O VAL I 330 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR I 332 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE I 304 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASN I 305 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU I 31 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA I 163 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LEU I 32 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE I 165 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ILE I 164 " --> pdb=" O HIS I 220 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 222 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR I 166 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR I 224 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN I 183 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU I 223 " --> pdb=" O GLN I 183 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE I 185 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS I 225 " --> pdb=" O PHE I 185 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 8 through 10 removed outlier: 4.359A pdb=" N ILE J 3 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN J 27 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE J 303 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY J 29 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN J 305 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU J 31 " --> pdb=" O ASN J 305 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA J 163 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU J 32 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N PHE J 165 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N ILE J 164 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR J 222 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR J 166 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR J 224 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 232 through 234 Processing sheet with id= S, first strand: chain 'K' and resid 3 through 5 removed outlier: 8.702A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA K 163 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N LEU K 32 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE K 165 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE K 164 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR K 222 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR K 166 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR K 224 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 232 through 234 Processing sheet with id= U, first strand: chain 'L' and resid 8 through 10 removed outlier: 4.397A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR L 367 " --> pdb=" O PHE L 327 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.754A 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: 6.689A pdb=" N LEU L 302 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR L 332 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE L 304 " --> pdb=" O TYR L 332 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA L 163 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU L 32 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE L 165 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ILE L 164 " --> pdb=" O HIS L 220 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR L 222 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR L 166 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR L 224 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 232 through 234 Processing sheet with id= W, first strand: chain 'M' and resid 67 through 70 removed outlier: 3.569A pdb=" N ALA M 69 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU M 27 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 35 through 37 Processing sheet with id= Y, first strand: chain 'M' and resid 125 through 127 removed outlier: 3.952A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 252 through 254 removed outlier: 6.665A pdb=" N VAL M 433 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR M 225 " --> pdb=" O VAL M 433 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE M 435 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU M 227 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN M 437 " --> pdb=" O LEU M 227 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE M 203 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL M 436 " --> pdb=" O ILE M 203 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL M 473 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N PHE M 206 " --> pdb=" O VAL M 473 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU M 475 " --> pdb=" O PHE M 206 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU M 173 " --> pdb=" O VAL M 513 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N THR M 515 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL M 175 " --> pdb=" O THR M 515 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA M 174 " --> pdb=" O SER M 530 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP M 532 " --> pdb=" O ALA M 174 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU M 176 " --> pdb=" O TRP M 532 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER M 534 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE M 161 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 292 through 294 Processing sheet with id= AB, first strand: chain 'M' and resid 356 through 358 Processing sheet with id= AC, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.620A pdb=" N ASP N 67 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ARG N 92 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY N 17 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN N 26 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL N 15 " --> pdb=" O ASN N 26 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 35 through 37 removed outlier: 3.602A pdb=" N SER N 43 " --> pdb=" O ALA N 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 125 through 127 removed outlier: 3.758A pdb=" N GLY N 100 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ARG N 64 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA N 98 " --> pdb=" O ARG N 64 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 252 through 254 removed outlier: 3.527A pdb=" N CYS N 252 " --> pdb=" O HIS N 224 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL N 433 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR N 225 " --> pdb=" O VAL N 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE N 435 " --> pdb=" O THR N 225 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU N 227 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN N 437 " --> pdb=" O LEU N 227 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE N 203 " --> pdb=" O HIS N 434 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL N 436 " --> pdb=" O ILE N 203 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE N 205 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL N 473 " --> pdb=" O VAL N 204 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE N 206 " --> pdb=" O VAL N 473 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU N 475 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER N 510 " --> pdb=" O THR N 472 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU N 173 " --> pdb=" O VAL N 513 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR N 515 " --> pdb=" O LEU N 173 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL N 175 " --> pdb=" O THR N 515 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN N 531 " --> pdb=" O ALA N 174 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LEU N 176 " --> pdb=" O ASN N 531 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE N 533 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL N 580 " --> pdb=" O ALA N 571 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL N 152 " --> pdb=" O SER N 583 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 298 through 301 removed outlier: 4.831A pdb=" N ILE N 298 " --> pdb=" O LEU N 310 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 356 through 358 Processing sheet with id= AI, first strand: chain 'O' and resid 67 through 70 removed outlier: 3.654A pdb=" N ASP O 67 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA O 69 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG O 92 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG O 24 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY O 17 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN O 26 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL O 15 " --> pdb=" O ASN O 26 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'O' and resid 124 through 127 removed outlier: 4.592A pdb=" N SER O 124 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE O 101 " --> pdb=" O ILE O 112 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 222 through 226 removed outlier: 6.384A pdb=" N VAL O 433 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR O 225 " --> pdb=" O VAL O 433 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE O 435 " --> pdb=" O THR O 225 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL O 473 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE O 206 " --> pdb=" O VAL O 473 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU O 475 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER O 510 " --> pdb=" O LEU O 474 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU O 476 " --> pdb=" O SER O 510 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE O 512 " --> pdb=" O LEU O 476 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU O 173 " --> pdb=" O VAL O 513 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N THR O 515 " --> pdb=" O LEU O 173 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL O 175 " --> pdb=" O THR O 515 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN O 531 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU O 176 " --> pdb=" O ASN O 531 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE O 533 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 298 through 301 removed outlier: 4.890A pdb=" N ILE O 298 " --> pdb=" O LEU O 310 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE O 308 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 67 through 70 removed outlier: 3.528A pdb=" N ASP P 67 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA P 69 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG P 92 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU P 27 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG P 22 " --> pdb=" O GLU P 19 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU P 19 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG P 24 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY P 17 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN P 26 " --> pdb=" O VAL P 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL P 15 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 35 through 37 Processing sheet with id= AP, first strand: chain 'P' and resid 125 through 127 removed outlier: 3.733A pdb=" N ILE P 52 " --> pdb=" O ALA P 63 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY P 100 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 222 through 226 removed outlier: 6.403A pdb=" N VAL P 433 " --> pdb=" O LYS P 223 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR P 225 " --> pdb=" O VAL P 433 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE P 435 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE P 203 " --> pdb=" O HIS P 434 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL P 436 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE P 205 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL P 473 " --> pdb=" O VAL P 204 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N PHE P 206 " --> pdb=" O VAL P 473 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU P 475 " --> pdb=" O PHE P 206 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU P 173 " --> pdb=" O VAL P 513 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR P 515 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL P 175 " --> pdb=" O THR P 515 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ALA P 174 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP P 532 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU P 176 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER P 534 " --> pdb=" O LEU P 176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE P 572 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 152 " --> pdb=" O SER P 583 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 67 through 70 removed outlier: 3.683A pdb=" N ALA Q 69 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG Q 92 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU Q 27 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Q 24 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY Q 17 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASN Q 26 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL Q 15 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 125 through 127 removed outlier: 3.536A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY Q 100 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA Q 98 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 222 through 226 removed outlier: 6.591A pdb=" N VAL Q 433 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR Q 225 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE Q 435 " --> pdb=" O THR Q 225 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE Q 203 " --> pdb=" O HIS Q 434 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL Q 436 " --> pdb=" O ILE Q 203 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE Q 205 " --> pdb=" O VAL Q 436 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL Q 473 " --> pdb=" O VAL Q 204 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER Q 510 " --> pdb=" O LEU Q 474 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU Q 476 " --> pdb=" O SER Q 510 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE Q 512 " --> pdb=" O LEU Q 476 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU Q 173 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR Q 515 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL Q 175 " --> pdb=" O THR Q 515 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN Q 531 " --> pdb=" O ALA Q 174 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU Q 176 " --> pdb=" O ASN Q 531 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE Q 533 " --> pdb=" O LEU Q 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 150 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE Q 161 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 13 through 19 removed outlier: 3.544A pdb=" N TYR R 14 " --> pdb=" O ASN R 26 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG R 24 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU R 18 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL R 62 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE R 101 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU R 60 " --> pdb=" O PHE R 101 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 100 through 104 removed outlier: 3.539A pdb=" N PHE R 101 " --> pdb=" O ILE R 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS R 103 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL R 110 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'R' and resid 512 through 515 removed outlier: 7.094A pdb=" N LEU R 173 " --> pdb=" O VAL R 513 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR R 515 " --> pdb=" O LEU R 173 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL R 175 " --> pdb=" O THR R 515 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA R 174 " --> pdb=" O ASN R 531 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE R 533 " --> pdb=" O ALA R 174 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 203 through 206 Processing sheet with id= AY, first strand: chain 'R' and resid 147 through 152 removed outlier: 3.508A pdb=" N ALA R 163 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 150 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE R 161 " --> pdb=" O LEU R 150 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 4794 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: 23.70 Time building geometry restraints manager: 21.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 21484 1.37 - 1.52: 22310 1.52 - 1.66: 22020 1.66 - 1.81: 242 1.81 - 1.96: 8 Bond restraints: 66064 Sorted by residual: bond pdb=" C2' AGS O 701 " pdb=" C3' AGS O 701 " ideal model delta sigma weight residual 1.530 1.282 0.248 1.30e-02 5.92e+03 3.64e+02 bond pdb=" C2' AGS N 701 " pdb=" C3' AGS N 701 " ideal model delta sigma weight residual 1.530 1.283 0.247 1.30e-02 5.92e+03 3.61e+02 bond pdb=" C2' AGS Q 701 " pdb=" C3' AGS Q 701 " ideal model delta sigma weight residual 1.530 1.288 0.242 1.30e-02 5.92e+03 3.47e+02 bond pdb=" C2' AGS P 701 " pdb=" C3' AGS P 701 " ideal model delta sigma weight residual 1.530 1.291 0.239 1.30e-02 5.92e+03 3.39e+02 bond pdb=" C2' AGS M 701 " pdb=" C3' AGS M 701 " ideal model delta sigma weight residual 1.530 1.291 0.239 1.30e-02 5.92e+03 3.39e+02 ... (remaining 66059 not shown) Histogram of bond angle deviations from ideal: 92.41 - 102.12: 145 102.12 - 111.83: 31157 111.83 - 121.54: 42341 121.54 - 131.25: 15584 131.25 - 140.96: 144 Bond angle restraints: 89371 Sorted by residual: angle pdb=" C5 AGS M 701 " pdb=" N7 AGS M 701 " pdb=" C8 AGS M 701 " ideal model delta sigma weight residual 103.67 108.44 -4.77 4.26e-01 5.51e+00 1.26e+02 angle pdb=" C5 AGS Q 701 " pdb=" N7 AGS Q 701 " pdb=" C8 AGS Q 701 " ideal model delta sigma weight residual 103.67 108.41 -4.74 4.26e-01 5.51e+00 1.24e+02 angle pdb=" C5 AGS O 701 " pdb=" N7 AGS O 701 " pdb=" C8 AGS O 701 " ideal model delta sigma weight residual 103.67 108.40 -4.73 4.26e-01 5.51e+00 1.23e+02 angle pdb=" C5 AGS P 701 " pdb=" N7 AGS P 701 " pdb=" C8 AGS P 701 " ideal model delta sigma weight residual 103.67 108.33 -4.66 4.26e-01 5.51e+00 1.20e+02 angle pdb=" C5 AGS N 701 " pdb=" C4 AGS N 701 " pdb=" N3 AGS N 701 " ideal model delta sigma weight residual 126.80 119.10 7.70 7.41e-01 1.82e+00 1.08e+02 ... (remaining 89366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 38487 35.54 - 71.08: 937 71.08 - 106.63: 109 106.63 - 142.17: 4 142.17 - 177.71: 3 Dihedral angle restraints: 39540 sinusoidal: 16314 harmonic: 23226 Sorted by residual: 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 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" O1B AGS N 701 " pdb=" O3B AGS N 701 " pdb=" PB AGS N 701 " pdb=" PG AGS N 701 " ideal model delta sinusoidal sigma weight residual 68.91 -108.80 177.71 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS Q 701 " pdb=" O3A AGS Q 701 " pdb=" PA AGS Q 701 " pdb=" PB AGS Q 701 " ideal model delta sinusoidal sigma weight residual -67.73 86.34 -154.07 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 39537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 9704 1.030 - 2.060: 0 2.060 - 3.090: 0 3.090 - 4.120: 0 4.120 - 5.151: 6 Chirality restraints: 9710 Sorted by residual: chirality pdb=" C2' AGS O 701 " pdb=" C1' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" O2' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.67 2.48 -5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" C4' AGS O 701 " pdb=" C3' AGS O 701 " pdb=" C5' AGS O 701 " pdb=" O4' AGS O 701 " both_signs ideal model delta sigma weight residual False -2.49 2.61 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C4' AGS P 701 " pdb=" C3' AGS P 701 " pdb=" C5' AGS P 701 " pdb=" O4' AGS P 701 " both_signs ideal model delta sigma weight residual False -2.49 2.60 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 9707 not shown) Planarity restraints: 11449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 324 " 0.038 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO K 325 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 325 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 325 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 297 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 298 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 470 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO R 471 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 471 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 471 " 0.030 5.00e-02 4.00e+02 ... (remaining 11446 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 8 2.09 - 2.79: 14922 2.79 - 3.49: 78403 3.49 - 4.20: 128557 4.20 - 4.90: 240132 Nonbonded interactions: 462022 Sorted by model distance: nonbonded pdb=" S1G AGS N 701 " pdb="MG MG N 702 " model vdw 1.383 2.530 nonbonded pdb=" S1G AGS M 701 " pdb="MG MG M 702 " model vdw 1.650 2.530 nonbonded pdb=" O2G AGS P 701 " pdb="MG MG P 702 " model vdw 1.806 2.170 nonbonded pdb=" S1G AGS O 701 " pdb="MG MG O 702 " model vdw 1.816 2.530 nonbonded pdb=" OE1 GLU M 211 " pdb="MG MG M 702 " model vdw 1.836 2.170 ... (remaining 462017 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 501)) selection = (chain 'B' and (resid 2 through 387 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 584)) selection = (chain 'N' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'O' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'P' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 355 or resid 375 through 484 or resid 498 through 584)) selection = (chain 'Q' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'R' and (resid 10 through 227 or resid 238 through 328 or resid 336 throu \ gh 355 or resid 375 through 484 or resid 498 through 584)) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 9.000 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 133.070 Find NCS groups from input model: 4.340 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 66064 Z= 0.310 Angle : 0.537 18.648 89371 Z= 0.332 Chirality : 0.132 5.151 9710 Planarity : 0.004 0.059 11449 Dihedral : 15.780 177.710 24688 Min Nonbonded Distance : 1.383 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.09), residues: 7933 helix: 0.53 (0.10), residues: 3036 sheet: 0.83 (0.17), residues: 1034 loop : -1.60 (0.09), residues: 3863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 116 HIS 0.005 0.001 HIS F 313 PHE 0.015 0.001 PHE F 288 TYR 0.020 0.001 TYR D 284 ARG 0.003 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2000 time to evaluate : 5.