Starting phenix.real_space_refine on Sat Feb 24 10:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj9_25159/02_2024/7sj9_25159_updated.pdb" } resolution = 3.8 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= 0.000 sd= 1.000 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 36 5.49 5 Mg 12 5.21 5 S 296 5.16 5 C 27204 2.51 5 N 7388 2.21 5 O 8304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "E PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "H ASP 26": "OD1" <-> "OD2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I ASP 39": "OD1" <-> "OD2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I ARG 359": "NH1" <-> "NH2" Residue "I GLU 383": "OE1" <-> "OE2" Residue "I GLU 401": "OE1" <-> "OE2" Residue "I ASP 404": "OD1" <-> "OD2" Residue "I GLU 405": "OE1" <-> "OE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J ASP 245": "OD1" <-> "OD2" Residue "J GLU 411": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K ASP 199": "OD1" <-> "OD2" Residue "K TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "L GLU 3": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L ASP 199": "OD1" <-> "OD2" Residue "L TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 411": "OE1" <-> "OE2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 43240 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "L" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.12, per 1000 atoms: 0.53 Number of scatterers: 43240 At special positions: 0 Unit cell: (168.36, 112.24, 212.52, 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 296 16.00 P 36 15.00 Mg 12 11.99 O 8304 8.00 N 7388 7.00 C 27204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.86 Conformation dependent library (CDL) restraints added in 8.9 seconds 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 233 helices and 30 sheets defined 46.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.89 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.750A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 183 through 196 removed outlier: 5.062A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.677A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.735A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 126 removed outlier: 4.612A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 241 removed outlier: 4.832A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 372 through 389 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 426 Processing helix chain 'C' and resid 10 through 27 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.781A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 Processing helix chain 'C' and resid 183 through 196 removed outlier: 5.084A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.676A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 383 through 400 Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.755A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 126 removed outlier: 4.562A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.822A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 323 through 335 Processing helix chain 'D' and resid 372 through 389 Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 405 through 427 Processing helix chain 'E' and resid 10 through 27 Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 111 through 127 removed outlier: 4.667A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 Processing helix chain 'E' and resid 183 through 196 removed outlier: 5.071A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.649A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 258 Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 383 through 400 Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.046A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 11 through 28 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 126 removed outlier: 4.588A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 241 removed outlier: 4.885A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 323 through 335 Processing helix chain 'F' and resid 372 through 389 Processing helix chain 'F' and resid 395 through 399 Processing helix chain 'F' and resid 405 through 427 Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 45 removed outlier: 3.613A pdb=" N GLU G 45 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 126 removed outlier: 4.600A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 158 Processing helix chain 'G' and resid 181 through 195 Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 241 removed outlier: 4.806A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 286 through 293 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 372 through 389 Processing helix chain 'G' and resid 395 through 401 removed outlier: 3.736A pdb=" N GLU G 401 " --> pdb=" O TRP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 426 Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 45 removed outlier: 3.625A pdb=" N GLU H 45 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 111 No H-bonds generated for 'chain 'H' and resid 109 through 111' Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 142 through 158 Processing helix chain 'H' and resid 181 through 195 Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 241 removed outlier: 4.796A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 293 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 323 through 335 Processing helix chain 'H' and resid 372 through 389 Processing helix chain 'H' and resid 395 through 399 Processing helix chain 'H' and resid 405 through 426 Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 126 removed outlier: 4.703A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 158 Processing