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7908 (m-30) cc_final: 0.7643 (m-30) REVERT: A 47 ASP cc_start: 0.8129 (m-30) cc_final: 0.7894 (m-30) REVERT: A 58 GLU cc_start: 0.7600 (mp0) cc_final: 0.7281 (mp0) REVERT: A 80 VAL cc_start: 0.8866 (t) cc_final: 0.8611 (p) REVERT: A 128 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 139 ASP cc_start: 0.7866 (t0) cc_final: 0.7466 (t0) REVERT: A 159 GLN cc_start: 0.8405 (mt0) cc_final: 0.8088 (mt0) REVERT: A 179 ASP cc_start: 0.8070 (t0) cc_final: 0.7862 (t70) REVERT: A 234 GLN cc_start: 0.8417 (pt0) cc_final: 0.8126 (pt0) REVERT: A 374 LYS cc_start: 0.8362 (mttt) cc_final: 0.8063 (mttm) REVERT: B 59 LEU cc_start: 0.8383 (mt) cc_final: 0.8181 (mt) REVERT: B 70 VAL cc_start: 0.8671 (t) cc_final: 0.8386 (m) REVERT: B 97 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8212 (ttmt) REVERT: B 102 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 132 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 202 ASP cc_start: 0.8349 (m-30) cc_final: 0.8084 (m-30) REVERT: B 205 PHE cc_start: 0.8976 (m-80) cc_final: 0.8773 (m-10) REVERT: B 233 TYR cc_start: 0.8028 (p90) cc_final: 0.7741 (p90) REVERT: B 240 VAL cc_start: 0.8690 (t) cc_final: 0.8468 (t) REVERT: B 257 ILE cc_start: 0.8417 (mm) cc_final: 0.8119 (mt) REVERT: B 258 ASN cc_start: 0.7944 (m-40) cc_final: 0.7528 (m-40) REVERT: B 289 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7913 (ttp80) REVERT: B 374 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8284 (mttp) REVERT: B 382 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 88 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7508 (mm-30) REVERT: C 104 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 180 LEU cc_start: 0.8150 (mt) cc_final: 0.7888 (mt) REVERT: C 202 ASP cc_start: 0.8035 (m-30) cc_final: 0.7828 (m-30) REVERT: C 286 GLU cc_start: 0.8074 (tp30) cc_final: 0.7841 (tp30) REVERT: C 296 SER cc_start: 0.8919 (m) cc_final: 0.8655 (t) REVERT: C 342 LYS cc_start: 0.8819 (mttp) cc_final: 0.8618 (mttp) REVERT: D 24 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8375 (mp10) REVERT: D 72 GLN cc_start: 0.6675 (tp40) cc_final: 0.6466 (mm-40) REVERT: D 76 ASP cc_start: 0.7305 (m-30) cc_final: 0.6840 (m-30) REVERT: D 109 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7519 (mtt-85) REVERT: D 113 SER cc_start: 0.8850 (m) cc_final: 0.8624 (t) REVERT: D 121 LYS cc_start: 0.8831 (ptmt) cc_final: 0.8622 (ttpt) REVERT: D 128 GLU cc_start: 0.7887 (mp0) cc_final: 0.7547 (mp0) REVERT: D 129 GLN cc_start: 0.8254 (mm110) cc_final: 0.7855 (mm-40) REVERT: D 131 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.8097 (ptm160) REVERT: D 137 LYS cc_start: 0.8359 (mttt) cc_final: 0.8063 (mmtp) REVERT: D 179 ASP cc_start: 0.7936 (t70) cc_final: 0.7690 (t70) REVERT: D 290 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7905 (mmt-90) REVERT: E 73 ILE cc_start: 0.7798 (mp) cc_final: 0.7590 (tt) REVERT: E 99 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8345 (ttp-170) REVERT: E 118 GLU cc_start: 0.7872 (tp30) cc_final: 0.7577 (tp30) REVERT: E 286 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7626 (tp30) REVERT: E 335 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7341 (mm-30) REVERT: F 11 ASN cc_start: 0.7906 (t0) cc_final: 0.7703 (p0) REVERT: F 14 ASP cc_start: 0.7343 (m-30) cc_final: 0.6479 (m-30) REVERT: F 17 SER cc_start: 0.8373 (m) cc_final: 0.8126 (t) REVERT: F 20 TYR cc_start: 0.8465 (t80) cc_final: 0.8230 (t80) REVERT: F 45 MET cc_start: 0.8253 (tpp) cc_final: 0.7810 (mmt) REVERT: F 109 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7672 (tpp80) REVERT: F 114 SER cc_start: 0.8741 (m) cc_final: 0.8217 (p) REVERT: F 137 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8305 (ttmm) REVERT: F 154 ASN cc_start: 0.7761 (m-40) cc_final: 0.7501 (m110) REVERT: F 233 TYR cc_start: 0.7682 (p90) cc_final: 0.7111 (p90) REVERT: F 286 GLU cc_start: 0.7157 (tp30) cc_final: 0.6767 (tp30) REVERT: F 296 SER cc_start: 0.8918 (m) cc_final: 0.8496 (t) REVERT: F 363 PHE cc_start: 0.8672 (m-80) cc_final: 0.8407 (m-80) REVERT: G 51 SER cc_start: 0.8732 (m) cc_final: 0.8378 (t) REVERT: G 53 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7692 (mtmt) REVERT: G 77 ASN cc_start: 0.8384 (t0) cc_final: 0.8167 (t0) REVERT: G 107 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 200 ASN cc_start: 0.8395 (m110) cc_final: 0.8075 (m-40) REVERT: G 202 ASP cc_start: 0.7629 (m-30) cc_final: 0.7332 (m-30) REVERT: G 225 LYS cc_start: 0.8641 (mttt) cc_final: 0.8402 (mtpt) REVERT: G 275 LYS cc_start: 0.8148 (mttt) cc_final: 0.7944 (mtpp) REVERT: G 291 PHE cc_start: 0.7945 (t80) cc_final: 0.7688 (t80) REVERT: G 353 LYS cc_start: 0.8422 (mttt) cc_final: 0.8158 (mttt) REVERT: G 403 ILE cc_start: 0.8258 (mt) cc_final: 0.7968 (tp) REVERT: H 43 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7801 (mtmm) REVERT: H 46 LYS cc_start: 0.8117 (mttt) cc_final: 0.7883 (mtpp) REVERT: H 65 ASP cc_start: 0.6985 (m-30) cc_final: 0.6718 (m-30) REVERT: H 68 LEU cc_start: 0.8638 (mt) cc_final: 0.8379 (mt) REVERT: H 107 GLU cc_start: 0.8190 (tp30) cc_final: 0.7783 (tp30) REVERT: H 110 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8276 (ttmm) REVERT: H 286 GLU cc_start: 0.8000 (tp30) cc_final: 0.7719 (tp30) REVERT: I 65 ASP cc_start: 0.8113 (m-30) cc_final: 0.7868 (m-30) REVERT: I 74 ASP cc_start: 0.7798 (m-30) cc_final: 0.7586 (m-30) REVERT: I 76 ASP cc_start: 0.7587 (m-30) cc_final: 0.6996 (m-30) REVERT: I 80 VAL cc_start: 0.8753 (t) cc_final: 0.8542 (p) REVERT: I 142 LYS cc_start: 0.8848 (tttt) cc_final: 0.8630 (ttmt) REVERT: I 250 ASP cc_start: 0.8196 (m-30) cc_final: 0.7831 (m-30) REVERT: I 342 LYS cc_start: 0.8378 (mttt) cc_final: 0.8154 (mtpp) REVERT: J 17 SER cc_start: 0.8014 (m) cc_final: 0.7726 (t) REVERT: J 99 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: J 300 THR cc_start: 0.8663 (m) cc_final: 0.8388 (p) REVERT: K 14 ASP cc_start: 0.6882 (m-30) cc_final: 0.6491 (m-30) REVERT: K 58 GLU cc_start: 0.7676 (pm20) cc_final: 0.7325 (pm20) REVERT: K 68 LEU cc_start: 0.8936 (mp) cc_final: 0.8721 (mt) REVERT: K 119 VAL cc_start: 0.7897 (p) cc_final: 0.7686 (t) REVERT: K 131 ARG cc_start: 0.8400 (ptm-80) cc_final: 0.8159 (ptm-80) REVERT: K 178 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7857 (mt-10) REVERT: K 255 ASP cc_start: 0.8515 (m-30) cc_final: 0.8299 (m-30) REVERT: K 262 PHE cc_start: 0.8565 (t80) cc_final: 0.8323 (t80) REVERT: K 266 GLN cc_start: 0.7883 (mt0) cc_final: 0.7552 (mt0) REVERT: K 291 PHE cc_start: 0.7868 (t80) cc_final: 0.7464 (t80) REVERT: L 63 LEU cc_start: 0.8049 (tp) cc_final: 0.7657 (tp) REVERT: L 142 LYS cc_start: 0.8528 (tttm) cc_final: 0.8321 (tttm) REVERT: L 233 TYR cc_start: 0.8185 (p90) cc_final: 0.7814 (p90) REVERT: L 293 GLU cc_start: 0.7739 (tt0) cc_final: 0.7464 (tt0) REVERT: L 374 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8300 (mtmt) REVERT: M 23 ILE cc_start: 0.8541 (mt) cc_final: 0.8316 (mt) REVERT: M 50 ASP cc_start: 0.8146 (m-30) cc_final: 0.7831 (m-30) REVERT: M 196 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7669 (mt-10) REVERT: M 204 VAL cc_start: 0.8427 (t) cc_final: 0.8075 (m) REVERT: M 254 LYS cc_start: 0.8844 (tttp) cc_final: 0.8580 (tttm) REVERT: M 271 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7512 (ttm-80) REVERT: M 300 LEU cc_start: 0.7976 (mt) cc_final: 0.7714 (mp) REVERT: M 318 ASN cc_start: 0.8460 (t0) cc_final: 0.8233 (t0) REVERT: M 319 GLN cc_start: 0.8679 (pp30) cc_final: 0.8461 (pp30) REVERT: M 327 ASP cc_start: 0.8458 (t0) cc_final: 0.8234 (t0) REVERT: M 386 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7422 (mt-10) REVERT: M 424 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6476 (mt-10) REVERT: M 428 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6316 (tm-30) REVERT: M 444 ASP cc_start: 0.7725 (m-30) cc_final: 0.7399 (m-30) REVERT: M 511 LEU cc_start: 0.7906 (mt) cc_final: 0.7642 (mt) REVERT: M 559 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8197 (mmpt) REVERT: M 560 GLN cc_start: 0.8378 (mt0) cc_final: 0.8158 (mt0) REVERT: M 574 SER cc_start: 0.8416 (p) cc_final: 0.8101 (t) REVERT: N 19 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7341 (mp0) REVERT: N 29 GLU cc_start: 0.6916 (mp0) cc_final: 0.6462 (mp0) REVERT: N 143 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7288 (mp0) REVERT: N 249 GLU cc_start: 0.7055 (pt0) cc_final: 0.6807 (pm20) REVERT: N 291 THR cc_start: 0.8836 (m) cc_final: 0.8418 (t) REVERT: N 302 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7864 (mttm) REVERT: N 315 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7032 (mtt180) REVERT: N 336 ARG cc_start: 0.8347 (ptp90) cc_final: 0.8037 (mtm-85) REVERT: N 355 CYS cc_start: 0.7875 (p) cc_final: 0.7530 (p) REVERT: N 383 GLN cc_start: 0.8135 (mt0) cc_final: 0.7882 (mm-40) REVERT: N 388 ILE cc_start: 0.8326 (tp) cc_final: 0.8083 (tt) REVERT: N 394 VAL cc_start: 0.8876 (t) cc_final: 0.8508 (p) REVERT: N 401 GLU cc_start: 0.7117 (mp0) cc_final: 0.6852 (mp0) REVERT: N 427 GLN cc_start: 0.7938 (mp10) cc_final: 0.7641 (mp10) REVERT: N 478 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7662 (mm-30) REVERT: N 506 LYS cc_start: 0.8568 (mttm) cc_final: 0.8366 (mtpp) REVERT: N 559 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8284 (mtmm) REVERT: O 19 GLU cc_start: 0.7470 (mp0) cc_final: 0.7198 (mp0) REVERT: O 43 SER cc_start: 0.8632 (p) cc_final: 0.8286 (t) REVERT: O 47 GLN cc_start: 0.8097 (pt0) cc_final: 0.7860 (pt0) REVERT: O 91 LEU cc_start: 0.8427 (tp) cc_final: 0.8128 (tp) REVERT: O 134 ASN cc_start: 0.8647 (t0) cc_final: 0.8416 (m-40) REVERT: O 166 ASP cc_start: 0.7713 (m-30) cc_final: 0.7291 (m-30) REVERT: O 171 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7272 (mmm-85) REVERT: O 352 GLU cc_start: 0.7911 (pp20) cc_final: 0.7565 (mm-30) REVERT: O 373 ASN cc_start: 0.7645 (m-40) cc_final: 0.7345 (m-40) REVERT: O 383 GLN cc_start: 0.7874 (mm110) cc_final: 0.7668 (mm110) REVERT: O 391 LYS cc_start: 0.8050 (tttp) cc_final: 0.7704 (ttpp) REVERT: O 517 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8026 (ttm-80) REVERT: O 539 ASN cc_start: 0.8305 (t0) cc_final: 0.8034 (t0) REVERT: O 559 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8541 (mtpp) REVERT: P 19 GLU cc_start: 0.7206 (mp0) cc_final: 0.6977 (mp0) REVERT: P 50 ASP cc_start: 0.7986 (m-30) cc_final: 0.7733 (m-30) REVERT: P 55 ASP cc_start: 0.8012 (p0) cc_final: 0.7745 (p0) REVERT: P 115 ASP cc_start: 0.7689 (p0) cc_final: 0.7416 (p0) REVERT: P 165 VAL cc_start: 0.8707 (p) cc_final: 0.8470 (t) REVERT: P 241 GLN cc_start: 0.7976 (mp10) cc_final: 0.7561 (mp10) REVERT: P 263 PHE cc_start: 0.8125 (t80) cc_final: 0.7915 (t80) REVERT: P 283 ASN cc_start: 0.8344 (m-40) cc_final: 0.8060 (m110) REVERT: P 349 LEU cc_start: 0.9006 (mm) cc_final: 0.8799 (mt) REVERT: P 401 GLU cc_start: 0.7986 (mp0) cc_final: 0.7697 (mp0) REVERT: P 411 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7251 (mtmt) REVERT: P 423 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7986 (mtmm) REVERT: P 444 ASP cc_start: 0.7233 (t0) cc_final: 0.6913 (t0) REVERT: P 459 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7620 (mm-30) REVERT: P 461 LEU cc_start: 0.8618 (tp) cc_final: 0.8404 (tp) REVERT: Q 67 ASP cc_start: 0.7713 (m-30) cc_final: 0.7458 (m-30) REVERT: Q 104 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7558 (ttm170) REVERT: Q 152 VAL cc_start: 0.8184 (t) cc_final: 0.7957 (p) REVERT: Q 170 SER cc_start: 0.8295 (t) cc_final: 0.7984 (p) REVERT: Q 209 ASN cc_start: 0.8576 (m110) cc_final: 0.8044 (m-40) REVERT: Q 211 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7421 (mt-10) REVERT: Q 242 LYS cc_start: 0.8107 (tppt) cc_final: 0.7906 (tppt) REVERT: Q 268 LYS cc_start: 0.8758 (tttm) cc_final: 0.8525 (ttmm) REVERT: Q 283 ASN cc_start: 0.8875 (m-40) cc_final: 0.8485 (m110) REVERT: Q 306 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6867 (tm-30) REVERT: Q 308 PHE cc_start: 0.7897 (t80) cc_final: 0.7390 (t80) REVERT: Q 311 TYR cc_start: 0.6614 (m-80) cc_final: 0.6303 (m-80) REVERT: Q 319 GLN cc_start: 0.7823 (pm20) cc_final: 0.7511 (pt0) REVERT: Q 327 ASP cc_start: 0.7705 (t0) cc_final: 0.7334 (t0) REVERT: Q 401 GLU cc_start: 0.7470 (tp30) cc_final: 0.7235 (tm-30) REVERT: Q 402 LEU cc_start: 0.7857 (mp) cc_final: 0.6436 (mp) REVERT: Q 440 ASN cc_start: 0.8552 (m-40) cc_final: 0.8345 (m110) REVERT: Q 468 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: Q 601 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7920 (mt-10) REVERT: R 140 ASP cc_start: 0.6726 (m-30) cc_final: 0.6486 (m-30) REVERT: R 189 LEU cc_start: 0.8703 (mp) cc_final: 0.8409 (mm) REVERT: R 245 LEU cc_start: 0.7036 (pp) cc_final: 0.6301 (mp) REVERT: R 294 LYS cc_start: 0.8199 (tppt) cc_final: 0.7324 (mptt) REVERT: R 371 PHE cc_start: 0.7843 (t80) cc_final: 0.7612 (t80) REVERT: R 418 ASP cc_start: 0.7535 (t70) cc_final: 0.7139 (t70) REVERT: R 423 LYS cc_start: 0.8445 (mptt) cc_final: 0.7840 (mmtm) REVERT: R 427 GLN cc_start: 0.7224 (tt0) cc_final: 0.6917 (tt0) REVERT: R 508 LYS cc_start: 0.7981 (mttp) cc_final: 0.7760 (mttp) REVERT: R 514 SER cc_start: 0.7676 (m) cc_final: 0.7475 (t) REVERT: R 516 GLN cc_start: 0.7732 (tt0) cc_final: 0.7499 (tt0) REVERT: R 559 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8106 (mtmt) outliers start: 1 outliers final: 0 residues processed: 2000 average time/residue: 0.6711 time to fit residues: 2184.1185 Evaluate side-chains 1665 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1665 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 672 optimal weight: 2.9990 chunk 603 optimal weight: 2.9990 chunk 334 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 406 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 chunk 623 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 379 optimal weight: 3.9990 chunk 464 optimal weight: 8.9990 chunk 722 optimal weight: 0.0010 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 200 ASN A 247 GLN C 129 GLN C 315 ASN D 5 GLN E 78 ASN E 129 GLN E 200 ASN F 324 ASN G 135 GLN G 154 ASN G 168 ASN G 218 HIS H 129 GLN I 258 ASN J 24 GLN J 183 GLN J 328 HIS K 78 ASN K 183 GLN L 234 GLN M 209 ASN N 544 GLN N 586 GLN O 221 ASN P 187 ASN P 586 GLN Q 427 GLN Q 556 GLN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66064 Z= 0.228 Angle : 0.541 13.298 89371 Z= 0.276 Chirality : 0.042 0.290 9710 Planarity : 0.004 0.058 11449 Dihedral : 9.786 166.704 9438 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.53 % Allowed : 9.00 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.72 (0.09), residues: 7933 helix: 0.41 (0.10), residues: 3064 sheet: 0.95 (0.17), residues: 998 loop : -1.64 (0.09), residues: 3871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 532 HIS 0.006 0.001 HIS Q 434 PHE 0.021 0.001 PHE M 462 TYR 0.022 0.001 TYR R 258 ARG 0.009 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1807 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1702 time to evaluate : 5.600 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 14 ASP cc_start: 0.7934 (m-30) cc_final: 0.7586 (m-30) REVERT: A 47 ASP cc_start: 0.8140 (m-30) cc_final: 0.7935 (m-30) REVERT: A 58 GLU cc_start: 0.7656 (mp0) cc_final: 0.7346 (mp0) REVERT: A 80 VAL cc_start: 0.8892 (t) cc_final: 0.8609 (p) REVERT: A 128 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 139 ASP cc_start: 0.7881 (t0) cc_final: 0.7518 (t0) REVERT: A 159 GLN cc_start: 0.8491 (mt0) cc_final: 0.8245 (mt0) REVERT: A 374 LYS cc_start: 0.8362 (mttt) cc_final: 0.8058 (mttm) REVERT: B 70 VAL cc_start: 0.8663 (t) cc_final: 0.8433 (m) REVERT: B 97 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8172 (ttmt) REVERT: B 102 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 107 GLU cc_start: 0.7319 (tp30) cc_final: 0.7115 (tt0) REVERT: B 132 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7813 (mp0) REVERT: B 179 ASP cc_start: 0.8335 (t0) cc_final: 0.8127 (t0) REVERT: B 202 ASP cc_start: 0.8402 (m-30) cc_final: 0.8125 (m-30) REVERT: B 205 PHE cc_start: 0.8978 (m-80) cc_final: 0.8773 (m-10) REVERT: B 233 TYR cc_start: 0.8026 (p90) cc_final: 0.7682 (p90) REVERT: B 240 VAL cc_start: 0.8755 (t) cc_final: 0.8512 (t) REVERT: B 257 ILE cc_start: 0.8517 (mm) cc_final: 0.8197 (mt) REVERT: B 258 ASN cc_start: 0.8147 (m-40) cc_final: 0.7699 (m-40) REVERT: B 374 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8327 (mttp) REVERT: B 382 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7568 (tp30) REVERT: C 58 GLU cc_start: 0.7827 (pm20) cc_final: 0.7522 (pm20) REVERT: C 88 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 102 GLU cc_start: 0.8042 (tp30) cc_final: 0.7794 (mm-30) REVERT: C 103 ASP cc_start: 0.7803 (t0) cc_final: 0.7586 (t0) REVERT: C 104 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7067 (mm-30) REVERT: C 132 GLU cc_start: 0.7713 (mp0) cc_final: 0.7331 (mp0) REVERT: C 202 ASP cc_start: 0.8039 (m-30) cc_final: 0.7827 (m-30) REVERT: C 286 GLU cc_start: 0.8138 (tp30) cc_final: 0.7898 (tp30) REVERT: C 316 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7543 (ttp-170) REVERT: D 24 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8421 (mp10) REVERT: D 72 GLN cc_start: 0.6773 (tp40) cc_final: 0.6527 (mm-40) REVERT: D 76 ASP cc_start: 0.7332 (m-30) cc_final: 0.6873 (m-30) REVERT: D 109 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7446 (mtt-85) REVERT: D 129 GLN cc_start: 0.8402 (mm110) cc_final: 0.8059 (mm110) REVERT: D 131 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.8161 (ptm160) REVERT: D 137 LYS cc_start: 0.8400 (mttt) cc_final: 0.8146 (mttm) REVERT: D 182 ILE cc_start: 0.8497 (mm) cc_final: 0.8093 (mt) REVERT: D 203 LEU cc_start: 0.8394 (mp) cc_final: 0.8172 (mt) REVERT: D 290 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7914 (mmt-90) REVERT: D 322 LEU cc_start: 0.8765 (mt) cc_final: 0.8506 (mt) REVERT: D 374 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8563 (mtmm) REVERT: E 77 ASN cc_start: 0.7738 (m-40) cc_final: 0.7483 (m-40) REVERT: E 99 ARG cc_start: 0.8725 (ttm-80) cc_final: 0.8452 (ttp-170) REVERT: E 100 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7617 (ttm110) REVERT: E 195 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (mm-40) REVERT: E 257 ILE cc_start: 0.8611 (mm) cc_final: 0.8401 (mt) REVERT: E 300 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8077 (p) REVERT: E 335 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7425 (mm-30) REVERT: E 341 THR cc_start: 0.8554 (m) cc_final: 0.8352 (p) REVERT: E 400 VAL cc_start: 0.8168 (t) cc_final: 0.7943 (m) REVERT: F 11 ASN cc_start: 0.7834 (t0) cc_final: 0.7523 (p0) REVERT: F 14 ASP cc_start: 0.7613 (m-30) cc_final: 0.6424 (m-30) REVERT: F 17 SER cc_start: 0.8371 (m) cc_final: 0.8102 (t) REVERT: F 20 TYR cc_start: 0.8588 (t80) cc_final: 0.8228 (t80) REVERT: F 43 LYS cc_start: 0.8497 (mttt) cc_final: 0.8269 (mttp) REVERT: F 45 MET cc_start: 0.8181 (tpp) cc_final: 0.7732 (mmt) REVERT: F 109 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7573 (tpp80) REVERT: F 114 SER cc_start: 0.8633 (m) cc_final: 0.8168 (p) REVERT: F 137 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8303 (ttmm) REVERT: F 154 ASN cc_start: 0.7763 (m-40) cc_final: 0.7538 (m110) REVERT: F 233 TYR cc_start: 0.7471 (p90) cc_final: 0.6858 (p90) REVERT: F 296 SER cc_start: 0.8939 (m) cc_final: 0.8528 (t) REVERT: F 317 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8168 (mt) REVERT: F 363 PHE cc_start: 0.8776 (m-80) cc_final: 0.8366 (m-80) REVERT: G 51 SER cc_start: 0.8553 (m) cc_final: 0.8289 (p) REVERT: G 77 ASN cc_start: 0.8457 (t0) cc_final: 0.8197 (t0) REVERT: G 107 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7712 (tm-30) REVERT: G 200 ASN cc_start: 0.8420 (m110) cc_final: 0.8055 (m110) REVERT: G 202 ASP cc_start: 0.7762 (m-30) cc_final: 0.7553 (m-30) REVERT: G 225 LYS cc_start: 0.8645 (mttt) cc_final: 0.8406 (mtpt) REVERT: G 242 GLU cc_start: 0.7764 (tt0) cc_final: 0.7545 (tt0) REVERT: G 255 ASP cc_start: 0.7968 (t0) cc_final: 0.7605 (t0) REVERT: G 275 LYS cc_start: 0.8286 (mttt) cc_final: 0.8057 (mtpp) REVERT: G 291 PHE cc_start: 0.8017 (t80) cc_final: 0.7767 (t80) REVERT: G 353 LYS cc_start: 0.8465 (mttt) cc_final: 0.8226 (mttt) REVERT: G 403 ILE cc_start: 0.8259 (mt) cc_final: 0.7962 (tp) REVERT: G 405 ASN cc_start: 0.7994 (t0) cc_final: 0.7396 (m110) REVERT: H 43 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7969 (mtmm) REVERT: H 46 LYS cc_start: 0.7933 (mttt) cc_final: 0.7670 (mtpp) REVERT: H 99 ARG cc_start: 0.8465 (ptm160) cc_final: 0.8254 (ptm160) REVERT: H 107 GLU cc_start: 0.8186 (tp30) cc_final: 0.7769 (tp30) REVERT: H 110 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8269 (ttmm) REVERT: H 118 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7553 (mm-30) REVERT: H 286 GLU cc_start: 0.8009 (tp30) cc_final: 0.7753 (tp30) REVERT: H 388 VAL cc_start: 0.8573 (p) cc_final: 0.8288 (m) REVERT: I 65 ASP cc_start: 0.8089 (m-30) cc_final: 0.7843 (m-30) REVERT: I 74 ASP cc_start: 0.7831 (m-30) cc_final: 0.7542 (m-30) REVERT: I 76 ASP cc_start: 0.7594 (m-30) cc_final: 0.6989 (m-30) REVERT: I 80 VAL cc_start: 0.8769 (t) cc_final: 0.8555 (p) REVERT: I 142 LYS cc_start: 0.8889 (tttt) cc_final: 0.8672 (ttmt) REVERT: I 288 PHE cc_start: 0.8441 (t80) cc_final: 0.8094 (m-80) REVERT: I 342 LYS cc_start: 0.8417 (mttt) cc_final: 0.8181 (mtpp) REVERT: J 17 SER cc_start: 0.8079 (m) cc_final: 0.7843 (t) REVERT: J 72 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6879 (mm-40) REVERT: J 202 ASP cc_start: 0.8176 (m-30) cc_final: 0.7956 (m-30) REVERT: J 233 TYR cc_start: 0.7903 (p90) cc_final: 0.7578 (p90) REVERT: J 300 THR cc_start: 0.8766 (m) cc_final: 0.8458 (p) REVERT: K 14 ASP cc_start: 0.6965 (m-30) cc_final: 0.6601 (m-30) REVERT: K 58 GLU cc_start: 0.7736 (pm20) cc_final: 0.7385 (pm20) REVERT: K 68 LEU cc_start: 0.8947 (mp) cc_final: 0.8731 (mt) REVERT: K 131 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.7902 (ptm-80) REVERT: K 250 ASP cc_start: 0.7885 (m-30) cc_final: 0.7675 (m-30) REVERT: K 255 ASP cc_start: 0.8441 (m-30) cc_final: 0.8237 (m-30) REVERT: K 262 PHE cc_start: 0.8567 (t80) cc_final: 0.8365 (t80) REVERT: K 286 GLU cc_start: 0.8093 (tp30) cc_final: 0.7887 (tp30) REVERT: K 379 SER cc_start: 0.8807 (m) cc_final: 0.8258 (t) REVERT: L 63 LEU cc_start: 0.8085 (tp) cc_final: 0.7658 (tp) REVERT: L 233 TYR cc_start: 0.8096 (p90) cc_final: 0.7778 (p90) REVERT: L 293 GLU cc_start: 0.7707 (tt0) cc_final: 0.7458 (tt0) REVERT: L 374 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8357 (mtmm) REVERT: M 24 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7521 (ttp-170) REVERT: M 50 ASP cc_start: 0.8193 (m-30) cc_final: 0.7829 (m-30) REVERT: M 191 THR cc_start: 0.8094 (m) cc_final: 0.7790 (p) REVERT: M 196 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7747 (mt-10) REVERT: M 254 LYS cc_start: 0.8884 (tttp) cc_final: 0.8570 (tttm) REVERT: M 271 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7551 (ttm-80) REVERT: M 318 ASN cc_start: 0.8472 (t0) cc_final: 0.8265 (t0) REVERT: M 319 GLN cc_start: 0.8737 (pp30) cc_final: 0.8526 (pp30) REVERT: M 327 ASP cc_start: 0.8370 (t0) cc_final: 0.8152 (t0) REVERT: M 333 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7346 (mmm160) REVERT: M 340 TRP cc_start: 0.8057 (m100) cc_final: 0.7751 (m100) REVERT: M 386 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7407 (mt-10) REVERT: M 424 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6507 (mt-10) REVERT: M 428 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6376 (tm-30) REVERT: M 444 ASP cc_start: 0.7820 (m-30) cc_final: 0.7616 (m-30) REVERT: M 478 GLU cc_start: 0.8188 (mp0) cc_final: 0.7823 (mp0) REVERT: M 511 LEU cc_start: 0.7936 (mt) cc_final: 0.7667 (mt) REVERT: M 560 GLN cc_start: 0.8352 (mt0) cc_final: 0.8094 (mt0) REVERT: M 574 SER cc_start: 0.8325 (p) cc_final: 0.8026 (t) REVERT: N 110 VAL cc_start: 0.8611 (p) cc_final: 0.8347 (m) REVERT: N 249 GLU cc_start: 0.7146 (pt0) cc_final: 0.6737 (pm20) REVERT: N 271 ARG cc_start: 0.7513 (mtt90) cc_final: 0.7300 (mtt180) REVERT: N 291 THR cc_start: 0.8810 (m) cc_final: 0.8371 (t) REVERT: N 301 GLU cc_start: 0.7631 (tt0) cc_final: 0.7199 (tt0) REVERT: N 336 ARG cc_start: 0.8375 (ptp90) cc_final: 0.8088 (mtm-85) REVERT: N 355 CYS cc_start: 0.8114 (p) cc_final: 0.7895 (p) REVERT: N 383 GLN cc_start: 0.8009 (mt0) cc_final: 0.7736 (mm-40) REVERT: N 394 VAL cc_start: 0.8905 (t) cc_final: 0.8495 (p) REVERT: N 401 GLU cc_start: 0.7170 (mp0) cc_final: 0.6930 (mp0) REVERT: N 427 GLN cc_start: 0.7953 (mp10) cc_final: 0.7652 (mp10) REVERT: N 478 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7720 (mm-30) REVERT: N 506 LYS cc_start: 0.8613 (mttm) cc_final: 0.8385 (mtpp) REVERT: O 134 ASN cc_start: 0.8679 (t0) cc_final: 0.8449 (m-40) REVERT: O 143 GLU cc_start: 0.7456 (mp0) cc_final: 0.7164 (mp0) REVERT: O 171 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7304 (mmm-85) REVERT: O 316 ASP cc_start: 0.8269 (p0) cc_final: 0.7965 (p0) REVERT: O 352 GLU cc_start: 0.7868 (pp20) cc_final: 0.7659 (mm-30) REVERT: O 373 ASN cc_start: 0.7553 (m-40) cc_final: 0.7303 (m-40) REVERT: O 383 GLN cc_start: 0.7916 (mm110) cc_final: 0.7669 (mm110) REVERT: O 391 LYS cc_start: 0.7966 (tttp) cc_final: 0.7639 (ttpp) REVERT: O 539 ASN cc_start: 0.8328 (t0) cc_final: 0.8081 (t0) REVERT: O 559 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8581 (mtpp) REVERT: P 19 GLU cc_start: 0.7297 (mp0) cc_final: 0.7044 (mp0) REVERT: P 50 ASP cc_start: 0.7966 (m-30) cc_final: 0.7716 (m-30) REVERT: P 55 ASP cc_start: 0.7979 (p0) cc_final: 0.7638 (p0) REVERT: P 115 ASP cc_start: 0.7636 (p0) cc_final: 0.7416 (p0) REVERT: P 156 THR cc_start: 0.8558 (m) cc_final: 0.8331 (p) REVERT: P 241 GLN cc_start: 0.8051 (mp10) cc_final: 0.7593 (mp10) REVERT: P 283 ASN cc_start: 0.8377 (m-40) cc_final: 0.8135 (m110) REVERT: P 401 GLU cc_start: 0.7996 (mp0) cc_final: 0.7676 (mp0) REVERT: P 411 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7309 (mtmt) REVERT: P 423 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7948 (mtmm) REVERT: P 444 ASP cc_start: 0.7326 (t0) cc_final: 0.6942 (t0) REVERT: P 459 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7636 (mm-30) REVERT: Q 94 ILE cc_start: 0.8309 (mt) cc_final: 0.7820 (tt) REVERT: Q 104 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7493 (ttm170) REVERT: Q 170 SER cc_start: 0.8262 (t) cc_final: 0.7600 (p) REVERT: Q 171 ARG cc_start: 0.6883 (mmt-90) cc_final: 0.6561 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8588 (m110) cc_final: 0.8039 (m-40) REVERT: Q 211 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7512 (mt-10) REVERT: Q 268 LYS cc_start: 0.8767 (tttm) cc_final: 0.8534 (ttmm) REVERT: Q 293 PHE cc_start: 0.8435 (t80) cc_final: 0.8140 (t80) REVERT: Q 306 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6907 (tm-30) REVERT: Q 308 PHE cc_start: 0.7888 (t80) cc_final: 0.7370 (t80) REVERT: Q 327 ASP cc_start: 0.7389 (t0) cc_final: 0.7184 (t0) REVERT: Q 401 GLU cc_start: 0.7512 (tp30) cc_final: 0.7304 (tm-30) REVERT: Q 402 LEU cc_start: 0.7966 (mp) cc_final: 0.6520 (mp) REVERT: Q 416 GLU cc_start: 0.8026 (tp30) cc_final: 0.7739 (tp30) REVERT: Q 440 ASN cc_start: 0.8550 (m-40) cc_final: 0.8336 (m110) REVERT: Q 468 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7334 (mtm180) REVERT: Q 544 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7854 (tp-100) REVERT: Q 601 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7966 (mt-10) REVERT: R 140 ASP cc_start: 0.6758 (m-30) cc_final: 0.6490 (m-30) REVERT: R 192 ARG cc_start: 0.7426 (tpp80) cc_final: 0.6209 (tpp80) REVERT: R 240 GLN cc_start: 0.8491 (mp10) cc_final: 0.8144 (mp10) REVERT: R 245 LEU cc_start: 0.7069 (pp) cc_final: 0.6635 (mp) REVERT: R 294 LYS cc_start: 0.8119 (tppt) cc_final: 0.7322 (mptt) REVERT: R 418 ASP cc_start: 0.7640 (t70) cc_final: 0.7215 (t70) REVERT: R 423 LYS cc_start: 0.8523 (mptt) cc_final: 0.7885 (mmtm) REVERT: R 427 GLN cc_start: 0.7248 (tt0) cc_final: 0.6963 (tt0) REVERT: R 439 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7466 (pttp) REVERT: R 475 LEU cc_start: 0.8621 (tp) cc_final: 0.8411 (tp) REVERT: R 508 LYS cc_start: 0.7999 (mttp) cc_final: 0.7772 (mttp) REVERT: R 516 GLN cc_start: 0.7786 (tt0) cc_final: 0.7554 (tt0) REVERT: R 559 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8132 (mtmt) outliers start: 105 outliers final: 76 residues processed: 1740 average time/residue: 0.6469 time to fit residues: 1830.4121 Evaluate side-chains 1724 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1644 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 234 GLN Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 353 PHE Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 554 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 439 LYS Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 401 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 chunk 601 optimal weight: 0.3980 chunk 492 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 724 optimal weight: 0.8980 chunk 782 optimal weight: 6.9990 chunk 644 optimal weight: 0.6980 chunk 718 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 580 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 313 HIS C 315 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 200 ASN F 324 ASN J 24 GLN J 183 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN Q 443 GLN R 277 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 66064 Z= 0.147 Angle : 0.488 14.932 89371 Z= 0.247 Chirality : 0.040 0.235 9710 Planarity : 0.003 0.053 11449 Dihedral : 9.056 168.787 9438 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.72 % Allowed : 11.38 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.09), residues: 7933 helix: 0.47 (0.10), residues: 3063 sheet: 1.01 (0.17), residues: 996 loop : -1.58 (0.09), residues: 3874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 409 HIS 0.004 0.001 HIS Q 480 PHE 0.016 0.001 PHE M 293 TYR 0.025 0.001 TYR R 258 ARG 0.009 0.000 ARG O 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1783 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1665 time to evaluate : 5.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7874 (m-30) cc_final: 0.7652 (m-30) REVERT: A 58 GLU cc_start: 0.7602 (mp0) cc_final: 0.7261 (mp0) REVERT: A 80 VAL cc_start: 0.8900 (t) cc_final: 0.8602 (p) REVERT: A 128 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 139 ASP cc_start: 0.7873 (t0) cc_final: 0.7512 (t0) REVERT: A 159 GLN cc_start: 0.8476 (mt0) cc_final: 0.8233 (mt0) REVERT: A 374 LYS cc_start: 0.8341 (mttt) cc_final: 0.8072 (mttm) REVERT: B 70 VAL cc_start: 0.8647 (t) cc_final: 0.8422 (m) REVERT: B 97 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8127 (ttmt) REVERT: B 102 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 132 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7762 (mp0) REVERT: B 179 ASP cc_start: 0.8324 (t0) cc_final: 0.8070 (t0) REVERT: B 233 TYR cc_start: 0.8042 (p90) cc_final: 0.7692 (p90) REVERT: B 240 VAL cc_start: 0.8764 (t) cc_final: 0.8521 (t) REVERT: B 257 ILE cc_start: 0.8492 (mm) cc_final: 0.8156 (mt) REVERT: B 258 ASN cc_start: 0.8154 (m-40) cc_final: 0.7675 (m-40) REVERT: B 374 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8319 (mttp) REVERT: B 382 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7566 (tp30) REVERT: C 58 GLU cc_start: 0.7887 (pm20) cc_final: 0.7546 (pm20) REVERT: C 88 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 102 GLU cc_start: 0.8046 (tp30) cc_final: 0.7694 (mm-30) REVERT: C 104 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7034 (mm-30) REVERT: C 132 GLU cc_start: 0.7717 (mp0) cc_final: 0.7364 (mp0) REVERT: C 202 ASP cc_start: 0.7992 (m-30) cc_final: 0.7788 (m-30) REVERT: C 286 GLU cc_start: 0.8122 (tp30) cc_final: 0.7887 (tp30) REVERT: C 316 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7527 (ttp-170) REVERT: D 24 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8381 (mp10) REVERT: D 72 GLN cc_start: 0.6793 (tp40) cc_final: 0.6567 (mm-40) REVERT: D 76 ASP cc_start: 0.7307 (m-30) cc_final: 0.6882 (m-30) REVERT: D 109 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7343 (mtt-85) REVERT: D 129 GLN cc_start: 0.8394 (mm110) cc_final: 0.8088 (mm110) REVERT: D 131 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.8075 (ptm160) REVERT: D 132 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7502 (mm-30) REVERT: D 137 LYS cc_start: 0.8402 (mttt) cc_final: 0.8155 (mttm) REVERT: D 182 ILE cc_start: 0.8533 (mm) cc_final: 0.8135 (mt) REVERT: D 203 LEU cc_start: 0.8442 (mp) cc_final: 0.8240 (mt) REVERT: D 238 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4549 (tt) REVERT: D 290 ARG cc_start: 0.8209 (mmt180) cc_final: 0.7918 (mmt-90) REVERT: E 47 ASP cc_start: 0.8294 (m-30) cc_final: 0.8066 (m-30) REVERT: E 77 ASN cc_start: 0.7686 (m-40) cc_final: 0.7419 (m-40) REVERT: E 98 THR cc_start: 0.8088 (m) cc_final: 0.7778 (m) REVERT: E 99 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8341 (ttp-170) REVERT: E 195 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7996 (mm110) REVERT: E 300 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 335 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7284 (mm-30) REVERT: E 400 VAL cc_start: 0.8119 (t) cc_final: 0.7907 (m) REVERT: F 11 ASN cc_start: 0.7832 (t0) cc_final: 0.7446 (p0) REVERT: F 14 ASP cc_start: 0.7495 (m-30) cc_final: 0.6326 (m-30) REVERT: F 17 SER cc_start: 0.8379 (m) cc_final: 0.8085 (t) REVERT: F 45 MET cc_start: 0.8187 (tpp) cc_final: 0.7742 (mmt) REVERT: F 109 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7541 (tpp80) REVERT: F 114 SER cc_start: 0.8651 (m) cc_final: 0.8168 (p) REVERT: F 128 GLU cc_start: 0.8039 (tp30) cc_final: 0.7728 (tp30) REVERT: F 137 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8239 (ttmm) REVERT: F 233 TYR cc_start: 0.7446 (p90) cc_final: 0.6797 (p90) REVERT: F 296 SER cc_start: 0.8898 (m) cc_final: 0.8518 (t) REVERT: F 317 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8167 (mt) REVERT: F 363 PHE cc_start: 0.8806 (m-80) cc_final: 0.8330 (m-80) REVERT: G 51 SER cc_start: 0.8606 (m) cc_final: 0.8255 (p) REVERT: G 77 ASN cc_start: 0.8371 (t0) cc_final: 0.8113 (t0) REVERT: G 107 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7736 (tm-30) REVERT: G 117 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8296 (tttm) REVERT: G 225 LYS cc_start: 0.8627 (mttt) cc_final: 0.8356 (mtpt) REVERT: G 242 GLU cc_start: 0.7767 (tt0) cc_final: 0.7553 (tt0) REVERT: G 255 ASP cc_start: 0.7980 (t0) cc_final: 0.7609 (t0) REVERT: G 275 LYS cc_start: 0.8285 (mttt) cc_final: 0.8041 (mtpp) REVERT: G 291 PHE cc_start: 0.8028 (t80) cc_final: 0.7775 (t80) REVERT: G 353 LYS cc_start: 0.8460 (mttt) cc_final: 0.8216 (mttt) REVERT: G 403 ILE cc_start: 0.8284 (mt) cc_final: 0.7993 (tp) REVERT: G 405 ASN cc_start: 0.7984 (t0) cc_final: 0.7453 (m110) REVERT: H 43 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7817 (mttp) REVERT: H 46 LYS cc_start: 0.7872 (mttt) cc_final: 0.7577 (mtpp) REVERT: H 110 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8230 (ttmm) REVERT: H 118 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7499 (mm-30) REVERT: H 202 ASP cc_start: 0.8636 (m-30) cc_final: 0.7852 (m-30) REVERT: H 286 GLU cc_start: 0.7955 (tp30) cc_final: 0.7711 (tp30) REVERT: H 388 VAL cc_start: 0.8571 (p) cc_final: 0.8299 (m) REVERT: I 74 ASP cc_start: 0.7816 (m-30) cc_final: 0.7533 (m-30) REVERT: I 76 ASP cc_start: 0.7582 (m-30) cc_final: 0.7016 (m-30) REVERT: I 142 LYS cc_start: 0.8882 (tttt) cc_final: 0.8599 (ttmt) REVERT: I 342 LYS cc_start: 0.8410 (mttt) cc_final: 0.8187 (mtpp) REVERT: J 17 SER cc_start: 0.8028 (m) cc_final: 0.7772 (t) REVERT: J 74 ASP cc_start: 0.7703 (m-30) cc_final: 0.7322 (t0) REVERT: J 99 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7615 (ttm-80) REVERT: J 233 TYR cc_start: 0.7833 (p90) cc_final: 0.7550 (p90) REVERT: J 300 THR cc_start: 0.8730 (m) cc_final: 0.8448 (p) REVERT: K 14 ASP cc_start: 0.6942 (m-30) cc_final: 0.6596 (m-30) REVERT: K 58 GLU cc_start: 0.7705 (pm20) cc_final: 0.7371 (pm20) REVERT: K 68 LEU cc_start: 0.8942 (mp) cc_final: 0.8739 (mt) REVERT: K 131 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.7955 (ptm-80) REVERT: K 255 ASP cc_start: 0.8460 (m-30) cc_final: 0.8227 (m-30) REVERT: K 262 PHE cc_start: 0.8563 (t80) cc_final: 0.8349 (t80) REVERT: K 286 GLU cc_start: 0.8117 (tp30) cc_final: 0.7893 (tp30) REVERT: K 296 SER cc_start: 0.8170 (m) cc_final: 0.7898 (t) REVERT: K 379 SER cc_start: 0.8767 (m) cc_final: 0.8247 (t) REVERT: L 63 LEU cc_start: 0.8030 (tp) cc_final: 0.7559 (tp) REVERT: L 233 TYR cc_start: 0.8080 (p90) cc_final: 0.7813 (p90) REVERT: L 293 GLU cc_start: 0.7719 (tt0) cc_final: 0.7465 (tt0) REVERT: L 374 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8362 (mtmm) REVERT: M 32 GLN cc_start: 0.7781 (mt0) cc_final: 0.7517 (mt0) REVERT: M 50 ASP cc_start: 0.8165 (m-30) cc_final: 0.7748 (m-30) REVERT: M 93 GLN cc_start: 0.8459 (mt0) cc_final: 0.8101 (mm-40) REVERT: M 271 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: M 318 ASN cc_start: 0.8459 (t0) cc_final: 0.8251 (t0) REVERT: M 327 ASP cc_start: 0.8310 (t0) cc_final: 0.8069 (t0) REVERT: M 386 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7342 (tp30) REVERT: M 421 PHE cc_start: 0.7436 (m-10) cc_final: 0.7171 (m-80) REVERT: M 424 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6500 (mt-10) REVERT: M 428 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6313 (tm-30) REVERT: M 503 GLU cc_start: 0.7846 (mp0) cc_final: 0.7495 (mp0) REVERT: M 574 SER cc_start: 0.8323 (p) cc_final: 0.8013 (t) REVERT: M 599 SER cc_start: 0.7724 (p) cc_final: 0.7209 (m) REVERT: N 244 GLU cc_start: 0.7047 (mp0) cc_final: 0.6838 (pm20) REVERT: N 249 GLU cc_start: 0.7137 (pt0) cc_final: 0.6730 (pm20) REVERT: N 271 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7296 (mtt180) REVERT: N 291 THR cc_start: 0.8758 (m) cc_final: 0.8326 (t) REVERT: N 301 GLU cc_start: 0.7669 (tt0) cc_final: 0.7261 (tt0) REVERT: N 336 ARG cc_start: 0.8351 (ptp90) cc_final: 0.8072 (mtm-85) REVERT: N 355 CYS cc_start: 0.8103 (p) cc_final: 0.7872 (p) REVERT: N 383 GLN cc_start: 0.7966 (mt0) cc_final: 0.7706 (mm-40) REVERT: N 394 VAL cc_start: 0.8871 (t) cc_final: 0.8432 (p) REVERT: N 401 GLU cc_start: 0.7175 (mp0) cc_final: 0.6949 (mp0) REVERT: N 478 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7701 (mm-30) REVERT: N 506 LYS cc_start: 0.8613 (mttm) cc_final: 0.8368 (mtpp) REVERT: O 134 ASN cc_start: 0.8645 (t0) cc_final: 0.8421 (m-40) REVERT: O 143 GLU cc_start: 0.7466 (mp0) cc_final: 0.7208 (mp0) REVERT: O 171 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: O 315 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: O 316 ASP cc_start: 0.8133 (p0) cc_final: 0.7931 (p0) REVERT: O 373 ASN cc_start: 0.7512 (m-40) cc_final: 0.7280 (m-40) REVERT: O 383 GLN cc_start: 0.7861 (mm110) cc_final: 0.7597 (mm110) REVERT: O 391 LYS cc_start: 0.7964 (tttp) cc_final: 0.7654 (ttpp) REVERT: O 559 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8567 (mtpp) REVERT: P 50 ASP cc_start: 0.7959 (m-30) cc_final: 0.7714 (m-30) REVERT: P 55 ASP cc_start: 0.7974 (p0) cc_final: 0.7601 (p0) REVERT: P 115 ASP cc_start: 0.7625 (p0) cc_final: 0.7389 (p0) REVERT: P 156 THR cc_start: 0.8609 (m) cc_final: 0.8402 (p) REVERT: P 241 GLN cc_start: 0.7976 (mp10) cc_final: 0.7593 (mp-120) REVERT: P 283 ASN cc_start: 0.8394 (m-40) cc_final: 0.8144 (m110) REVERT: P 401 GLU cc_start: 0.7979 (mp0) cc_final: 0.7677 (mp0) REVERT: P 411 LYS cc_start: 0.7550 (mtmt) cc_final: 0.7293 (mtmt) REVERT: P 413 MET cc_start: 0.7691 (ttm) cc_final: 0.7407 (ttm) REVERT: P 423 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7960 (mtmm) REVERT: P 444 ASP cc_start: 0.7286 (t0) cc_final: 0.6901 (t0) REVERT: P 459 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7592 (mm-30) REVERT: P 559 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8179 (mtmm) REVERT: Q 94 ILE cc_start: 0.8299 (mt) cc_final: 0.7806 (tt) REVERT: Q 104 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7473 (ttm170) REVERT: Q 170 SER cc_start: 0.8251 (t) cc_final: 0.7666 (p) REVERT: Q 171 ARG cc_start: 0.6895 (mmt-90) cc_final: 0.6577 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8565 (m110) cc_final: 0.8019 (m-40) REVERT: Q 211 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7525 (mt-10) REVERT: Q 268 LYS cc_start: 0.8757 (tttm) cc_final: 0.8522 (ttmm) REVERT: Q 293 PHE cc_start: 0.8389 (t80) cc_final: 0.8146 (t80) REVERT: Q 297 ASN cc_start: 0.6737 (t0) cc_final: 0.6392 (t0) REVERT: Q 306 GLU cc_start: 0.7475 (tm-30) cc_final: 0.6914 (tm-30) REVERT: Q 308 PHE cc_start: 0.7828 (t80) cc_final: 0.7302 (t80) REVERT: Q 327 ASP cc_start: 0.7256 (t0) cc_final: 0.7027 (t0) REVERT: Q 402 LEU cc_start: 0.7936 (mp) cc_final: 0.6487 (mp) REVERT: Q 468 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7820 (mtm180) REVERT: Q 477 GLU cc_start: 0.8233 (tp30) cc_final: 0.7975 (tp30) REVERT: Q 544 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7869 (tp-100) REVERT: R 16 VAL cc_start: 0.8487 (p) cc_final: 0.8275 (t) REVERT: R 140 ASP cc_start: 0.6759 (m-30) cc_final: 0.6498 (m-30) REVERT: R 160 LYS cc_start: 0.8271 (mppt) cc_final: 0.7851 (mppt) REVERT: R 192 ARG cc_start: 0.7408 (tpp80) cc_final: 0.6221 (tpp80) REVERT: R 198 TYR cc_start: 0.8888 (m-80) cc_final: 0.8510 (m-80) REVERT: R 245 LEU cc_start: 0.7386 (pp) cc_final: 0.6873 (mp) REVERT: R 282 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8185 (mmm-85) REVERT: R 294 LYS cc_start: 0.8104 (tppt) cc_final: 0.7379 (mptt) REVERT: R 418 ASP cc_start: 0.7634 (t70) cc_final: 0.7240 (t70) REVERT: R 423 LYS cc_start: 0.8551 (mptt) cc_final: 0.8243 (mmtm) REVERT: R 439 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7460 (pttp) REVERT: R 508 LYS cc_start: 0.8000 (mttp) cc_final: 0.7774 (mttp) REVERT: R 516 GLN cc_start: 0.7753 (tt0) cc_final: 0.7511 (tt0) REVERT: R 559 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8133 (mtmt) REVERT: R 578 LEU cc_start: 0.7744 (tt) cc_final: 0.7503 (mp) outliers start: 118 outliers final: 84 residues processed: 1707 average time/residue: 0.6558 time to fit residues: 1818.6759 Evaluate side-chains 1715 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1626 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain O residue 554 ASN Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 472 THR Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 439 LYS Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 715 optimal weight: 0.7980 chunk 544 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 486 optimal weight: 0.8980 chunk 726 optimal weight: 7.9990 chunk 769 optimal weight: 0.5980 chunk 379 optimal weight: 2.9990 chunk 688 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN C 315 ASN D 313 HIS ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN G 200 ASN G 247 GLN H 258 ASN J 24 GLN J 183 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN Q 172 HIS Q 443 GLN R 277 GLN R 318 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 66064 Z= 0.269 Angle : 0.545 16.769 89371 Z= 0.277 Chirality : 0.043 0.198 9710 Planarity : 0.004 0.055 11449 Dihedral : 9.000 167.346 9438 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.26 % Allowed : 12.73 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 7933 helix: 0.38 (0.10), residues: 3075 sheet: 0.88 (0.17), residues: 1009 loop : -1.65 (0.09), residues: 3849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 409 HIS 0.009 0.001 HIS Q 434 PHE 0.019 0.002 PHE M 462 TYR 0.025 0.002 TYR R 258 ARG 0.009 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1822 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1667 time to evaluate : 5.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7963 (m-30) cc_final: 0.7670 (m-30) REVERT: A 58 GLU cc_start: 0.7669 (mp0) cc_final: 0.7307 (mp0) REVERT: A 80 VAL cc_start: 0.8886 (t) cc_final: 0.8568 (p) REVERT: A 128 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 374 LYS cc_start: 0.8361 (mttt) cc_final: 0.8084 (mttm) REVERT: B 70 VAL cc_start: 0.8689 (t) cc_final: 0.8452 (m) REVERT: B 102 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 132 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7625 (mp0) REVERT: B 179 ASP cc_start: 0.8373 (t0) cc_final: 0.8096 (t0) REVERT: B 233 TYR cc_start: 0.8079 (p90) cc_final: 0.7641 (p90) REVERT: B 240 VAL cc_start: 0.8776 (t) cc_final: 0.8546 (t) REVERT: B 257 ILE cc_start: 0.8544 (mm) cc_final: 0.8188 (mt) REVERT: B 258 ASN cc_start: 0.8269 (m-40) cc_final: 0.7803 (m-40) REVERT: B 374 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8305 (mttp) REVERT: B 382 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7541 (tp30) REVERT: C 73 ILE cc_start: 0.8234 (mm) cc_final: 0.8033 (mt) REVERT: C 88 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7516 (mm-30) REVERT: C 102 GLU cc_start: 0.8073 (tp30) cc_final: 0.7692 (mm-30) REVERT: C 103 ASP cc_start: 0.7828 (t0) cc_final: 0.7528 (t0) REVERT: C 110 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7757 (mtmt) REVERT: C 132 GLU cc_start: 0.7742 (mp0) cc_final: 0.7355 (mp0) REVERT: C 202 ASP cc_start: 0.8044 (m-30) cc_final: 0.7836 (m-30) REVERT: C 286 GLU cc_start: 0.8153 (tp30) cc_final: 0.7926 (tp30) REVERT: C 316 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7543 (ttp-170) REVERT: C 386 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.6227 (m-10) REVERT: D 24 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8396 (mp10) REVERT: D 72 GLN cc_start: 0.6973 (tp40) cc_final: 0.6378 (tp-100) REVERT: D 76 ASP cc_start: 0.7253 (m-30) cc_final: 0.6645 (m-30) REVERT: D 100 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7479 (mtm-85) REVERT: D 106 GLU cc_start: 0.7896 (tp30) cc_final: 0.7668 (tp30) REVERT: D 107 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8118 (tp30) REVERT: D 109 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7360 (mtt-85) REVERT: D 131 ARG cc_start: 0.8432 (ptm-80) cc_final: 0.8169 (ptm160) REVERT: D 137 LYS cc_start: 0.8391 (mttt) cc_final: 0.8148 (mttm) REVERT: D 182 ILE cc_start: 0.8627 (mm) cc_final: 0.8354 (mt) REVERT: D 238 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4600 (tt) REVERT: D 290 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7961 (mmt-90) REVERT: E 77 ASN cc_start: 0.7739 (m-40) cc_final: 0.7349 (m-40) REVERT: E 99 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8488 (ttp-170) REVERT: E 257 ILE cc_start: 0.8625 (mm) cc_final: 0.8386 (mt) REVERT: E 335 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7358 (mm-30) REVERT: E 400 VAL cc_start: 0.8125 (t) cc_final: 0.7886 (m) REVERT: F 11 ASN cc_start: 0.7817 (t0) cc_final: 0.7276 (p0) REVERT: F 14 ASP cc_start: 0.7484 (m-30) cc_final: 0.6222 (m-30) REVERT: F 17 SER cc_start: 0.8396 (m) cc_final: 0.8084 (t) REVERT: F 45 MET cc_start: 0.8348 (tpp) cc_final: 0.7845 (mmt) REVERT: F 76 ASP cc_start: 0.7200 (m-30) cc_final: 0.6618 (m-30) REVERT: F 81 ASN cc_start: 0.8752 (p0) cc_final: 0.8435 (p0) REVERT: F 109 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7763 (tpp80) REVERT: F 114 SER cc_start: 0.8679 (m) cc_final: 0.8166 (p) REVERT: F 128 GLU cc_start: 0.8046 (tp30) cc_final: 0.7728 (tp30) REVERT: F 137 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8209 (ttmm) REVERT: F 233 TYR cc_start: 0.7569 (p90) cc_final: 0.6941 (p90) REVERT: F 296 SER cc_start: 0.8950 (m) cc_final: 0.8575 (t) REVERT: F 317 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8238 (mm) REVERT: F 363 PHE cc_start: 0.8913 (m-80) cc_final: 0.8431 (m-80) REVERT: G 53 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7687 (mttt) REVERT: G 77 ASN cc_start: 0.8308 (t0) cc_final: 0.8030 (t0) REVERT: G 107 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7440 (tm-30) REVERT: G 117 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8276 (tttm) REVERT: G 159 GLN cc_start: 0.7527 (pm20) cc_final: 0.7242 (pm20) REVERT: G 166 THR cc_start: 0.8959 (t) cc_final: 0.8602 (p) REVERT: G 200 ASN cc_start: 0.8454 (m110) cc_final: 0.8169 (m-40) REVERT: G 225 LYS cc_start: 0.8660 (mttt) cc_final: 0.8458 (mtpt) REVERT: G 255 ASP cc_start: 0.7993 (t0) cc_final: 0.7553 (t0) REVERT: G 275 LYS cc_start: 0.8410 (mttt) cc_final: 0.8140 (mtpp) REVERT: G 353 LYS cc_start: 0.8476 (mttt) cc_final: 0.8250 (mttt) REVERT: G 403 ILE cc_start: 0.8312 (mt) cc_final: 0.8025 (tp) REVERT: G 405 ASN cc_start: 0.7958 (t0) cc_final: 0.7505 (m110) REVERT: H 43 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7946 (mttp) REVERT: H 46 LYS cc_start: 0.8039 (mttt) cc_final: 0.7805 (mtpp) REVERT: H 110 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8251 (ttmm) REVERT: H 118 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7672 (mm-30) REVERT: H 202 ASP cc_start: 0.8648 (m-30) cc_final: 0.7907 (m-30) REVERT: H 264 ARG cc_start: 0.6650 (mtt90) cc_final: 0.6294 (mtt90) REVERT: H 286 GLU cc_start: 0.7991 (tp30) cc_final: 0.7734 (tp30) REVERT: H 337 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7403 (ttpp) REVERT: H 388 VAL cc_start: 0.8553 (p) cc_final: 0.8280 (m) REVERT: I 50 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8090 (ttpp) REVERT: I 74 ASP cc_start: 0.7841 (m-30) cc_final: 0.7435 (m-30) REVERT: I 76 ASP cc_start: 0.7618 (m-30) cc_final: 0.7069 (m-30) REVERT: I 142 LYS cc_start: 0.8894 (tttt) cc_final: 0.8622 (ttmt) REVERT: I 266 GLN cc_start: 0.7819 (pp30) cc_final: 0.7504 (pp30) REVERT: I 342 LYS cc_start: 0.8401 (mttt) cc_final: 0.8188 (mtpp) REVERT: J 17 SER cc_start: 0.8063 (m) cc_final: 0.7802 (t) REVERT: J 74 ASP cc_start: 0.7736 (m-30) cc_final: 0.7361 (t0) REVERT: J 202 ASP cc_start: 0.8141 (m-30) cc_final: 0.7901 (m-30) REVERT: J 233 TYR cc_start: 0.7822 (p90) cc_final: 0.7545 (p90) REVERT: J 300 THR cc_start: 0.8766 (m) cc_final: 0.8465 (p) REVERT: K 14 ASP cc_start: 0.7099 (m-30) cc_final: 0.6694 (m-30) REVERT: K 68 LEU cc_start: 0.8927 (mp) cc_final: 0.8698 (mt) REVERT: K 131 ARG cc_start: 0.8323 (ptm-80) cc_final: 0.7929 (ptm-80) REVERT: K 286 GLU cc_start: 0.8113 (tp30) cc_final: 0.7860 (tp30) REVERT: K 296 SER cc_start: 0.8257 (m) cc_final: 0.7973 (t) REVERT: K 379 SER cc_start: 0.8780 (m) cc_final: 0.8301 (t) REVERT: L 14 ASP cc_start: 0.7399 (m-30) cc_final: 0.7107 (m-30) REVERT: L 63 LEU cc_start: 0.8022 (tp) cc_final: 0.7562 (tp) REVERT: L 70 VAL cc_start: 0.8572 (t) cc_final: 0.8195 (p) REVERT: L 116 TYR cc_start: 0.8587 (m-80) cc_final: 0.8212 (m-80) REVERT: L 233 TYR cc_start: 0.8143 (p90) cc_final: 0.7824 (p90) REVERT: L 293 GLU cc_start: 0.7691 (tt0) cc_final: 0.7459 (tt0) REVERT: L 374 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8345 (mtmm) REVERT: M 50 ASP cc_start: 0.8217 (m-30) cc_final: 0.7858 (m-30) REVERT: M 196 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7857 (mt-10) REVERT: M 271 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: M 327 ASP cc_start: 0.8249 (t0) cc_final: 0.8014 (t0) REVERT: M 386 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7417 (mt-10) REVERT: M 424 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6385 (mt-10) REVERT: M 428 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6324 (tm-30) REVERT: M 478 GLU cc_start: 0.8224 (mp0) cc_final: 0.7741 (mp0) REVERT: M 550 MET cc_start: 0.7252 (ppp) cc_final: 0.6920 (ppp) REVERT: M 574 SER cc_start: 0.8309 (p) cc_final: 0.8017 (t) REVERT: M 599 SER cc_start: 0.7932 (p) cc_final: 0.7448 (m) REVERT: N 244 GLU cc_start: 0.7083 (mp0) cc_final: 0.6865 (pm20) REVERT: N 249 GLU cc_start: 0.7227 (pt0) cc_final: 0.6734 (pm20) REVERT: N 301 GLU cc_start: 0.7752 (tt0) cc_final: 0.7330 (tt0) REVERT: N 336 ARG cc_start: 0.8351 (ptp90) cc_final: 0.8058 (mtm-85) REVERT: N 383 GLN cc_start: 0.8006 (mt0) cc_final: 0.7732 (mm-40) REVERT: N 394 VAL cc_start: 0.8872 (t) cc_final: 0.8419 (p) REVERT: N 401 GLU cc_start: 0.7202 (mp0) cc_final: 0.6970 (mp0) REVERT: N 506 LYS cc_start: 0.8643 (mttm) cc_final: 0.8321 (mtpp) REVERT: O 91 LEU cc_start: 0.8638 (tp) cc_final: 0.8360 (tp) REVERT: O 171 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: O 316 ASP cc_start: 0.8166 (p0) cc_final: 0.7954 (p0) REVERT: O 373 ASN cc_start: 0.7495 (m-40) cc_final: 0.7275 (m-40) REVERT: O 391 LYS cc_start: 0.7989 (tttp) cc_final: 0.7679 (ttpp) REVERT: O 559 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8561 (mtpp) REVERT: P 50 ASP cc_start: 0.7916 (m-30) cc_final: 0.7677 (m-30) REVERT: P 55 ASP cc_start: 0.7988 (p0) cc_final: 0.7615 (p0) REVERT: P 115 ASP cc_start: 0.7639 (p0) cc_final: 0.7407 (p0) REVERT: P 239 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7420 (tmtt) REVERT: P 283 ASN cc_start: 0.8491 (m-40) cc_final: 0.8200 (m110) REVERT: P 303 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5335 (p0) REVERT: P 401 GLU cc_start: 0.8010 (mp0) cc_final: 0.7706 (mp0) REVERT: P 411 LYS cc_start: 0.7602 (mtmt) cc_final: 0.7357 (mtmt) REVERT: P 413 MET cc_start: 0.7702 (ttm) cc_final: 0.7399 (ttm) REVERT: P 423 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7971 (mtmm) REVERT: P 444 ASP cc_start: 0.7542 (t0) cc_final: 0.7137 (t0) REVERT: P 459 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7645 (mm-30) REVERT: P 559 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8194 (mtmm) REVERT: Q 94 ILE cc_start: 0.8295 (mt) cc_final: 0.7820 (tt) REVERT: Q 104 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7532 (ttm170) REVERT: Q 170 SER cc_start: 0.8248 (t) cc_final: 0.7738 (p) REVERT: Q 171 ARG cc_start: 0.7004 (mmt-90) cc_final: 0.6679 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8555 (m110) cc_final: 0.8022 (m-40) REVERT: Q 211 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7476 (mt-10) REVERT: Q 268 LYS cc_start: 0.8768 (tttm) cc_final: 0.8556 (ttmm) REVERT: Q 297 ASN cc_start: 0.6733 (t0) cc_final: 0.6444 (t0) REVERT: Q 306 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6903 (tm-30) REVERT: Q 308 PHE cc_start: 0.7846 (t80) cc_final: 0.7276 (t80) REVERT: Q 416 GLU cc_start: 0.7992 (tp30) cc_final: 0.7723 (tp30) REVERT: Q 468 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7813 (mtm180) REVERT: Q 544 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7869 (tm-30) REVERT: Q 601 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8066 (mt-10) REVERT: R 16 VAL cc_start: 0.8509 (p) cc_final: 0.8262 (t) REVERT: R 24 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7368 (mtp85) REVERT: R 160 LYS cc_start: 0.8325 (mppt) cc_final: 0.7862 (mppt) REVERT: R 192 ARG cc_start: 0.7274 (tpp80) cc_final: 0.5999 (tpp80) REVERT: R 198 TYR cc_start: 0.8930 (m-80) cc_final: 0.8671 (m-80) REVERT: R 245 LEU cc_start: 0.7549 (pp) cc_final: 0.6923 (mt) REVERT: R 294 LYS cc_start: 0.8113 (tppt) cc_final: 0.7391 (mptt) REVERT: R 417 VAL cc_start: 0.8311 (t) cc_final: 0.8029 (m) REVERT: R 418 ASP cc_start: 0.7669 (t70) cc_final: 0.7313 (t70) REVERT: R 423 LYS cc_start: 0.8593 (mptt) cc_final: 0.8324 (mmtm) REVERT: R 439 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7569 (pttp) REVERT: R 508 LYS cc_start: 0.8031 (mttp) cc_final: 0.7812 (mttp) REVERT: R 516 GLN cc_start: 0.7793 (tt0) cc_final: 0.7480 (tt0) REVERT: R 559 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8111 (mtmt) outliers start: 155 outliers final: 113 residues processed: 1723 average time/residue: 0.6802 time to fit residues: 1901.4801 Evaluate side-chains 1755 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1636 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 585 ASN Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 273 SER Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 407 THR Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 242 LYS Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 578 LEU Chi-restraints excluded: chain P residue 599 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 316 ASP Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 381 ILE Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 200 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 439 LYS Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 640 optimal weight: 0.9980 chunk 436 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 572 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 656 optimal weight: 0.0970 chunk 531 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 392 optimal weight: 0.0270 chunk 690 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 overall best weight: 0.8838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 313 HIS C 315 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN J 24 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 382 GLN R 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66064 Z= 0.166 Angle : 0.491 15.629 89371 Z= 0.250 Chirality : 0.040 0.167 9710 Planarity : 0.003 0.052 11449 Dihedral : 8.783 169.023 9438 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.07 % Allowed : 14.12 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.66 (0.09), residues: 7933 helix: 0.48 (0.10), residues: 3068 sheet: 0.95 (0.17), residues: 1019 loop : -1.63 (0.09), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 409 HIS 0.006 0.001 HIS Q 480 PHE 0.021 0.001 PHE K 262 TYR 0.027 0.001 TYR R 258 ARG 0.008 0.000 ARG R 505 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1807 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1665 time to evaluate : 5.