helix chain 'I' and resid 181 through 195 Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 241 removed outlier: 4.790A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 293 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 323 through 335 Processing helix chain 'I' and resid 372 through 389 Processing helix chain 'I' and resid 395 through 401 removed outlier: 3.715A pdb=" N GLU I 401 " --> pdb=" O TRP I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 426 Processing helix chain 'J' and resid 10 through 27 Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 112 through 128 removed outlier: 4.625A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 Processing helix chain 'J' and resid 183 through 196 removed outlier: 5.088A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 215 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.700A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 258 Processing helix chain 'J' and resid 278 through 281 No H-bonds generated for 'chain 'J' and resid 278 through 281' Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 383 through 400 Processing helix chain 'J' and resid 405 through 411 removed outlier: 3.876A pdb=" N GLU J 411 " --> pdb=" O TRP J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 27 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 72 through 80 Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.781A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 Processing helix chain 'K' and resid 183 through 196 removed outlier: 5.060A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 215 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.737A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 383 through 400 Processing helix chain 'K' and resid 405 through 411 removed outlier: 3.797A pdb=" N GLU K 411 " --> pdb=" O TRP K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 27 Processing helix chain 'L' and resid 48 through 50 No H-bonds generated for 'chain 'L' and resid 48 through 50' Processing helix chain 'L' and resid 72 through 80 Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.636A pdb=" N ILE L 114 " --> pdb=" O GLY L 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ASP L 116 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 127 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN L 128 " --> pdb=" O LEU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 Processing helix chain 'L' and resid 183 through 196 removed outlier: 4.948A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.696A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 258 Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 383 through 400 Processing helix chain 'L' and resid 405 through 411 removed outlier: 3.812A pdb=" N GLU L 411 " --> pdb=" O TRP L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'M' and resid 17 through 28 Processing helix chain 'M' and resid 35 through 40 Processing helix chain 'M' and resid 42 through 51 Processing helix chain 'M' and resid 68 through 85 Processing helix chain 'M' and resid 93 through 97 Processing helix chain 'M' and resid 101 through 117 Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 35 through 40 Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 68 through 85 Processing helix chain 'N' and resid 93 through 97 Processing helix chain 'N' and resid 101 through 117 Processing helix chain 'N' and resid 126 through 130 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.003A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.042A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS B 137 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.746A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.145A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 271 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.048A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'C' and resid 269 through 273 Processing sheet with id= J, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.082A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA D 9 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS D 137 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N HIS D 137 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE D 167 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.772A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 199 through 201 removed outlier: 7.190A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 271 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.972A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'E' and resid 269 through 273 Processing sheet with id= P, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.043A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA F 9 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS F 137 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE F 163 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU F 135 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS F 137 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE F 167 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.904A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 199 through 201 removed outlier: 7.032A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA F 271 " --> pdb=" O SER F 365 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.124A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL G 5 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE G 133 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE G 7 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU G 135 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA G 9 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS G 137 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE G 163 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU G 135 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN G 165 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS G 137 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE G 167 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU G 198 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N SER G 168 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR G 200 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL G 170 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE G 202 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ASP G 203 " --> pdb=" O PRO G 268 " (cutoff:3.500A) removed outlier: 11.916A pdb=" N PHE G 270 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA G 271 " --> pdb=" O SER G 365 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.754A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.108A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA H 9 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS H 137 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 163 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU H 135 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS H 137 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE H 167 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU H 198 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER H 168 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR H 200 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL H 170 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE H 202 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP H 203 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 11.910A pdb=" N PHE H 270 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA H 271 " --> pdb=" O SER H 365 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.872A pdb=" N LYS H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.139A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL I 5 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE I 133 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE I 7 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU I 135 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA I 9 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS I 137 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE I 163 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU I 135 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN I 165 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N HIS I 137 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE I 167 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU I 198 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER I 168 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR I 200 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL I 170 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE I 202 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ASP I 203 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N PHE I 270 " --> pdb=" O ASP I 203 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA I 271 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.904A pdb=" N LYS I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.102A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA J 270 " --> pdb=" O MET J 203 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP J 205 " --> pdb=" O ALA J 270 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N TYR J 272 " --> pdb=" O ASP J 205 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE J 267 " --> pdb=" O THR J 381 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.153A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA K 270 " --> pdb=" O MET K 203 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP K 205 " --> pdb=" O ALA K 270 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N TYR K 272 " --> pdb=" O ASP K 205 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE K 267 " --> pdb=" O THR K 381 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR K 381 " --> pdb=" O PHE K 267 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AC, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.104A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA L 270 " --> pdb=" O MET L 203 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP L 205 " --> pdb=" O ALA L 270 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N TYR L 272 " --> pdb=" O ASP L 205 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE L 267 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 53 through 55 1884 hydrogen bonds defined for protein. 5013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 20.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10694 1.33 - 1.45: 9222 1.45 - 1.58: 23790 1.58 - 1.70: 60 1.70 - 1.82: 466 Bond restraints: 44232 Sorted by residual: bond pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.40e+01 bond pdb=" CA PRO I 358 " pdb=" C PRO I 358 " ideal model delta sigma weight residual 1.529 1.554 -0.025 1.08e-02 8.57e+03 5.49e+00 bond pdb=" CA ARG I 359 " pdb=" C ARG I 359 " ideal model delta sigma weight residual 1.527 1.556 -0.029 1.30e-02 5.92e+03 5.12e+00 bond pdb=" CA PRO G 358 " pdb=" C PRO G 358 " ideal model delta sigma weight residual 1.522 1.547 -0.026 1.18e-02 7.18e+03 4.73e+00 ... (remaining 44227 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.09: 763 104.09 - 111.58: 19387 111.58 - 119.07: 16030 119.07 - 126.55: 23273 126.55 - 134.04: 599 Bond angle restraints: 60052 Sorted by residual: angle pdb=" N ARG I 359 " pdb=" CA ARG I 359 " pdb=" C ARG I 359 " ideal model delta sigma weight residual 111.39 126.49 -15.10 1.38e+00 5.25e-01 1.20e+02 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.10 121.03 -10.93 1.49e+00 4.50e-01 5.39e+01 angle pdb=" CA PRO H 358 " pdb=" C PRO H 358 " pdb=" O PRO H 358 " ideal model delta sigma weight residual 121.38 115.94 5.44 7.70e-01 1.69e+00 4.99e+01 angle pdb=" CA PRO D 358 " pdb=" C PRO D 358 " pdb=" O PRO D 358 " ideal model delta sigma weight residual 121.38 115.97 5.41 7.70e-01 1.69e+00 4.93e+01 angle pdb=" N PRO D 358 " pdb=" CA PRO D 358 " pdb=" C PRO D 358 " ideal model delta sigma weight residual 113.12 122.57 -9.45 1.65e+00 3.67e-01 3.28e+01 ... (remaining 60047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 25870 34.10 - 68.19: 326 68.19 - 102.29: 50 102.29 - 136.38: 6 136.38 - 170.48: 18 Dihedral angle restraints: 26270 sinusoidal: 10506 harmonic: 15764 Sorted by residual: dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -120.25 -170.48 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.18 -166.55 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -129.48 -161.25 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 26267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 6407 0.113 - 0.226: 140 0.226 - 0.340: 4 0.340 - 0.453: 0 0.453 - 0.566: 1 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA ARG D 359 " pdb=" N ARG D 359 " pdb=" C ARG D 359 " pdb=" CB ARG D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG F 359 " pdb=" N ARG F 359 " pdb=" C ARG F 359 " pdb=" CB ARG F 359 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 6549 not shown) Planarity restraints: 7788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 357 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C PRO G 357 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO G 357 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO G 358 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 357 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C PRO B 357 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO B 357 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO B 358 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 357 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO I 357 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO I 357 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO I 358 " -0.019 2.00e-02 2.50e+03 ... (remaining 7785 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 679 2.63 - 3.20: 41670 3.20 - 3.76: 68873 3.76 - 4.33: 95958 4.33 - 4.90: 157396 Nonbonded interactions: 364576 Sorted by model distance: nonbonded pdb=" OG1 THR E 223 " pdb=" OE1 GLN G 245 " model vdw 2.061 2.440 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.065 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.067 2.170 nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 2.068 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.070 2.170 ... (remaining 364571 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' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'M' selection = chain 'N' } 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 group one per residue 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: 12.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 31.050 Check model and map are aligned: 0.720 Set scattering table: 0.410 Process input model: 118.940 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.003 0.049 44232 Z= 0.201 Angle : 0.670 15.102 60052 Z= 0.366 Chirality : 0.047 0.566 6552 Planarity : 0.005 0.094 7788 Dihedral : 13.669 170.480 16142 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.43 % Favored : 96.53 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 5394 helix: 1.19 (0.11), residues: 2484 sheet: -0.13 (0.19), residues: 786 loop : -1.18 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 397 HIS 0.011 0.001 HIS F 190 PHE 0.027 0.002 PHE J 343 TYR 0.018 0.002 TYR D 50 ARG 0.015 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1993 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1987 time to evaluate : 5.501 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.9237 (m110) cc_final: 0.8962 (m110) REVERT: A 155 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 166 LYS cc_start: 0.9230 (mtmm) cc_final: 0.9018 (mttp) REVERT: A 169 PHE cc_start: 0.9159 (m-10) cc_final: 0.8941 (m-10) REVERT: A 202 PHE cc_start: 0.8382 (m-80) cc_final: 0.7621 (m-80) REVERT: A 211 ASP cc_start: 0.8693 (t70) cc_final: 0.8109 (t0) REVERT: A 280 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8604 (ttpp) REVERT: A 306 ASP cc_start: 0.8933 (p0) cc_final: 0.7755 (p0) REVERT: A 308 ARG cc_start: 0.8817 (mtm110) cc_final: 0.8504 (mtm-85) REVERT: A 324 VAL cc_start: 0.8996 (t) cc_final: 0.8708 (p) REVERT: A 338 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8776 (mtmt) REVERT: A 392 ASP cc_start: 0.9116 (m-30) cc_final: 0.8842 (m-30) REVERT: A 417 GLU cc_start: 0.8885 (tt0) cc_final: 0.8615 (mt-10) REVERT: B 3 GLU cc_start: 0.8130 (mp0) cc_final: 0.7557 (mp0) REVERT: B 14 ASN cc_start: 0.9044 (m110) cc_final: 0.8643 (m110) REVERT: B 31 ASP cc_start: 0.8734 (t0) cc_final: 0.8419 (t0) REVERT: B 124 CYS cc_start: 0.8997 (m) cc_final: 0.8425 (p) REVERT: B 198 GLU cc_start: 0.8622 (pt0) cc_final: 0.8367 (pt0) REVERT: B 207 LEU cc_start: 0.9666 (mm) cc_final: 0.9282 (mt) REVERT: B 252 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8764 (mtpp) REVERT: B 288 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 297 LYS cc_start: 0.8913 (pttt) cc_final: 0.8685 (pttt) REVERT: B 298 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8404 (t0) REVERT: B 307 HIS cc_start: 0.9038 (m-70) cc_final: 0.8693 (m-70) REVERT: B 329 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8983 (mm-40) REVERT: B 331 LEU cc_start: 0.9485 (tp) cc_final: 0.7767 (tp) REVERT: B 375 