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7927 (m-30) cc_final: 0.7618 (m-30) REVERT: A 58 GLU cc_start: 0.7672 (mp0) cc_final: 0.7307 (mp0) REVERT: A 80 VAL cc_start: 0.8901 (t) cc_final: 0.8578 (p) REVERT: A 139 ASP cc_start: 0.7948 (t0) cc_final: 0.7607 (t0) REVERT: A 374 LYS cc_start: 0.8335 (mttt) cc_final: 0.8038 (mttm) REVERT: B 70 VAL cc_start: 0.8747 (t) cc_final: 0.8506 (m) REVERT: B 102 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7592 (mm-30) REVERT: B 132 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7591 (mp0) REVERT: B 179 ASP cc_start: 0.8346 (t0) cc_final: 0.8036 (t0) REVERT: B 233 TYR cc_start: 0.8071 (p90) cc_final: 0.7649 (p90) REVERT: B 240 VAL cc_start: 0.8770 (t) cc_final: 0.8538 (t) REVERT: B 257 ILE cc_start: 0.8543 (mm) cc_final: 0.8168 (mt) REVERT: B 258 ASN cc_start: 0.8268 (m-40) cc_final: 0.7782 (m-40) REVERT: B 374 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8253 (mttp) REVERT: B 382 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7545 (tp30) REVERT: C 102 GLU cc_start: 0.8086 (tp30) cc_final: 0.7697 (mm-30) REVERT: C 110 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7672 (mtmt) REVERT: C 132 GLU cc_start: 0.7738 (mp0) cc_final: 0.7356 (mp0) REVERT: C 286 GLU cc_start: 0.8123 (tp30) cc_final: 0.7887 (tp30) REVERT: C 316 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7547 (ttp-170) REVERT: D 24 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8363 (mp10) REVERT: D 72 GLN cc_start: 0.6975 (tp40) cc_final: 0.6536 (tp-100) REVERT: D 100 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7475 (mtm-85) REVERT: D 106 GLU cc_start: 0.7900 (tp30) cc_final: 0.7671 (tp30) REVERT: D 109 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7322 (mtt-85) REVERT: D 131 ARG cc_start: 0.8422 (ptm-80) cc_final: 0.8130 (ptm160) REVERT: D 132 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7514 (mm-30) REVERT: D 137 LYS cc_start: 0.8396 (mttt) cc_final: 0.8150 (mttm) REVERT: D 182 ILE cc_start: 0.8624 (mm) cc_final: 0.8342 (mt) REVERT: D 238 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4568 (tt) REVERT: D 290 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7933 (mmt-90) REVERT: D 343 VAL cc_start: 0.8356 (t) cc_final: 0.8151 (t) REVERT: D 350 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7443 (mm-30) REVERT: E 63 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8275 (tp) REVERT: E 77 ASN cc_start: 0.7699 (m-40) cc_final: 0.7482 (m-40) REVERT: E 98 THR cc_start: 0.8178 (m) cc_final: 0.7839 (m) REVERT: E 99 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8384 (ttp-170) REVERT: E 195 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (mm110) REVERT: E 283 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7134 (m) REVERT: E 300 THR cc_start: 0.8390 (m) cc_final: 0.8129 (p) REVERT: E 335 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7286 (mm-30) REVERT: E 400 VAL cc_start: 0.8138 (t) cc_final: 0.7889 (m) REVERT: F 11 ASN cc_start: 0.7766 (t0) cc_final: 0.7200 (p0) REVERT: F 14 ASP cc_start: 0.7477 (m-30) cc_final: 0.6130 (m-30) REVERT: F 17 SER cc_start: 0.8334 (m) cc_final: 0.8084 (t) REVERT: F 45 MET cc_start: 0.8344 (tpp) cc_final: 0.7827 (mmt) REVERT: F 76 ASP cc_start: 0.7187 (m-30) cc_final: 0.6613 (m-30) REVERT: F 81 ASN cc_start: 0.8780 (p0) cc_final: 0.8447 (p0) REVERT: F 97 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8540 (ttmm) REVERT: F 109 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7593 (tpp80) REVERT: F 114 SER cc_start: 0.8686 (m) cc_final: 0.8183 (p) REVERT: F 128 GLU cc_start: 0.8061 (tp30) cc_final: 0.7741 (tp30) REVERT: F 137 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8192 (ttmm) REVERT: F 233 TYR cc_start: 0.7536 (p90) cc_final: 0.6864 (p90) REVERT: F 296 SER cc_start: 0.8935 (m) cc_final: 0.8559 (t) REVERT: F 317 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8304 (mt) REVERT: G 51 SER cc_start: 0.8538 (m) cc_final: 0.7969 (p) REVERT: G 53 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7553 (mttt) REVERT: G 77 ASN cc_start: 0.8221 (t0) cc_final: 0.7960 (t0) REVERT: G 107 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7407 (tm-30) REVERT: G 117 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8304 (tttp) REVERT: G 166 THR cc_start: 0.8928 (t) cc_final: 0.8586 (p) REVERT: G 255 ASP cc_start: 0.8020 (t0) cc_final: 0.7532 (t0) REVERT: G 275 LYS cc_start: 0.8364 (mttt) cc_final: 0.8104 (mtpp) REVERT: G 353 LYS cc_start: 0.8480 (mttt) cc_final: 0.8236 (mttt) REVERT: G 403 ILE cc_start: 0.8318 (mt) cc_final: 0.8029 (tp) REVERT: G 405 ASN cc_start: 0.7927 (t0) cc_final: 0.7517 (m110) REVERT: H 43 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7905 (mttm) REVERT: H 46 LYS cc_start: 0.8021 (mttt) cc_final: 0.7769 (mtpp) REVERT: H 65 ASP cc_start: 0.7056 (m-30) cc_final: 0.6818 (m-30) REVERT: H 110 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8248 (ttmm) REVERT: H 118 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7603 (mm-30) REVERT: H 202 ASP cc_start: 0.8597 (m-30) cc_final: 0.7834 (m-30) REVERT: H 286 GLU cc_start: 0.7970 (tp30) cc_final: 0.7705 (tp30) REVERT: H 337 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7438 (ttpt) REVERT: H 388 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8285 (m) REVERT: I 50 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8099 (ttpp) REVERT: I 74 ASP cc_start: 0.7814 (m-30) cc_final: 0.7375 (m-30) REVERT: I 76 ASP cc_start: 0.7606 (m-30) cc_final: 0.7062 (m-30) REVERT: I 104 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7107 (mt-10) REVERT: I 142 LYS cc_start: 0.8890 (tttt) cc_final: 0.8602 (ttmt) REVERT: I 266 GLN cc_start: 0.7790 (pp30) cc_final: 0.7530 (pp30) REVERT: I 342 LYS cc_start: 0.8421 (mttt) cc_final: 0.8202 (mtpp) REVERT: J 17 SER cc_start: 0.8016 (m) cc_final: 0.7729 (t) REVERT: J 74 ASP cc_start: 0.7715 (m-30) cc_final: 0.7350 (t0) REVERT: J 99 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: J 202 ASP cc_start: 0.8133 (m-30) cc_final: 0.7885 (m-30) REVERT: J 233 TYR cc_start: 0.7781 (p90) cc_final: 0.7557 (p90) REVERT: J 242 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7618 (tt0) REVERT: J 300 THR cc_start: 0.8734 (m) cc_final: 0.8463 (p) REVERT: K 14 ASP cc_start: 0.7038 (m-30) cc_final: 0.6657 (m-30) REVERT: K 68 LEU cc_start: 0.8938 (mp) cc_final: 0.8700 (mt) REVERT: K 202 ASP cc_start: 0.8393 (m-30) cc_final: 0.8183 (m-30) REVERT: K 286 GLU cc_start: 0.8114 (tp30) cc_final: 0.7867 (tp30) REVERT: K 296 SER cc_start: 0.8087 (m) cc_final: 0.7844 (t) REVERT: K 379 SER cc_start: 0.8772 (m) cc_final: 0.8291 (t) REVERT: L 70 VAL cc_start: 0.8562 (t) cc_final: 0.8186 (p) REVERT: L 156 GLN cc_start: 0.7873 (mt0) cc_final: 0.7669 (mt0) REVERT: L 233 TYR cc_start: 0.8100 (p90) cc_final: 0.7802 (p90) REVERT: L 293 GLU cc_start: 0.7690 (tt0) cc_final: 0.7466 (tt0) REVERT: L 374 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8358 (mtmm) REVERT: M 50 ASP cc_start: 0.8179 (m-30) cc_final: 0.7803 (m-30) REVERT: M 196 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7926 (mt-10) REVERT: M 271 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7483 (ttm-80) REVERT: M 327 ASP cc_start: 0.8216 (t0) cc_final: 0.7981 (t0) REVERT: M 386 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7363 (mt-10) REVERT: M 424 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6381 (mt-10) REVERT: M 428 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6344 (tm-30) REVERT: M 478 GLU cc_start: 0.8208 (mp0) cc_final: 0.7695 (mp0) REVERT: M 506 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7754 (tmtt) REVERT: M 550 MET cc_start: 0.7198 (ppp) cc_final: 0.6939 (ppp) REVERT: M 574 SER cc_start: 0.8269 (p) cc_final: 0.7955 (t) REVERT: M 599 SER cc_start: 0.7926 (p) cc_final: 0.7445 (m) REVERT: N 19 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7173 (mt-10) REVERT: N 249 GLU cc_start: 0.7241 (pt0) cc_final: 0.6681 (pm20) REVERT: N 301 GLU cc_start: 0.7708 (tt0) cc_final: 0.7406 (tt0) REVERT: N 336 ARG cc_start: 0.8360 (ptp90) cc_final: 0.8026 (mtm-85) REVERT: N 383 GLN cc_start: 0.8047 (mt0) cc_final: 0.7774 (mm-40) REVERT: N 394 VAL cc_start: 0.8851 (t) cc_final: 0.8391 (p) REVERT: N 401 GLU cc_start: 0.7201 (mp0) cc_final: 0.6974 (mp0) REVERT: N 506 LYS cc_start: 0.8642 (mttm) cc_final: 0.8313 (mtpp) REVERT: O 50 ASP cc_start: 0.8029 (m-30) cc_final: 0.7745 (m-30) REVERT: O 91 LEU cc_start: 0.8630 (tp) cc_final: 0.8393 (tp) REVERT: O 171 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7354 (mmm-85) REVERT: O 316 ASP cc_start: 0.8196 (p0) cc_final: 0.7967 (p0) REVERT: O 373 ASN cc_start: 0.7467 (m-40) cc_final: 0.7257 (m-40) REVERT: O 391 LYS cc_start: 0.7975 (tttp) cc_final: 0.7667 (ttpp) REVERT: O 559 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8554 (mtpp) REVERT: P 50 ASP cc_start: 0.7908 (m-30) cc_final: 0.7684 (m-30) REVERT: P 55 ASP cc_start: 0.7994 (p0) cc_final: 0.7587 (p0) REVERT: P 115 ASP cc_start: 0.7616 (p0) cc_final: 0.7358 (p0) REVERT: P 153 ASP cc_start: 0.7536 (p0) cc_final: 0.7271 (p0) REVERT: P 239 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7436 (tmtt) REVERT: P 283 ASN cc_start: 0.8454 (m-40) cc_final: 0.8148 (m110) REVERT: P 303 ASP cc_start: 0.6093 (OUTLIER) cc_final: 0.5286 (p0) REVERT: P 401 GLU cc_start: 0.8011 (mp0) cc_final: 0.7806 (mp0) REVERT: P 411 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7342 (mtmt) REVERT: P 413 MET cc_start: 0.7711 (ttm) cc_final: 0.7429 (ttm) REVERT: P 423 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7993 (mtmm) REVERT: P 444 ASP cc_start: 0.7388 (t0) cc_final: 0.7009 (t0) REVERT: P 459 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7576 (mm-30) REVERT: P 559 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8227 (mtmm) REVERT: Q 94 ILE cc_start: 0.8272 (mt) cc_final: 0.7795 (tt) REVERT: Q 104 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7502 (ttm170) REVERT: Q 159 VAL cc_start: 0.8886 (m) cc_final: 0.8571 (p) REVERT: Q 170 SER cc_start: 0.8231 (t) cc_final: 0.7737 (p) REVERT: Q 171 ARG cc_start: 0.6996 (mmt-90) cc_final: 0.6678 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8547 (m110) cc_final: 0.8017 (m-40) REVERT: Q 268 LYS cc_start: 0.8731 (tttm) cc_final: 0.8517 (ttmm) REVERT: Q 297 ASN cc_start: 0.6751 (t0) cc_final: 0.6469 (t0) REVERT: Q 306 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6882 (tm-30) REVERT: Q 308 PHE cc_start: 0.7803 (t80) cc_final: 0.7288 (t80) REVERT: Q 468 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7789 (mtm180) REVERT: Q 517 ARG cc_start: 0.8430 (mmt90) cc_final: 0.8163 (mmt180) REVERT: Q 544 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7865 (tp-100) REVERT: R 14 TYR cc_start: 0.7797 (p90) cc_final: 0.7447 (p90) REVERT: R 16 VAL cc_start: 0.8460 (p) cc_final: 0.8228 (t) REVERT: R 24 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7351 (mtp85) REVERT: R 158 THR cc_start: 0.6387 (p) cc_final: 0.6159 (p) REVERT: R 160 LYS cc_start: 0.8232 (mppt) cc_final: 0.7843 (mppt) REVERT: R 189 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8470 (mt) REVERT: R 192 ARG cc_start: 0.7262 (tpp80) cc_final: 0.5986 (tpp80) REVERT: R 198 TYR cc_start: 0.8880 (m-80) cc_final: 0.8670 (m-80) REVERT: R 240 GLN cc_start: 0.7267 (mp10) cc_final: 0.6934 (mt0) REVERT: R 245 LEU cc_start: 0.7566 (pp) cc_final: 0.6896 (mt) REVERT: R 294 LYS cc_start: 0.8066 (tppt) cc_final: 0.7378 (mptt) REVERT: R 417 VAL cc_start: 0.8292 (t) cc_final: 0.8076 (p) REVERT: R 418 ASP cc_start: 0.7649 (t70) cc_final: 0.7289 (t70) REVERT: R 423 LYS cc_start: 0.8520 (mptt) cc_final: 0.8240 (mmtm) REVERT: R 439 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7505 (pttp) REVERT: R 477 GLU cc_start: 0.6863 (tp30) cc_final: 0.6510 (tp30) REVERT: R 508 LYS cc_start: 0.8011 (mttp) cc_final: 0.7797 (mttp) REVERT: R 514 SER cc_start: 0.7550 (m) cc_final: 0.6882 (p) REVERT: R 559 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8105 (mtmt) outliers start: 142 outliers final: 105 residues processed: 1726 average time/residue: 0.6511 time to fit residues: 1818.8843 Evaluate side-chains 1757 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1642 time to evaluate : 5.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 515 THR Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 477 GLU Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 348 THR Chi-restraints excluded: chain P residue 382 GLN Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 599 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 381 ILE Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 439 LYS Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 258 optimal weight: 4.9990 chunk 692 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 451 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 770 optimal weight: 7.9990 chunk 639 optimal weight: 0.0010 chunk 356 optimal weight: 3.9990 chunk 64 optimal weight: 0.0040 chunk 254 optimal weight: 0.9980 chunk 404 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS C 315 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN G 315 ASN H 364 ASN I 365 GLN K 278 HIS ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 214 GLN P 382 GLN Q 214 GLN Q 443 GLN Q 556 GLN R 240 GLN R 277 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66064 Z= 0.129 Angle : 0.465 14.836 89371 Z= 0.236 Chirality : 0.040 0.176 9710 Planarity : 0.003 0.049 11449 Dihedral : 8.524 170.141 9438 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.97 % Allowed : 15.00 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.52 (0.09), residues: 7933 helix: 0.62 (0.10), residues: 3062 sheet: 1.06 (0.17), residues: 1012 loop : -1.58 (0.09), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 409 HIS 0.006 0.001 HIS Q 480 PHE 0.019 0.001 PHE Q 293 TYR 0.026 0.001 TYR R 258 ARG 0.014 0.000 ARG M 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1796 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1661 time to evaluate : 5.531 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7888 (m-30) cc_final: 0.7612 (m-30) REVERT: A 58 GLU cc_start: 0.7637 (mp0) cc_final: 0.7271 (mp0) REVERT: A 80 VAL cc_start: 0.8909 (t) cc_final: 0.8575 (p) REVERT: A 139 ASP cc_start: 0.7926 (t0) cc_final: 0.7575 (t0) REVERT: A 374 LYS cc_start: 0.8297 (mttt) cc_final: 0.8015 (mttm) REVERT: B 70 VAL cc_start: 0.8755 (t) cc_final: 0.8515 (m) REVERT: B 102 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 132 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7724 (mp0) REVERT: B 179 ASP cc_start: 0.8312 (t0) cc_final: 0.7980 (t0) REVERT: B 233 TYR cc_start: 0.8041 (p90) cc_final: 0.7649 (p90) REVERT: B 240 VAL cc_start: 0.8766 (t) cc_final: 0.8529 (t) REVERT: B 257 ILE cc_start: 0.8515 (mm) cc_final: 0.8120 (mt) REVERT: B 258 ASN cc_start: 0.8250 (m-40) cc_final: 0.7758 (m-40) REVERT: B 374 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8242 (mttp) REVERT: B 382 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7562 (tp30) REVERT: C 102 GLU cc_start: 0.8088 (tp30) cc_final: 0.7692 (mm-30) REVERT: C 110 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7635 (mtmt) REVERT: C 132 GLU cc_start: 0.7711 (mp0) cc_final: 0.7356 (mp0) REVERT: C 286 GLU cc_start: 0.8114 (tp30) cc_final: 0.7884 (tp30) REVERT: C 316 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7539 (ttp-170) REVERT: D 24 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8329 (mp10) REVERT: D 72 GLN cc_start: 0.6971 (tp40) cc_final: 0.6553 (tp-100) REVERT: D 100 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7469 (mtm-85) REVERT: D 106 GLU cc_start: 0.7898 (tp30) cc_final: 0.7680 (tp30) REVERT: D 131 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.8120 (ptm160) REVERT: D 132 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7511 (mm-30) REVERT: D 137 LYS cc_start: 0.8342 (mttt) cc_final: 0.8095 (mttm) REVERT: D 182 ILE cc_start: 0.8622 (mm) cc_final: 0.8354 (mt) REVERT: D 208 VAL cc_start: 0.8028 (t) cc_final: 0.7781 (m) REVERT: D 238 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4528 (tt) REVERT: D 289 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8245 (ttp-170) REVERT: D 290 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7900 (mmt-90) REVERT: D 343 VAL cc_start: 0.8303 (t) cc_final: 0.8079 (t) REVERT: D 350 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7368 (mm-30) REVERT: E 77 ASN cc_start: 0.7597 (m-40) cc_final: 0.7210 (m-40) REVERT: E 84 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8357 (mp) REVERT: E 98 THR cc_start: 0.8086 (m) cc_final: 0.7762 (m) REVERT: E 99 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8345 (ttp-170) REVERT: E 195 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7977 (mm110) REVERT: E 300 THR cc_start: 0.8308 (m) cc_final: 0.8050 (p) REVERT: E 335 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7126 (tp30) REVERT: E 400 VAL cc_start: 0.8122 (t) cc_final: 0.7874 (m) REVERT: F 45 MET cc_start: 0.8209 (tpp) cc_final: 0.7967 (mmt) REVERT: F 76 ASP cc_start: 0.7169 (m-30) cc_final: 0.6587 (m-30) REVERT: F 81 ASN cc_start: 0.8780 (p0) cc_final: 0.8450 (p0) REVERT: F 97 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8545 (ttmm) REVERT: F 109 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7530 (tpp80) REVERT: F 114 SER cc_start: 0.8691 (m) cc_final: 0.8187 (p) REVERT: F 128 GLU cc_start: 0.8042 (tp30) cc_final: 0.7732 (tp30) REVERT: F 137 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8160 (ttmm) REVERT: F 233 TYR cc_start: 0.7448 (p90) cc_final: 0.6810 (p90) REVERT: F 296 SER cc_start: 0.8877 (m) cc_final: 0.8533 (t) REVERT: G 51 SER cc_start: 0.8506 (m) cc_final: 0.7946 (p) REVERT: G 53 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7638 (mttt) REVERT: G 77 ASN cc_start: 0.8101 (t0) cc_final: 0.7836 (t0) REVERT: G 107 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7303 (tm-30) REVERT: G 117 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8306 (tttp) REVERT: G 166 THR cc_start: 0.8863 (t) cc_final: 0.8596 (m) REVERT: G 255 ASP cc_start: 0.8012 (t0) cc_final: 0.7507 (t0) REVERT: G 275 LYS cc_start: 0.8386 (mttt) cc_final: 0.8141 (mtpp) REVERT: G 403 ILE cc_start: 0.8322 (mt) cc_final: 0.8025 (tp) REVERT: G 405 ASN cc_start: 0.7925 (t0) cc_final: 0.7549 (m110) REVERT: H 43 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7795 (mttm) REVERT: H 46 LYS cc_start: 0.8017 (mttt) cc_final: 0.7629 (mtpp) REVERT: H 65 ASP cc_start: 0.7071 (m-30) cc_final: 0.6827 (m-30) REVERT: H 110 LYS cc_start: 0.8594 (ttmt) cc_final: 0.8223 (ttmm) REVERT: H 202 ASP cc_start: 0.8541 (m-30) cc_final: 0.8066 (m-30) REVERT: H 286 GLU cc_start: 0.7916 (tp30) cc_final: 0.7651 (tp30) REVERT: H 337 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7432 (ttpt) REVERT: H 388 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8240 (m) REVERT: I 74 ASP cc_start: 0.7811 (m-30) cc_final: 0.7360 (m-30) REVERT: I 76 ASP cc_start: 0.7588 (m-30) cc_final: 0.7019 (m-30) REVERT: I 104 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7126 (mt-10) REVERT: I 106 GLU cc_start: 0.7610 (pp20) cc_final: 0.7376 (pp20) REVERT: I 142 LYS cc_start: 0.8881 (tttt) cc_final: 0.8604 (ttmt) REVERT: I 266 GLN cc_start: 0.7777 (pp30) cc_final: 0.7520 (pp30) REVERT: I 342 LYS cc_start: 0.8420 (mttt) cc_final: 0.8193 (mtpp) REVERT: J 17 SER cc_start: 0.7998 (m) cc_final: 0.7695 (t) REVERT: J 99 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7397 (ttm-80) REVERT: J 202 ASP cc_start: 0.8121 (m-30) cc_final: 0.7891 (m-30) REVERT: J 242 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7573 (tt0) REVERT: J 300 THR cc_start: 0.8689 (m) cc_final: 0.8380 (p) REVERT: K 14 ASP cc_start: 0.7005 (m-30) cc_final: 0.6629 (m-30) REVERT: K 68 LEU cc_start: 0.8940 (mp) cc_final: 0.8706 (mt) REVERT: K 202 ASP cc_start: 0.8388 (m-30) cc_final: 0.8176 (m-30) REVERT: K 286 GLU cc_start: 0.8106 (tp30) cc_final: 0.7895 (tp30) REVERT: K 379 SER cc_start: 0.8757 (m) cc_final: 0.8271 (t) REVERT: L 70 VAL cc_start: 0.8549 (t) cc_final: 0.8170 (p) REVERT: L 156 GLN cc_start: 0.7856 (mt0) cc_final: 0.7642 (mt0) REVERT: L 233 TYR cc_start: 0.8055 (p90) cc_final: 0.7811 (p90) REVERT: L 293 GLU cc_start: 0.7692 (tt0) cc_final: 0.7464 (tt0) REVERT: L 374 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8357 (mtmm) REVERT: M 50 ASP cc_start: 0.8159 (m-30) cc_final: 0.7740 (m-30) REVERT: M 271 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: M 327 ASP cc_start: 0.8198 (t0) cc_final: 0.7925 (t0) REVERT: M 386 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7323 (mt-10) REVERT: M 424 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6386 (mt-10) REVERT: M 428 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6485 (tm-30) REVERT: M 478 GLU cc_start: 0.8209 (mp0) cc_final: 0.7698 (mp0) REVERT: M 550 MET cc_start: 0.7221 (ppp) cc_final: 0.6978 (ppp) REVERT: M 574 SER cc_start: 0.8260 (p) cc_final: 0.7948 (t) REVERT: M 599 SER cc_start: 0.7877 (p) cc_final: 0.7398 (m) REVERT: N 19 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7186 (mt-10) REVERT: N 153 ASP cc_start: 0.7710 (p0) cc_final: 0.7364 (p0) REVERT: N 187 ASN cc_start: 0.8593 (m110) cc_final: 0.8319 (m110) REVERT: N 249 GLU cc_start: 0.7188 (pt0) cc_final: 0.6614 (pm20) REVERT: N 301 GLU cc_start: 0.7679 (tt0) cc_final: 0.7389 (tt0) REVERT: N 336 ARG cc_start: 0.8336 (ptp90) cc_final: 0.8025 (mtm-85) REVERT: N 383 GLN cc_start: 0.8068 (mt0) cc_final: 0.7798 (mm-40) REVERT: N 394 VAL cc_start: 0.8843 (t) cc_final: 0.8363 (p) REVERT: N 401 GLU cc_start: 0.7202 (mp0) cc_final: 0.6977 (mp0) REVERT: N 457 PHE cc_start: 0.8650 (t80) cc_final: 0.8293 (t80) REVERT: N 506 LYS cc_start: 0.8632 (mttm) cc_final: 0.8303 (mtpp) REVERT: O 50 ASP cc_start: 0.8053 (m-30) cc_final: 0.7747 (m-30) REVERT: O 91 LEU cc_start: 0.8613 (tp) cc_final: 0.8408 (tp) REVERT: O 171 ARG cc_start: 0.7711 (mmm-85) cc_final: 0.7346 (mmm-85) REVERT: O 373 ASN cc_start: 0.7496 (m-40) cc_final: 0.7288 (m-40) REVERT: O 391 LYS cc_start: 0.7942 (tttp) cc_final: 0.7635 (ttpp) REVERT: O 559 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8550 (mtpp) REVERT: P 40 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8489 (mmtp) REVERT: P 50 ASP cc_start: 0.7921 (m-30) cc_final: 0.7706 (m-30) REVERT: P 55 ASP cc_start: 0.7962 (p0) cc_final: 0.7595 (p0) REVERT: P 115 ASP cc_start: 0.7606 (p0) cc_final: 0.7334 (p0) REVERT: P 153 ASP cc_start: 0.7636 (p0) cc_final: 0.7292 (p0) REVERT: P 239 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7357 (tmtt) REVERT: P 283 ASN cc_start: 0.8429 (m-40) cc_final: 0.8129 (m110) REVERT: P 303 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5118 (p0) REVERT: P 411 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7326 (mtmt) REVERT: P 413 MET cc_start: 0.7698 (ttm) cc_final: 0.7435 (ttm) REVERT: P 423 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7991 (mtmm) REVERT: P 444 ASP cc_start: 0.7360 (t0) cc_final: 0.6986 (t0) REVERT: P 459 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7529 (mm-30) REVERT: P 559 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8161 (mtmm) REVERT: Q 104 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7482 (ttm170) REVERT: Q 170 SER cc_start: 0.8267 (t) cc_final: 0.7781 (p) REVERT: Q 171 ARG cc_start: 0.6985 (mmt-90) cc_final: 0.6682 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8523 (m110) cc_final: 0.8273 (m-40) REVERT: Q 297 ASN cc_start: 0.6760 (t0) cc_final: 0.6466 (t0) REVERT: Q 306 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6863 (tm-30) REVERT: Q 308 PHE cc_start: 0.7814 (t80) cc_final: 0.7239 (t80) REVERT: Q 416 GLU cc_start: 0.8070 (tp30) cc_final: 0.7780 (tp30) REVERT: Q 468 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7787 (mtm180) REVERT: Q 544 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7846 (tp-100) REVERT: R 14 TYR cc_start: 0.7751 (p90) cc_final: 0.7195 (p90) REVERT: R 16 VAL cc_start: 0.8450 (p) cc_final: 0.8200 (t) REVERT: R 24 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7293 (mtp85) REVERT: R 158 THR cc_start: 0.6455 (p) cc_final: 0.6154 (p) REVERT: R 159 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8134 (t) REVERT: R 160 LYS cc_start: 0.8155 (mppt) cc_final: 0.7780 (mppt) REVERT: R 189 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8465 (mt) REVERT: R 192 ARG cc_start: 0.7276 (tpp80) cc_final: 0.6022 (tpp80) REVERT: R 245 LEU cc_start: 0.7615 (pp) cc_final: 0.6946 (mt) REVERT: R 270 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7021 (tt) REVERT: R 294 LYS cc_start: 0.8059 (tppt) cc_final: 0.7343 (mptt) REVERT: R 417 VAL cc_start: 0.8252 (t) cc_final: 0.8020 (p) REVERT: R 418 ASP cc_start: 0.7633 (t70) cc_final: 0.7298 (t70) REVERT: R 423 LYS cc_start: 0.8519 (mptt) cc_final: 0.8254 (mmtm) REVERT: R 476 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7759 (mt) REVERT: R 477 GLU cc_start: 0.6898 (tp30) cc_final: 0.6548 (tp30) REVERT: R 508 LYS cc_start: 0.8002 (mttp) cc_final: 0.7790 (mttp) REVERT: R 514 SER cc_start: 0.7705 (m) cc_final: 0.6948 (p) REVERT: R 550 MET cc_start: 0.8116 (ppp) cc_final: 0.7549 (ppp) REVERT: R 559 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8097 (mtmt) outliers start: 135 outliers final: 98 residues processed: 1717 average time/residue: 0.6493 time to fit residues: 1803.8527 Evaluate side-chains 1710 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1603 time to evaluate : 5.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 139 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 483 LEU Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 344 LYS Chi-restraints excluded: chain P residue 382 GLN Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 381 ILE Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 556 GLN Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 742 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 438 optimal weight: 4.9990 chunk 562 optimal weight: 3.9990 chunk 435 optimal weight: 2.9990 chunk 648 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 767 optimal weight: 8.9990 chunk 480 optimal weight: 0.7980 chunk 467 optimal weight: 4.9990 chunk 354 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS C 315 ASN F 324 ASN G 254 ASN I 365 GLN J 24 GLN K 278 HIS ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 466 GLN O 107 ASN P 214 GLN P 240 GLN P 382 GLN Q 480 HIS ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 66064 Z= 0.225 Angle : 0.507 14.967 89371 Z= 0.257 Chirality : 0.041 0.199 9710 Planarity : 0.004 0.052 11449 Dihedral : 8.616 170.202 9438 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.22 % Allowed : 15.39 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.09), residues: 7933 helix: 0.59 (0.10), residues: 3058 sheet: 1.02 (0.17), residues: 1011 loop : -1.59 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 409 HIS 0.006 0.001 HIS Q 434 PHE 0.022 0.001 PHE M 507 TYR 0.027 0.001 TYR R 258 ARG 0.012 0.000 ARG M 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1629 time to evaluate : 5.462 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7979 (m-30) cc_final: 0.7698 (m-30) REVERT: A 58 GLU cc_start: 0.7700 (mp0) cc_final: 0.7321 (mp0) REVERT: A 374 LYS cc_start: 0.8337 (mttt) cc_final: 0.8062 (mttm) REVERT: B 70 VAL cc_start: 0.8745 (t) cc_final: 0.8503 (m) REVERT: B 102 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 129 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8644 (mm-40) REVERT: B 132 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7562 (mp0) REVERT: B 179 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0) REVERT: B 233 TYR cc_start: 0.8055 (p90) cc_final: 0.7689 (p90) REVERT: B 240 VAL cc_start: 0.8764 (t) cc_final: 0.8526 (t) REVERT: B 257 ILE cc_start: 0.8565 (mm) cc_final: 0.8197 (mt) REVERT: B 258 ASN cc_start: 0.8302 (m-40) cc_final: 0.7813 (m-40) REVERT: B 374 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8245 (mttp) REVERT: B 382 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7556 (tp30) REVERT: C 102 GLU cc_start: 0.8104 (tp30) cc_final: 0.7615 (mm-30) REVERT: C 110 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7717 (mtmt) REVERT: D 24 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8357 (mp10) REVERT: D 72 GLN cc_start: 0.7022 (tp40) cc_final: 0.6588 (tp-100) REVERT: D 100 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7479 (mtm-85) REVERT: D 109 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7265 (mtt-85) REVERT: D 131 ARG cc_start: 0.8425 (ptm-80) cc_final: 0.8138 (ptm160) REVERT: D 132 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 137 LYS cc_start: 0.8403 (mttt) cc_final: 0.8149 (mttm) REVERT: D 182 ILE cc_start: 0.8646 (mm) cc_final: 0.8400 (mt) REVERT: D 238 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4330 (tt) REVERT: D 289 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8269 (ttp-170) REVERT: D 290 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7945 (mmt-90) REVERT: D 343 VAL cc_start: 0.8305 (t) cc_final: 0.8080 (t) REVERT: E 77 ASN cc_start: 0.7656 (m-40) cc_final: 0.7288 (m-40) REVERT: E 84 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (mp) REVERT: E 99 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8384 (ttp-170) REVERT: E 133 LYS cc_start: 0.8653 (mttm) cc_final: 0.8388 (mttp) REVERT: E 283 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7192 (m) REVERT: E 300 THR cc_start: 0.8406 (m) cc_final: 0.8124 (p) REVERT: E 335 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7172 (tp30) REVERT: E 400 VAL cc_start: 0.8138 (t) cc_final: 0.7909 (m) REVERT: F 45 MET cc_start: 0.8246 (tpp) cc_final: 0.8001 (mmt) REVERT: F 76 ASP cc_start: 0.7213 (m-30) cc_final: 0.6614 (m-30) REVERT: F 81 ASN cc_start: 0.8791 (p0) cc_final: 0.8471 (p0) REVERT: F 97 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8536 (ttmm) REVERT: F 109 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7644 (tpp80) REVERT: F 114 SER cc_start: 0.8697 (m) cc_final: 0.8205 (p) REVERT: F 128 GLU cc_start: 0.8076 (tp30) cc_final: 0.7777 (tp30) REVERT: F 137 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8178 (ttmm) REVERT: F 233 TYR cc_start: 0.7490 (p90) cc_final: 0.6830 (p90) REVERT: F 296 SER cc_start: 0.8928 (m) cc_final: 0.8570 (t) REVERT: G 51 SER cc_start: 0.8545 (m) cc_final: 0.7971 (p) REVERT: G 53 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7699 (mttt) REVERT: G 74 ASP cc_start: 0.7572 (m-30) cc_final: 0.7170 (t0) REVERT: G 77 ASN cc_start: 0.8123 (t0) cc_final: 0.7860 (t0) REVERT: G 107 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7309 (tm-30) REVERT: G 117 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8326 (tttp) REVERT: G 166 THR cc_start: 0.8868 (t) cc_final: 0.8612 (m) REVERT: G 255 ASP cc_start: 0.8035 (t0) cc_final: 0.7492 (t0) REVERT: G 275 LYS cc_start: 0.8406 (mttt) cc_final: 0.8145 (mtpp) REVERT: G 403 ILE cc_start: 0.8338 (mt) cc_final: 0.8046 (tp) REVERT: G 405 ASN cc_start: 0.7938 (t0) cc_final: 0.7492 (m110) REVERT: H 43 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7894 (mttt) REVERT: H 65 ASP cc_start: 0.7080 (m-30) cc_final: 0.6817 (m-30) REVERT: H 110 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8248 (ttmm) REVERT: H 202 ASP cc_start: 0.8555 (m-30) cc_final: 0.8072 (m-30) REVERT: H 286 GLU cc_start: 0.7951 (tp30) cc_final: 0.7670 (tp30) REVERT: H 337 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7513 (ttpt) REVERT: H 388 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8270 (m) REVERT: I 50 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (ttpp) REVERT: I 74 ASP cc_start: 0.7813 (m-30) cc_final: 0.7326 (m-30) REVERT: I 76 ASP cc_start: 0.7609 (m-30) cc_final: 0.7071 (m-30) REVERT: I 104 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7245 (mt-10) REVERT: I 142 LYS cc_start: 0.8885 (tttt) cc_final: 0.8602 (ttmt) REVERT: I 266 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7476 (pp30) REVERT: I 342 LYS cc_start: 0.8425 (mttt) cc_final: 0.8210 (mtpp) REVERT: J 17 SER cc_start: 0.8011 (m) cc_final: 0.7732 (t) REVERT: J 99 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7546 (ttm-80) REVERT: J 202 ASP cc_start: 0.8136 (m-30) cc_final: 0.7900 (m-30) REVERT: J 242 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7588 (tm-30) REVERT: J 300 THR cc_start: 0.8727 (m) cc_final: 0.8466 (p) REVERT: K 14 ASP cc_start: 0.7068 (m-30) cc_final: 0.6682 (m-30) REVERT: K 68 LEU cc_start: 0.8957 (mp) cc_final: 0.8717 (mt) REVERT: K 131 ARG cc_start: 0.8252 (ptm-80) cc_final: 0.7884 (ptm-80) REVERT: K 202 ASP cc_start: 0.8371 (m-30) cc_final: 0.8121 (m-30) REVERT: K 286 GLU cc_start: 0.8119 (tp30) cc_final: 0.7895 (tp30) REVERT: K 379 SER cc_start: 0.8754 (m) cc_final: 0.8281 (t) REVERT: L 70 VAL cc_start: 0.8573 (t) cc_final: 0.8207 (p) REVERT: L 116 TYR cc_start: 0.8598 (m-80) cc_final: 0.8234 (m-80) REVERT: L 233 TYR cc_start: 0.8088 (p90) cc_final: 0.7830 (p90) REVERT: L 255 ASP cc_start: 0.7998 (m-30) cc_final: 0.7599 (m-30) REVERT: L 293 GLU cc_start: 0.7678 (tt0) cc_final: 0.7451 (tt0) REVERT: L 374 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8352 (mtmm) REVERT: M 50 ASP cc_start: 0.8178 (m-30) cc_final: 0.7762 (m-30) REVERT: M 271 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: M 327 ASP cc_start: 0.8228 (t0) cc_final: 0.7982 (t0) REVERT: M 386 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7377 (tp30) REVERT: M 424 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6381 (mt-10) REVERT: M 428 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6523 (tm-30) REVERT: M 478 GLU cc_start: 0.8222 (mp0) cc_final: 0.7725 (mp0) REVERT: M 503 GLU cc_start: 0.7828 (mp0) cc_final: 0.7503 (mp0) REVERT: M 506 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7721 (ptmm) REVERT: M 507 PHE cc_start: 0.8243 (m-10) cc_final: 0.7950 (m-10) REVERT: M 574 SER cc_start: 0.8256 (p) cc_final: 0.7956 (t) REVERT: M 599 SER cc_start: 0.7959 (p) cc_final: 0.7501 (m) REVERT: N 19 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7208 (mt-10) REVERT: N 153 ASP cc_start: 0.7688 (p0) cc_final: 0.7365 (p0) REVERT: N 249 GLU cc_start: 0.7245 (pt0) cc_final: 0.6668 (pm20) REVERT: N 301 GLU cc_start: 0.7711 (tt0) cc_final: 0.7406 (tt0) REVERT: N 336 ARG cc_start: 0.8380 (ptp90) cc_final: 0.8060 (mtm-85) REVERT: N 383 GLN cc_start: 0.8102 (mt0) cc_final: 0.7817 (mm-40) REVERT: N 394 VAL cc_start: 0.8849 (t) cc_final: 0.8392 (p) REVERT: N 401 GLU cc_start: 0.7204 (mp0) cc_final: 0.6976 (mp0) REVERT: N 457 PHE cc_start: 0.8643 (t80) cc_final: 0.8440 (t80) REVERT: N 506 LYS cc_start: 0.8670 (mttm) cc_final: 0.8327 (mtpp) REVERT: O 43 SER cc_start: 0.8492 (p) cc_final: 0.8251 (t) REVERT: O 91 LEU cc_start: 0.8654 (tp) cc_final: 0.8419 (tp) REVERT: O 171 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7375 (mmm-85) REVERT: O 373 ASN cc_start: 0.7557 (m-40) cc_final: 0.7326 (m-40) REVERT: O 391 LYS cc_start: 0.7984 (tttp) cc_final: 0.7668 (ttpp) REVERT: O 539 ASN cc_start: 0.8289 (t0) cc_final: 0.7965 (t0) REVERT: O 559 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8546 (mtpp) REVERT: O 580 VAL cc_start: 0.8495 (p) cc_final: 0.8230 (t) REVERT: P 50 ASP cc_start: 0.7908 (m-30) cc_final: 0.7683 (m-30) REVERT: P 55 ASP cc_start: 0.8007 (p0) cc_final: 0.7594 (p0) REVERT: P 115 ASP cc_start: 0.7609 (p0) cc_final: 0.7334 (p0) REVERT: P 153 ASP cc_start: 0.7570 (p0) cc_final: 0.7265 (p0) REVERT: P 239 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7411 (tmtt) REVERT: P 283 ASN cc_start: 0.8473 (m-40) cc_final: 0.8171 (m110) REVERT: P 303 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5389 (p0) REVERT: P 411 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7349 (mtmt) REVERT: P 413 MET cc_start: 0.7753 (ttm) cc_final: 0.7493 (ttm) REVERT: P 423 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7982 (mtmm) REVERT: P 444 ASP cc_start: 0.7440 (t0) cc_final: 0.7069 (t0) REVERT: P 459 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7553 (mm-30) REVERT: P 559 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8181 (mtmm) REVERT: Q 94 ILE cc_start: 0.8273 (mt) cc_final: 0.7795 (tt) REVERT: Q 170 SER cc_start: 0.8301 (t) cc_final: 0.7785 (p) REVERT: Q 171 ARG cc_start: 0.7030 (mmt-90) cc_final: 0.6723 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8513 (m110) cc_final: 0.8299 (m-40) REVERT: Q 249 GLU cc_start: 0.8035 (pp20) cc_final: 0.7761 (pp20) REVERT: Q 297 ASN cc_start: 0.6763 (t0) cc_final: 0.6465 (t0) REVERT: Q 306 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6849 (tm-30) REVERT: Q 308 PHE cc_start: 0.7857 (t80) cc_final: 0.7252 (t80) REVERT: Q 459 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8163 (mm-30) REVERT: Q 468 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7783 (mtm180) REVERT: Q 544 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7836 (tp-100) REVERT: R 14 TYR cc_start: 0.7768 (p90) cc_final: 0.7108 (p90) REVERT: R 24 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7404 (mtp85) REVERT: R 158 THR cc_start: 0.6539 (p) cc_final: 0.6282 (p) REVERT: R 159 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (p) REVERT: R 160 LYS cc_start: 0.8151 (mppt) cc_final: 0.7779 (mppt) REVERT: R 189 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8493 (mt) REVERT: R 192 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6022 (tpp80) REVERT: R 245 LEU cc_start: 0.7635 (pp) cc_final: 0.7055 (mp) REVERT: R 270 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7084 (tt) REVERT: R 283 ASN cc_start: 0.7668 (m110) cc_final: 0.7315 (m110) REVERT: R 294 LYS cc_start: 0.8058 (tppt) cc_final: 0.7434 (mptt) REVERT: R 418 ASP cc_start: 0.7676 (t70) cc_final: 0.7326 (t70) REVERT: R 423 LYS cc_start: 0.8477 (mptt) cc_final: 0.8198 (mmtm) REVERT: R 508 LYS cc_start: 0.8015 (mttp) cc_final: 0.7808 (mttp) REVERT: R 559 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8115 (mtmt) outliers start: 152 outliers final: 116 residues processed: 1693 average time/residue: 0.6620 time to fit residues: 1818.3634 Evaluate side-chains 1735 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1609 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 121 LYS Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 344 LYS Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 381 ILE Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 200 ASN Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 474 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 458 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 150 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 487 optimal weight: 0.9990 chunk 522 optimal weight: 2.9990 chunk 379 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 603 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS C 315 ASN F 324 ASN K 278 HIS M 224 HIS P 214 GLN Q 214 GLN Q 443 GLN ** Q 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66064 Z= 0.145 Angle : 0.480 15.040 89371 Z= 0.242 Chirality : 0.040 0.182 9710 Planarity : 0.003 0.060 11449 Dihedral : 8.471 171.320 9438 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.83 % Allowed : 16.03 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.47 (0.09), residues: 7933 helix: 0.70 (0.10), residues: 3042 sheet: 1.07 (0.17), residues: 1000 loop : -1.57 (0.09), residues: 3891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 409 HIS 0.003 0.001 HIS J 313 PHE 0.019 0.001 PHE M 462 TYR 0.026 0.001 TYR R 258 ARG 0.013 0.000 ARG R 505 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1606 time to evaluate : 5.529 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7940 (m-30) cc_final: 0.7669 (m-30) REVERT: A 58 GLU cc_start: 0.7671 (mp0) cc_final: 0.7292 (mp0) REVERT: A 353 LYS cc_start: 0.8196 (mttt) cc_final: 0.7792 (mttp) REVERT: A 374 LYS cc_start: 0.8301 (mttt) cc_final: 0.8025 (mttm) REVERT: B 70 VAL cc_start: 0.8756 (t) cc_final: 0.8513 (m) REVERT: B 102 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 132 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7722 (mp0) REVERT: B 179 ASP cc_start: 0.8310 (t0) cc_final: 0.8027 (t0) REVERT: B 233 TYR cc_start: 0.8026 (p90) cc_final: 0.7629 (p90) REVERT: B 240 VAL cc_start: 0.8763 (t) cc_final: 0.8525 (t) REVERT: B 257 ILE cc_start: 0.8564 (mm) cc_final: 0.8181 (mt) REVERT: B 258 ASN cc_start: 0.8292 (m-40) cc_final: 0.7794 (m-40) REVERT: B 374 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8226 (mttp) REVERT: B 382 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7557 (tp30) REVERT: C 102 GLU cc_start: 0.8068 (tp30) cc_final: 0.7770 (mm-30) REVERT: C 104 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7474 (mm-30) REVERT: C 110 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7655 (mtmt) REVERT: D 24 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8361 (mp10) REVERT: D 100 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7471 (mtm-85) REVERT: D 107 GLU cc_start: 0.8332 (tp30) cc_final: 0.7965 (tp30) REVERT: D 129 GLN cc_start: 0.8484 (mm110) cc_final: 0.8142 (mm110) REVERT: D 131 ARG cc_start: 0.8417 (ptm-80) cc_final: 0.8115 (ptm160) REVERT: D 137 LYS cc_start: 0.8357 (mttt) cc_final: 0.8098 (mttm) REVERT: D 182 ILE cc_start: 0.8639 (mm) cc_final: 0.8406 (mt) REVERT: D 238 LEU cc_start: 0.4817 (OUTLIER) cc_final: 0.4564 (tt) REVERT: D 289 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8254 (ttp-170) REVERT: D 290 ARG cc_start: 0.8241 (mmt180) cc_final: 0.8005 (mmt-90) REVERT: D 343 VAL cc_start: 0.8263 (t) cc_final: 0.8031 (t) REVERT: E 84 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8392 (mp) REVERT: E 98 THR cc_start: 0.8078 (m) cc_final: 0.7798 (m) REVERT: E 99 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8341 (ttp-170) REVERT: E 118 GLU cc_start: 0.8091 (tp30) cc_final: 0.7810 (tp30) REVERT: E 133 LYS cc_start: 0.8643 (mttm) cc_final: 0.8378 (mttp) REVERT: E 335 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7119 (tp30) REVERT: F 45 MET cc_start: 0.8197 (tpp) cc_final: 0.7958 (mmt) REVERT: F 76 ASP cc_start: 0.7197 (m-30) cc_final: 0.6597 (m-30) REVERT: F 81 ASN cc_start: 0.8791 (p0) cc_final: 0.8472 (p0) REVERT: F 97 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8538 (ttmm) REVERT: F 109 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7570 (tpp80) REVERT: F 114 SER cc_start: 0.8695 (m) cc_final: 0.8208 (p) REVERT: F 128 GLU cc_start: 0.8133 (tp30) cc_final: 0.7843 (tp30) REVERT: F 137 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8115 (ttmm) REVERT: F 233 TYR cc_start: 0.7450 (p90) cc_final: 0.6771 (p90) REVERT: F 296 SER cc_start: 0.8903 (m) cc_final: 0.8543 (t) REVERT: G 51 SER cc_start: 0.8502 (m) cc_final: 0.7925 (p) REVERT: G 53 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7668 (mttt) REVERT: G 77 ASN cc_start: 0.8068 (t0) cc_final: 0.7794 (t0) REVERT: G 107 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7271 (tm-30) REVERT: G 117 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8322 (tttp) REVERT: G 255 ASP cc_start: 0.8026 (t0) cc_final: 0.7495 (t0) REVERT: G 275 LYS cc_start: 0.8382 (mttt) cc_final: 0.8125 (mtpp) REVERT: G 403 ILE cc_start: 0.8345 (mt) cc_final: 0.8053 (tp) REVERT: G 405 ASN cc_start: 0.7920 (t0) cc_final: 0.7510 (m110) REVERT: H 65 ASP cc_start: 0.7112 (m-30) cc_final: 0.6898 (m-30) REVERT: H 110 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8239 (ttmm) REVERT: H 202 ASP cc_start: 0.8497 (m-30) cc_final: 0.7979 (m-30) REVERT: H 286 GLU cc_start: 0.7912 (tp30) cc_final: 0.7631 (tp30) REVERT: H 337 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7490 (ttpt) REVERT: H 388 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8225 (m) REVERT: I 74 ASP cc_start: 0.7802 (m-30) cc_final: 0.7299 (m-30) REVERT: I 76 ASP cc_start: 0.7601 (m-30) cc_final: 0.7048 (m-30) REVERT: I 104 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7127 (mt-10) REVERT: I 142 LYS cc_start: 0.8894 (tttt) cc_final: 0.8611 (ttmt) REVERT: I 266 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7491 (pp30) REVERT: I 342 LYS cc_start: 0.8416 (mttt) cc_final: 0.8215 (mtpp) REVERT: J 17 SER cc_start: 0.8022 (m) cc_final: 0.7714 (t) REVERT: J 99 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: J 202 ASP cc_start: 0.8125 (m-30) cc_final: 0.7899 (m-30) REVERT: J 242 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7582 (tm-30) REVERT: J 300 THR cc_start: 0.8725 (m) cc_final: 0.8412 (p) REVERT: K 14 ASP cc_start: 0.6995 (m-30) cc_final: 0.6638 (m-30) REVERT: K 68 LEU cc_start: 0.8948 (mp) cc_final: 0.8704 (mt) REVERT: K 202 ASP cc_start: 0.8303 (m-30) cc_final: 0.8074 (m-30) REVERT: K 286 GLU cc_start: 0.8110 (tp30) cc_final: 0.7902 (tp30) REVERT: K 379 SER cc_start: 0.8750 (m) cc_final: 0.8261 (t) REVERT: L 70 VAL cc_start: 0.8562 (t) cc_final: 0.8196 (p) REVERT: L 233 TYR cc_start: 0.8070 (p90) cc_final: 0.7830 (p90) REVERT: L 255 ASP cc_start: 0.7998 (m-30) cc_final: 0.7608 (m-30) REVERT: L 293 GLU cc_start: 0.7689 (tt0) cc_final: 0.7476 (tt0) REVERT: L 374 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8361 (mtmm) REVERT: M 50 ASP cc_start: 0.8174 (m-30) cc_final: 0.7769 (m-30) REVERT: M 271 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7434 (ttm-80) REVERT: M 327 ASP cc_start: 0.8189 (t0) cc_final: 0.7940 (t0) REVERT: M 386 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7327 (mt-10) REVERT: M 424 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6369 (mt-10) REVERT: M 428 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6540 (tm-30) REVERT: M 478 GLU cc_start: 0.8212 (mp0) cc_final: 0.7674 (mp0) REVERT: M 574 SER cc_start: 0.8252 (p) cc_final: 0.7950 (t) REVERT: M 599 SER cc_start: 0.7965 (p) cc_final: 0.7507 (m) REVERT: N 153 ASP cc_start: 0.7642 (p0) cc_final: 0.7312 (p0) REVERT: N 187 ASN cc_start: 0.8598 (m110) cc_final: 0.8329 (m110) REVERT: N 249 GLU cc_start: 0.7224 (pt0) cc_final: 0.6650 (pm20) REVERT: N 301 GLU cc_start: 0.7693 (tt0) cc_final: 0.7391 (tt0) REVERT: N 336 ARG cc_start: 0.8352 (ptp90) cc_final: 0.8029 (mtm-85) REVERT: N 383 GLN cc_start: 0.8070 (mt0) cc_final: 0.7784 (mm-40) REVERT: N 394 VAL cc_start: 0.8846 (t) cc_final: 0.8369 (p) REVERT: N 401 GLU cc_start: 0.7208 (mp0) cc_final: 0.6982 (mp0) REVERT: N 478 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7534 (mm-30) REVERT: N 506 LYS cc_start: 0.8664 (mttm) cc_final: 0.8315 (mtpp) REVERT: O 91 LEU cc_start: 0.8619 (tp) cc_final: 0.8397 (tp) REVERT: O 171 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7359 (mmm-85) REVERT: O 373 ASN cc_start: 0.7517 (m-40) cc_final: 0.7314 (m-40) REVERT: O 391 LYS cc_start: 0.7942 (tttp) cc_final: 0.7637 (ttpp) REVERT: O 559 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8536 (mtpp) REVERT: P 40 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8501 (mmtp) REVERT: P 50 ASP cc_start: 0.7925 (m-30) cc_final: 0.7688 (m-30) REVERT: P 55 ASP cc_start: 0.7964 (p0) cc_final: 0.7595 (p0) REVERT: P 115 ASP cc_start: 0.7591 (p0) cc_final: 0.7301 (p0) REVERT: P 153 ASP cc_start: 0.7568 (p0) cc_final: 0.7196 (p0) REVERT: P 239 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7490 (tmtt) REVERT: P 283 ASN cc_start: 0.8444 (m-40) cc_final: 0.8136 (m110) REVERT: P 303 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5248 (p0) REVERT: P 411 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7326 (mtmt) REVERT: P 413 MET cc_start: 0.7760 (ttm) cc_final: 0.7490 (ttm) REVERT: P 423 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7976 (mtmm) REVERT: P 444 ASP cc_start: 0.7386 (t0) cc_final: 0.7023 (t0) REVERT: P 459 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7552 (mm-30) REVERT: P 559 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8212 (mtmt) REVERT: Q 170 SER cc_start: 0.8294 (t) cc_final: 0.7773 (p) REVERT: Q 171 ARG cc_start: 0.7033 (mmt-90) cc_final: 0.6719 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8485 (m110) cc_final: 0.8000 (m-40) REVERT: Q 211 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7404 (mp0) REVERT: Q 249 GLU cc_start: 0.8075 (pp20) cc_final: 0.7807 (pp20) REVERT: Q 297 ASN cc_start: 0.6759 (t0) cc_final: 0.6456 (t0) REVERT: Q 306 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6852 (tm-30) REVERT: Q 308 PHE cc_start: 0.7848 (t80) cc_final: 0.7254 (t80) REVERT: Q 459 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8130 (mm-30) REVERT: Q 464 ARG cc_start: 0.8799 (ttp-170) cc_final: 0.8599 (ttm170) REVERT: Q 468 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7782 (mtm180) REVERT: Q 544 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7840 (tp-100) REVERT: R 14 TYR cc_start: 0.7721 (p90) cc_final: 0.7021 (p90) REVERT: R 24 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7300 (mtp85) REVERT: R 158 THR cc_start: 0.6516 (p) cc_final: 0.6247 (p) REVERT: R 159 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8163 (p) REVERT: R 160 LYS cc_start: 0.8142 (mppt) cc_final: 0.7770 (mppt) REVERT: R 189 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (mt) REVERT: R 192 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6024 (tpp80) REVERT: R 245 LEU cc_start: 0.7598 (pp) cc_final: 0.7162 (mp) REVERT: R 270 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6999 (tt) REVERT: R 283 ASN cc_start: 0.7635 (m110) cc_final: 0.7276 (m110) REVERT: R 294 LYS cc_start: 0.8131 (tppt) cc_final: 0.7476 (mptt) REVERT: R 418 ASP cc_start: 0.7650 (t70) cc_final: 0.7308 (t70) REVERT: R 423 LYS cc_start: 0.8468 (mptt) cc_final: 0.8176 (mmtm) REVERT: R 508 LYS cc_start: 0.8048 (mttp) cc_final: 0.7847 (mttp) REVERT: R 550 MET cc_start: 0.8115 (ppp) cc_final: 0.7541 (ppp) REVERT: R 559 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8110 (mtmt) outliers start: 125 outliers final: 104 residues processed: 1664 average time/residue: 0.6815 time to fit residues: 1840.2630 Evaluate side-chains 1711 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1599 time to evaluate : 5.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 534 SER Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 344 LYS Chi-restraints excluded: chain P residue 380 ILE Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 378 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 200 ASN Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 697 optimal weight: 2.9990 chunk 735 optimal weight: 5.9990 chunk 670 optimal weight: 8.9990 chunk 714 optimal weight: 0.0870 chunk 734 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 561 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 646 optimal weight: 2.9990 chunk 676 optimal weight: 0.8980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS C 315 ASN E 154 ASN F 324 ASN K 278 HIS Q 382 GLN ** Q 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 66064 Z= 0.249 Angle : 0.526 16.081 89371 Z= 0.268 Chirality : 0.042 0.165 9710 Planarity : 0.004 0.064 11449 Dihedral : 8.625 169.736 9438 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.85 % Allowed : 16.43 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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 (0.09), residues: 7933 helix: 0.62 (0.10), residues: 3043 sheet: 0.98 (0.17), residues: 992 loop : -1.60 (0.09), residues: 3898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 409 HIS 0.006 0.001 HIS F 227 PHE 0.024 0.001 PHE M 507 TYR 0.027 0.001 TYR R 258 ARG 0.014 0.000 ARG E 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1628 time to evaluate : 5.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7972 (m-30) cc_final: 0.7634 (m-30) REVERT: A 58 GLU cc_start: 0.7708 (mp0) cc_final: 0.7316 (mp0) REVERT: A 353 LYS cc_start: 0.8209 (mttt) cc_final: 0.7818 (mttp) REVERT: A 374 LYS cc_start: 0.8351 (mttt) cc_final: 0.8046 (mttm) REVERT: B 70 VAL cc_start: 0.8746 (t) cc_final: 0.8501 (m) REVERT: B 102 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 132 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7580 (mp0) REVERT: B 179 ASP cc_start: 0.8334 (t0) cc_final: 0.8094 (t0) REVERT: B 233 TYR cc_start: 0.8068 (p90) cc_final: 0.7644 (p90) REVERT: B 240 VAL cc_start: 0.8769 (t) cc_final: 0.8540 (t) REVERT: B 257 ILE cc_start: 0.8586 (mm) cc_final: 0.8213 (mt) REVERT: B 258 ASN cc_start: 0.8360 (m-40) cc_final: 0.7884 (m-40) REVERT: B 374 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8265 (mttp) REVERT: B 382 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7559 (tp30) REVERT: C 83 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: C 102 GLU cc_start: 0.8064 (tp30) cc_final: 0.7617 (mm-30) REVERT: C 103 ASP cc_start: 0.7847 (t0) cc_final: 0.7575 (t0) REVERT: C 110 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7735 (mtmt) REVERT: D 24 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8383 (mp10) REVERT: D 43 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8161 (mttp) REVERT: D 100 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7477 (mtm-85) REVERT: D 107 GLU cc_start: 0.8287 (tp30) cc_final: 0.7921 (tp30) REVERT: D 109 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7294 (mtt-85) REVERT: D 129 GLN cc_start: 0.8507 (mm110) cc_final: 0.8162 (mm110) REVERT: D 131 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.8146 (ptm160) REVERT: D 137 LYS cc_start: 0.8412 (mttt) cc_final: 0.8148 (mttm) REVERT: D 182 ILE cc_start: 0.8647 (mm) cc_final: 0.8424 (mt) REVERT: D 238 LEU cc_start: 0.4612 (OUTLIER) cc_final: 0.4365 (tt) REVERT: D 290 ARG cc_start: 0.8280 (mmt180) cc_final: 0.8018 (mmt-90) REVERT: D 343 VAL cc_start: 0.8294 (t) cc_final: 0.8070 (t) REVERT: E 77 ASN cc_start: 0.7578 (m-40) cc_final: 0.7229 (m-40) REVERT: E 84 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (mp) REVERT: E 99 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8416 (ttp-170) REVERT: E 133 LYS cc_start: 0.8665 (mttm) cc_final: 0.8399 (mttp) REVERT: E 283 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.6156 (p) REVERT: E 335 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7190 (tp30) REVERT: E 382 GLU cc_start: 0.7672 (mp0) cc_final: 0.7419 (mp0) REVERT: F 45 MET cc_start: 0.8288 (tpp) cc_final: 0.8050 (mmt) REVERT: F 76 ASP cc_start: 0.7262 (m-30) cc_final: 0.6660 (m-30) REVERT: F 81 ASN cc_start: 0.8824 (p0) cc_final: 0.8493 (p0) REVERT: F 109 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7773 (tpp80) REVERT: F 114 SER cc_start: 0.8711 (m) cc_final: 0.8208 (p) REVERT: F 128 GLU cc_start: 0.8151 (tp30) cc_final: 0.7857 (tp30) REVERT: F 137 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8198 (ttmm) REVERT: F 233 TYR cc_start: 0.7537 (p90) cc_final: 0.6890 (p90) REVERT: F 296 SER cc_start: 0.8927 (m) cc_final: 0.8552 (t) REVERT: G 40 CYS cc_start: 0.8155 (m) cc_final: 0.7842 (m) REVERT: G 51 SER cc_start: 0.8544 (m) cc_final: 0.7949 (p) REVERT: G 53 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7670 (mttt) REVERT: G 77 ASN cc_start: 0.8129 (t0) cc_final: 0.7867 (t0) REVERT: G 107 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7336 (tm-30) REVERT: G 117 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8341 (tttp) REVERT: G 255 ASP cc_start: 0.8011 (t0) cc_final: 0.7454 (t0) REVERT: G 275 LYS cc_start: 0.8437 (mttt) cc_final: 0.8174 (mtpp) REVERT: G 401 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7406 (tm-30) REVERT: G 403 ILE cc_start: 0.8363 (mt) cc_final: 0.8068 (tp) REVERT: G 405 ASN cc_start: 0.8049 (t0) cc_final: 0.7674 (m110) REVERT: H 65 ASP cc_start: 0.7103 (m-30) cc_final: 0.6872 (m-30) REVERT: H 110 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8234 (ttmm) REVERT: H 202 ASP cc_start: 0.8537 (m-30) cc_final: 0.8075 (m-30) REVERT: H 286 GLU cc_start: 0.7951 (tp30) cc_final: 0.7672 (tp30) REVERT: H 337 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7551 (ttpt) REVERT: H 388 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8256 (m) REVERT: I 50 LYS cc_start: 0.8433 (ptmt) cc_final: 0.8088 (ttpp) REVERT: I 74 ASP cc_start: 0.7855 (m-30) cc_final: 0.7285 (m-30) REVERT: I 76 ASP cc_start: 0.7639 (m-30) cc_final: 0.7092 (m-30) REVERT: I 104 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7256 (mt-10) REVERT: I 106 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (pp20) REVERT: I 142 LYS cc_start: 0.8893 (tttt) cc_final: 0.8611 (ttmt) REVERT: I 266 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7411 (pp30) REVERT: I 342 LYS cc_start: 0.8435 (mttt) cc_final: 0.8220 (mtpp) REVERT: J 17 SER cc_start: 0.8022 (m) cc_final: 0.7738 (t) REVERT: J 99 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: J 202 ASP cc_start: 0.8112 (m-30) cc_final: 0.7875 (m-30) REVERT: J 242 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7611 (tm-30) REVERT: K 14 ASP cc_start: 0.7086 (m-30) cc_final: 0.6692 (m-30) REVERT: K 68 LEU cc_start: 0.8950 (mp) cc_final: 0.8705 (mt) REVERT: K 202 ASP cc_start: 0.8362 (m-30) cc_final: 0.8146 (m-30) REVERT: K 286 GLU cc_start: 0.8120 (tp30) cc_final: 0.7896 (tp30) REVERT: K 379 SER cc_start: 0.8739 (m) cc_final: 0.8279 (t) REVERT: L 70 VAL cc_start: 0.8581 (t) cc_final: 0.8226 (p) REVERT: L 233 TYR cc_start: 0.8096 (p90) cc_final: 0.7837 (p90) REVERT: L 374 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8348 (mtmm) REVERT: M 50 ASP cc_start: 0.8191 (m-30) cc_final: 0.7799 (m-30) REVERT: M 212 TYR cc_start: 0.8302 (m-80) cc_final: 0.7998 (m-80) REVERT: M 271 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: M 327 ASP cc_start: 0.8235 (t0) cc_final: 0.7989 (t0) REVERT: M 386 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7376 (mt-10) REVERT: M 424 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6373 (mt-10) REVERT: M 428 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6516 (tm-30) REVERT: M 478 GLU cc_start: 0.8223 (mp0) cc_final: 0.7699 (mp0) REVERT: M 574 SER cc_start: 0.8267 (p) cc_final: 0.7969 (t) REVERT: M 599 SER cc_start: 0.8112 (p) cc_final: 0.7637 (m) REVERT: N 153 ASP cc_start: 0.7678 (p0) cc_final: 0.7335 (p0) REVERT: N 249 GLU cc_start: 0.7246 (pt0) cc_final: 0.6673 (pm20) REVERT: N 301 GLU cc_start: 0.7733 (tt0) cc_final: 0.7420 (tt0) REVERT: N 336 ARG cc_start: 0.8345 (ptp90) cc_final: 0.8065 (mtm-85) REVERT: N 383 GLN cc_start: 0.8087 (mt0) cc_final: 0.7816 (mm-40) REVERT: N 394 VAL cc_start: 0.8856 (t) cc_final: 0.8396 (p) REVERT: N 401 GLU cc_start: 0.7214 (mp0) cc_final: 0.6991 (mp0) REVERT: N 457 PHE cc_start: 0.8633 (t80) cc_final: 0.8429 (t80) REVERT: N 478 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7554 (mm-30) REVERT: N 506 LYS cc_start: 0.8675 (mttm) cc_final: 0.8330 (mtpp) REVERT: N 560 GLN cc_start: 0.8503 (mt0) cc_final: 0.8255 (mt0) REVERT: O 91 LEU cc_start: 0.8663 (tp) cc_final: 0.8427 (tp) REVERT: O 171 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: O 373 ASN cc_start: 0.7577 (m-40) cc_final: 0.7341 (m-40) REVERT: O 391 LYS cc_start: 0.7990 (tttp) cc_final: 0.7675 (ttpp) REVERT: O 539 ASN cc_start: 0.8288 (t0) cc_final: 0.7960 (t0) REVERT: O 559 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8542 (mtpp) REVERT: O 580 VAL cc_start: 0.8530 (p) cc_final: 0.8260 (t) REVERT: P 50 ASP cc_start: 0.7941 (m-30) cc_final: 0.7718 (m-30) REVERT: P 55 ASP cc_start: 0.8011 (p0) cc_final: 0.7596 (p0) REVERT: P 115 ASP cc_start: 0.7590 (p0) cc_final: 0.7301 (p0) REVERT: P 153 ASP cc_start: 0.7543 (p0) cc_final: 0.7178 (p0) REVERT: P 241 GLN cc_start: 0.7955 (mp10) cc_final: 0.7729 (mp-120) REVERT: P 283 ASN cc_start: 0.8498 (m-40) cc_final: 0.8182 (m110) REVERT: P 303 ASP cc_start: 0.6270 (OUTLIER) cc_final: 0.5397 (p0) REVERT: P 411 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7341 (mtmt) REVERT: P 413 MET cc_start: 0.7785 (ttm) cc_final: 0.7585 (ttm) REVERT: P 423 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7982 (mtmm) REVERT: P 444 ASP cc_start: 0.7457 (t0) cc_final: 0.7064 (t0) REVERT: P 459 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7573 (mm-30) REVERT: P 559 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8172 (mtmm) REVERT: Q 21 GLU cc_start: 0.7434 (tp30) cc_final: 0.7223 (tp30) REVERT: Q 170 SER cc_start: 0.8283 (t) cc_final: 0.7741 (p) REVERT: Q 171 ARG cc_start: 0.7072 (mmt-90) cc_final: 0.6747 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8477 (m110) cc_final: 0.8012 (m-40) REVERT: Q 211 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7412 (mp0) REVERT: Q 306 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6849 (tm-30) REVERT: Q 308 PHE cc_start: 0.7844 (t80) cc_final: 0.7240 (t80) REVERT: Q 459 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8135 (mm-30) REVERT: Q 464 ARG cc_start: 0.8809 (ttp-170) cc_final: 0.8602 (ttm170) REVERT: Q 468 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7786 (mtm180) REVERT: Q 544 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7847 (tp-100) REVERT: R 14 TYR cc_start: 0.7765 (p90) cc_final: 0.7055 (p90) REVERT: R 24 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7298 (mtp85) REVERT: R 159 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8193 (p) REVERT: R 160 LYS cc_start: 0.8138 (mppt) cc_final: 0.7808 (mppt) REVERT: R 189 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8516 (mt) REVERT: R 192 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6074 (tpp80) REVERT: R 245 LEU cc_start: 0.7613 (pp) cc_final: 0.7218 (mp) REVERT: R 270 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6885 (tt) REVERT: R 283 ASN cc_start: 0.7671 (m110) cc_final: 0.7290 (m-40) REVERT: R 294 LYS cc_start: 0.8130 (tppt) cc_final: 0.7453 (mptt) REVERT: R 417 VAL cc_start: 0.8318 (t) cc_final: 0.8087 (p) REVERT: R 418 ASP cc_start: 0.7667 (t70) cc_final: 0.7420 (t70) REVERT: R 423 LYS cc_start: 0.8478 (mptt) cc_final: 0.8228 (mmtm) REVERT: R 508 LYS cc_start: 0.8061 (mttp) cc_final: 0.7838 (mttp) REVERT: R 536 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7387 (ttt90) REVERT: R 559 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8084 (mtmt) outliers start: 127 outliers final: 104 residues processed: 1685 average time/residue: 0.6625 time to fit residues: 1807.6159 Evaluate side-chains 1738 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1623 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 344 LYS Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain P residue 484 ARG Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 599 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 311 TYR Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 382 GLN Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 200 ASN Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 712 optimal weight: 1.9990 chunk 469 optimal weight: 0.0770 chunk 756 optimal weight: 6.9990 chunk 461 optimal weight: 4.9990 chunk 358 optimal weight: 2.9990 chunk 525 optimal weight: 1.9990 chunk 793 optimal weight: 0.5980 chunk 729 optimal weight: 0.4980 chunk 631 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 487 optimal weight: 0.8980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS C 315 ASN E 24 GLN E 154 ASN K 278 HIS Q 556 GLN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 66064 Z= 0.163 Angle : 0.503 15.657 89371 Z= 0.253 Chirality : 0.040 0.178 9710 Planarity : 0.003 0.070 11449 Dihedral : 8.507 170.968 9438 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.64 % Allowed : 16.85 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.09), residues: 7933 helix: 0.69 (0.10), residues: 3038 sheet: 1.02 (0.17), residues: 998 loop : -1.58 (0.09), residues: 3897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 409 HIS 0.004 0.001 HIS J 313 PHE 0.025 0.001 PHE K 262 TYR 0.027 0.001 TYR R 258 ARG 0.016 0.000 ARG Q 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1614 time to evaluate : 5.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7980 (m-30) cc_final: 0.7698 (m-30) REVERT: A 58 GLU cc_start: 0.7686 (mp0) cc_final: 0.7299 (mp0) REVERT: B 70 VAL cc_start: 0.8736 (t) cc_final: 0.8486 (m) REVERT: B 102 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 179 ASP cc_start: 0.8315 (t0) cc_final: 0.8041 (t0) REVERT: B 233 TYR cc_start: 0.8055 (p90) cc_final: 0.7637 (p90) REVERT: B 240 VAL cc_start: 0.8759 (t) cc_final: 0.8522 (t) REVERT: B 257 ILE cc_start: 0.8582 (mm) cc_final: 0.8185 (mt) REVERT: B 258 ASN cc_start: 0.8319 (m-40) cc_final: 0.7818 (m-40) REVERT: B 374 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8224 (mttp) REVERT: B 382 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7567 (tp30) REVERT: C 110 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7679 (mtmt) REVERT: C 118 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 24 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8353 (mp10) REVERT: D 43 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8134 (mttp) REVERT: D 100 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7474 (mtm-85) REVERT: D 107 GLU cc_start: 0.8300 (tp30) cc_final: 0.7907 (tp30) REVERT: D 129 GLN cc_start: 0.8502 (mm110) cc_final: 0.8159 (mm110) REVERT: D 131 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.8123 (ptm160) REVERT: D 137 LYS cc_start: 0.8373 (mttt) cc_final: 0.8113 (mttm) REVERT: D 182 ILE cc_start: 0.8648 (mm) cc_final: 0.8433 (mt) REVERT: D 238 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4340 (tt) REVERT: D 290 ARG cc_start: 0.8263 (mmt180) cc_final: 0.8011 (mmt-90) REVERT: D 343 VAL cc_start: 0.8287 (t) cc_final: 0.8048 (t) REVERT: E 5 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7584 (tp40) REVERT: E 84 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8415 (mp) REVERT: E 99 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8371 (ttp-170) REVERT: E 118 GLU cc_start: 0.8111 (tp30) cc_final: 0.7825 (tp30) REVERT: E 133 LYS cc_start: 0.8650 (mttm) cc_final: 0.8388 (mttp) REVERT: E 185 PHE cc_start: 0.8601 (m-80) cc_final: 0.8280 (m-80) REVERT: E 283 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7134 (m) REVERT: E 335 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7189 (mm-30) REVERT: E 382 GLU cc_start: 0.7637 (mp0) cc_final: 0.7194 (mp0) REVERT: F 45 MET cc_start: 0.8245 (tpp) cc_final: 0.8013 (mmt) REVERT: F 76 ASP cc_start: 0.7264 (m-30) cc_final: 0.6655 (m-30) REVERT: F 97 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8525 (ttmm) REVERT: F 109 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7623 (tpp80) REVERT: F 114 SER cc_start: 0.8710 (m) cc_final: 0.8214 (p) REVERT: F 128 GLU cc_start: 0.8142 (tp30) cc_final: 0.7849 (tp30) REVERT: F 137 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8143 (ttmm) REVERT: F 233 TYR cc_start: 0.7512 (p90) cc_final: 0.6873 (p90) REVERT: F 296 SER cc_start: 0.8891 (m) cc_final: 0.8517 (t) REVERT: G 40 CYS cc_start: 0.8153 (m) cc_final: 0.7829 (m) REVERT: G 51 SER cc_start: 0.8522 (m) cc_final: 0.7923 (p) REVERT: G 53 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7657 (mttt) REVERT: G 77 ASN cc_start: 0.8096 (t0) cc_final: 0.7830 (t0) REVERT: G 107 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7266 (tm-30) REVERT: G 117 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8273 (tttm) REVERT: G 255 ASP cc_start: 0.8002 (t0) cc_final: 0.7454 (t0) REVERT: G 275 LYS cc_start: 0.8408 (mttt) cc_final: 0.8137 (mtpp) REVERT: G 403 ILE cc_start: 0.8370 (mt) cc_final: 0.8057 (tp) REVERT: H 65 ASP cc_start: 0.7117 (m-30) cc_final: 0.6888 (m-30) REVERT: H 110 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8236 (ttmm) REVERT: H 202 ASP cc_start: 0.8493 (m-30) cc_final: 0.7459 (m-30) REVERT: H 286 GLU cc_start: 0.7924 (tp30) cc_final: 0.7641 (tp30) REVERT: H 337 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7524 (ttpt) REVERT: H 388 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8225 (m) REVERT: I 74 ASP cc_start: 0.7844 (m-30) cc_final: 0.7280 (m-30) REVERT: I 76 ASP cc_start: 0.7625 (m-30) cc_final: 0.7072 (m-30) REVERT: I 104 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7127 (mt-10) REVERT: I 106 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: I 142 LYS cc_start: 0.8896 (tttt) cc_final: 0.8621 (ttmt) REVERT: I 266 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: I 342 LYS cc_start: 0.8436 (mttt) cc_final: 0.8196 (mtpp) REVERT: J 17 SER cc_start: 0.8014 (m) cc_final: 0.7728 (t) REVERT: J 99 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7481 (ttm-80) REVERT: J 202 ASP cc_start: 0.8093 (m-30) cc_final: 0.7855 (m-30) REVERT: J 242 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7629 (tt0) REVERT: J 300 THR cc_start: 0.8719 (m) cc_final: 0.8410 (p) REVERT: K 14 ASP cc_start: 0.7017 (m-30) cc_final: 0.6663 (m-30) REVERT: K 68 LEU cc_start: 0.8956 (mp) cc_final: 0.8714 (mt) REVERT: K 202 ASP cc_start: 0.8345 (m-30) cc_final: 0.8132 (m-30) REVERT: K 286 GLU cc_start: 0.8113 (tp30) cc_final: 0.7895 (tp30) REVERT: K 379 SER cc_start: 0.8740 (m) cc_final: 0.8271 (t) REVERT: L 70 VAL cc_start: 0.8578 (t) cc_final: 0.8251 (p) REVERT: L 233 TYR cc_start: 0.8071 (p90) cc_final: 0.7781 (p90) REVERT: L 374 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8359 (mtmm) REVERT: M 50 ASP cc_start: 0.8190 (m-30) cc_final: 0.7782 (m-30) REVERT: M 212 TYR cc_start: 0.8389 (m-80) cc_final: 0.8142 (m-80) REVERT: M 271 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: M 327 ASP cc_start: 0.8212 (t0) cc_final: 0.7973 (t0) REVERT: M 386 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7341 (mt-10) REVERT: M 424 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6357 (mt-10) REVERT: M 428 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6449 (tm-30) REVERT: M 478 GLU cc_start: 0.8207 (mp0) cc_final: 0.7697 (mp0) REVERT: M 506 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7551 (tmtt) REVERT: M 507 PHE cc_start: 0.8017 (m-10) cc_final: 0.7525 (m-10) REVERT: M 574 SER cc_start: 0.8253 (p) cc_final: 0.7961 (t) REVERT: M 599 SER cc_start: 0.8084 (p) cc_final: 0.7613 (m) REVERT: N 153 ASP cc_start: 0.7644 (p0) cc_final: 0.7314 (p0) REVERT: N 187 ASN cc_start: 0.8602 (m110) cc_final: 0.8311 (m110) REVERT: N 249 GLU cc_start: 0.7242 (pt0) cc_final: 0.6660 (pm20) REVERT: N 301 GLU cc_start: 0.7718 (tt0) cc_final: 0.7415 (tt0) REVERT: N 302 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7933 (mttm) REVERT: N 336 ARG cc_start: 0.8359 (ptp90) cc_final: 0.8033 (mtm-85) REVERT: N 383 GLN cc_start: 0.8076 (mt0) cc_final: 0.7786 (mm-40) REVERT: N 394 VAL cc_start: 0.8838 (t) cc_final: 0.8374 (p) REVERT: N 401 GLU cc_start: 0.7214 (mp0) cc_final: 0.6984 (mp0) REVERT: N 478 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7547 (mm-30) REVERT: N 497 TYR cc_start: 0.6480 (p90) cc_final: 0.5117 (p90) REVERT: N 498 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7156 (mp0) REVERT: N 506 LYS cc_start: 0.8674 (mttm) cc_final: 0.8326 (mtpp) REVERT: O 91 LEU cc_start: 0.8629 (tp) cc_final: 0.8412 (tp) REVERT: O 171 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.7356 (mmm-85) REVERT: O 373 ASN cc_start: 0.7527 (m-40) cc_final: 0.7316 (m-40) REVERT: O 391 LYS cc_start: 0.7962 (tttp) cc_final: 0.7659 (ttpp) REVERT: O 539 ASN cc_start: 0.8271 (t0) cc_final: 0.7936 (t0) REVERT: O 559 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8534 (mtpp) REVERT: P 50 ASP cc_start: 0.7931 (m-30) cc_final: 0.7720 (m-30) REVERT: P 55 ASP cc_start: 0.7972 (p0) cc_final: 0.7604 (p0) REVERT: P 115 ASP cc_start: 0.7569 (p0) cc_final: 0.7280 (p0) REVERT: P 153 ASP cc_start: 0.7548 (p0) cc_final: 0.7173 (p0) REVERT: P 241 GLN cc_start: 0.7952 (mp10) cc_final: 0.7730 (mp-120) REVERT: P 283 ASN cc_start: 0.8470 (m-40) cc_final: 0.8148 (m110) REVERT: P 303 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5298 (p0) REVERT: P 344 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8515 (tptp) REVERT: P 411 LYS cc_start: 0.7565 (mtmt) cc_final: 0.7342 (mtmt) REVERT: P 423 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7971 (mtmm) REVERT: P 444 ASP cc_start: 0.7445 (t0) cc_final: 0.7125 (t0) REVERT: P 459 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7525 (mm-30) REVERT: P 559 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8154 (mtmm) REVERT: Q 21 GLU cc_start: 0.7424 (tp30) cc_final: 0.7211 (tp30) REVERT: Q 170 SER cc_start: 0.8286 (t) cc_final: 0.7738 (p) REVERT: Q 171 ARG cc_start: 0.7069 (mmt-90) cc_final: 0.6741 (mmt-90) REVERT: Q 209 ASN cc_start: 0.8472 (m110) cc_final: 0.8008 (m-40) REVERT: Q 211 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7402 (mp0) REVERT: Q 297 ASN cc_start: 0.6767 (t0) cc_final: 0.6460 (t0) REVERT: Q 308 PHE cc_start: 0.7821 (t80) cc_final: 0.7306 (t80) REVERT: Q 459 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8121 (mm-30) REVERT: Q 468 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7772 (mtm180) REVERT: Q 544 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7763 (tp-100) REVERT: R 14 TYR cc_start: 0.7713 (p90) cc_final: 0.6946 (p90) REVERT: R 24 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7293 (mtp85) REVERT: R 159 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8179 (p) REVERT: R 160 LYS cc_start: 0.8137 (mppt) cc_final: 0.7787 (mppt) REVERT: R 192 ARG cc_start: 0.7343 (tpp80) cc_final: 0.6065 (tpp80) REVERT: R 245 LEU cc_start: 0.7586 (pp) cc_final: 0.7247 (mp) REVERT: R 270 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6809 (tt) REVERT: R 283 ASN cc_start: 0.7645 (m110) cc_final: 0.7269 (m-40) REVERT: R 294 LYS cc_start: 0.8120 (tppt) cc_final: 0.7455 (mptt) REVERT: R 417 VAL cc_start: 0.8333 (t) cc_final: 0.8093 (p) REVERT: R 508 LYS cc_start: 0.7965 (mttp) cc_final: 0.7764 (mttp) REVERT: R 536 ARG cc_start: 0.7711 (ttm170) cc_final: 0.7288 (ttt90) REVERT: R 550 MET cc_start: 0.8117 (ppp) cc_final: 0.7521 (ppp) REVERT: R 559 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8069 (mtmt) outliers start: 112 outliers final: 94 residues processed: 1666 average time/residue: 0.6513 time to fit residues: 1751.8577 Evaluate side-chains 1716 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1612 time to evaluate : 5.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 183 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 342 LYS Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 168 ASN Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 319 LEU Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 404 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 597 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 248 GLU Chi-restraints excluded: chain N residue 267 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 297 ASN Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 483 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 297 ASN Chi-restraints excluded: chain O residue 313 ASP Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 384 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 521 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 289 ASN Chi-restraints excluded: chain P residue 297 ASN Chi-restraints excluded: chain P residue 303 ASP Chi-restraints excluded: chain P residue 344 LYS Chi-restraints excluded: chain P residue 396 LEU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 285 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 374 VAL Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain Q residue 423 LYS Chi-restraints excluded: chain Q residue 525 VAL Chi-restraints excluded: chain Q residue 550 MET Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 200 ASN Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 472 THR Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 517 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 387 optimal weight: 2.9990 chunk 501 optimal weight: 0.0470 chunk 672 optimal weight: 0.9990 chunk 193 optimal weight: 0.1980 chunk 582 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 632 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 649 optimal weight: 0.4980 chunk 80 optimal weight: 0.2980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS E 24 GLN E 154 ASN G 247 GLN I 365 GLN K 278 HIS O 187 ASN Q 443 GLN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104149 restraints weight = 96037.055| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.65 r_work: 0.3101 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 66064 Z= 0.125 Angle : 0.477 14.036 89371 Z= 0.239 Chirality : 0.039 0.179 9710 Planarity : 0.003 0.068 11449 Dihedral : 8.133 173.672 9438 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.29 % Allowed : 17.46 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.33 (0.10), residues: 7933 helix: 0.83 (0.10), residues: 3029 sheet: 1.12 (0.17), residues: 1025 loop : -1.50 (0.09), residues: 3879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 340 HIS 0.004 0.000 HIS K 278 PHE 0.023 0.001 PHE K 262 TYR 0.026 0.001 TYR R 258 ARG 0.016 0.000 ARG Q 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24094.02 seconds wall clock time: 417 minutes 19.21 seconds (25039.21 seconds total)