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7108 (pp30) REVERT: B 376 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 379 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8542 (mtmt) REVERT: B 404 ASP cc_start: 0.8451 (p0) cc_final: 0.7840 (p0) REVERT: B 407 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 3 GLU cc_start: 0.7621 (mp0) cc_final: 0.7199 (mp0) REVERT: C 50 ASN cc_start: 0.8782 (t160) cc_final: 0.8451 (t0) REVERT: C 76 ASP cc_start: 0.9104 (m-30) cc_final: 0.8873 (m-30) REVERT: C 152 LEU cc_start: 0.9509 (tp) cc_final: 0.8998 (tp) REVERT: C 163 LYS cc_start: 0.8573 (mmpt) cc_final: 0.8040 (mmmt) REVERT: C 183 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8483 (mt-10) REVERT: C 211 ASP cc_start: 0.8868 (t0) cc_final: 0.8658 (t0) REVERT: C 280 LYS cc_start: 0.5111 (mmtt) cc_final: 0.4520 (mmtt) REVERT: C 324 VAL cc_start: 0.8388 (t) cc_final: 0.7784 (t) REVERT: C 376 CYS cc_start: 0.9071 (t) cc_final: 0.8648 (t) REVERT: C 377 MET cc_start: 0.8554 (ttp) cc_final: 0.7973 (tmm) REVERT: C 378 LEU cc_start: 0.9541 (mt) cc_final: 0.8972 (mt) REVERT: C 423 GLU cc_start: 0.8742 (mp0) cc_final: 0.8449 (mp0) REVERT: D 41 ASP cc_start: 0.8623 (p0) cc_final: 0.7843 (p0) REVERT: D 45 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7897 (mm-30) REVERT: D 154 LYS cc_start: 0.9572 (mmmm) cc_final: 0.9348 (mmmm) REVERT: D 195 ASN cc_start: 0.8806 (m-40) cc_final: 0.8340 (m110) REVERT: D 198 GLU cc_start: 0.8875 (pt0) cc_final: 0.8463 (pt0) REVERT: D 252 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8528 (ttmm) REVERT: D 298 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8341 (t0) REVERT: D 307 HIS cc_start: 0.9232 (m-70) cc_final: 0.8677 (m-70) REVERT: D 327 ASP cc_start: 0.9130 (m-30) cc_final: 0.8925 (m-30) REVERT: D 379 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8876 (mtmt) REVERT: D 404 ASP cc_start: 0.8915 (p0) cc_final: 0.8671 (p0) REVERT: D 407 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8330 (mt-10) REVERT: E 69 ASP cc_start: 0.9006 (t0) cc_final: 0.8434 (t0) REVERT: E 71 GLU cc_start: 0.7879 (pt0) cc_final: 0.7114 (pt0) REVERT: E 76 ASP cc_start: 0.9024 (m-30) cc_final: 0.8789 (m-30) REVERT: E 88 HIS cc_start: 0.8838 (t70) cc_final: 0.8254 (t70) REVERT: E 150 THR cc_start: 0.9474 (m) cc_final: 0.9078 (t) REVERT: E 152 LEU cc_start: 0.9316 (tp) cc_final: 0.9004 (tp) REVERT: E 155 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8766 (mt-10) REVERT: E 164 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8506 (mmmm) REVERT: E 199 ASP cc_start: 0.8213 (m-30) cc_final: 0.7936 (m-30) REVERT: E 205 ASP cc_start: 0.8780 (t0) cc_final: 0.8533 (t0) REVERT: E 232 SER cc_start: 0.9427 (p) cc_final: 0.8932 (m) REVERT: E 245 ASP cc_start: 0.8990 (t70) cc_final: 0.8696 (t0) REVERT: E 269 LEU cc_start: 0.9084 (pp) cc_final: 0.8139 (pp) REVERT: E 284 GLU cc_start: 0.7646 (pp20) cc_final: 0.7299 (pp20) REVERT: E 293 ASN cc_start: 0.9300 (m-40) cc_final: 0.9087 (m-40) REVERT: E 324 VAL cc_start: 0.9058 (t) cc_final: 0.8822 (p) REVERT: E 341 ILE cc_start: 0.9323 (mp) cc_final: 0.8820 (mp) REVERT: E 357 TYR cc_start: 0.9060 (m-80) cc_final: 0.8810 (m-80) REVERT: E 392 ASP cc_start: 0.9444 (m-30) cc_final: 0.9051 (m-30) REVERT: E 396 ASP cc_start: 0.9025 (m-30) cc_final: 0.8747 (m-30) REVERT: E 411 GLU cc_start: 0.8124 (tp30) cc_final: 0.7809 (tp30) REVERT: E 414 GLU cc_start: 0.8430 (mp0) cc_final: 0.8145 (mp0) REVERT: E 415 GLU cc_start: 0.8005 (tt0) cc_final: 0.7719 (tt0) REVERT: E 423 GLU cc_start: 0.8858 (mp0) cc_final: 0.8517 (mp0) REVERT: E 425 MET cc_start: 0.9241 (mmm) cc_final: 0.8866 (mmt) REVERT: E 431 ASP cc_start: 0.8463 (m-30) cc_final: 0.8145 (m-30) REVERT: F 41 ASP cc_start: 0.8901 (p0) cc_final: 0.8255 (p0) REVERT: F 45 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7974 (mm-30) REVERT: F 106 TYR cc_start: 0.8924 (m-80) cc_final: 0.8644 (m-80) REVERT: F 147 MET cc_start: 0.9140 (tpp) cc_final: 0.8931 (tpp) REVERT: F 252 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8861 (ttmm) REVERT: F 323 MET cc_start: 0.8420 (mmm) cc_final: 0.8080 (mmm) REVERT: F 325 GLU cc_start: 0.9146 (tt0) cc_final: 0.8870 (tt0) REVERT: F 327 ASP cc_start: 0.9062 (m-30) cc_final: 0.8851 (m-30) REVERT: F 375 GLN cc_start: 0.8345 (pp30) cc_final: 0.7380 (pp30) REVERT: F 376 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8197 (mt-10) REVERT: F 379 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8793 (mtmt) REVERT: F 404 ASP cc_start: 0.8547 (p0) cc_final: 0.8203 (p0) REVERT: F 423 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8590 (tp-100) REVERT: G 3 GLU cc_start: 0.8322 (mp0) cc_final: 0.7887 (mp0) REVERT: G 92 PHE cc_start: 0.9480 (p90) cc_final: 0.9212 (p90) REVERT: G 106 TYR cc_start: 0.9232 (m-80) cc_final: 0.8792 (m-80) REVERT: G 129 CYS cc_start: 0.8837 (t) cc_final: 0.8613 (t) REVERT: G 159 TYR cc_start: 0.9127 (m-80) cc_final: 0.8858 (m-80) REVERT: G 198 GLU cc_start: 0.8996 (pt0) cc_final: 0.8438 (pt0) REVERT: G 208 TYR cc_start: 0.9143 (m-10) cc_final: 0.8866 (m-80) REVERT: G 281 TYR cc_start: 0.9279 (m-80) cc_final: 0.9006 (m-80) REVERT: G 284 LEU cc_start: 0.9070 (mt) cc_final: 0.8385 (pt) REVERT: G 291 GLN cc_start: 0.8681 (pp30) cc_final: 0.8327 (pp30) REVERT: G 350 LYS cc_start: 0.9299 (tptp) cc_final: 0.8617 (tppt) REVERT: G 362 LYS cc_start: 0.8861 (tmmt) cc_final: 0.8446 (tmmt) REVERT: G 407 GLU cc_start: 0.8222 (pt0) cc_final: 0.7874 (pt0) REVERT: G 410 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8791 (mt-10) REVERT: G 412 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8423 (tm-30) REVERT: H 19 LYS cc_start: 0.8721 (tptm) cc_final: 0.8155 (tptt) REVERT: H 194 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7804 (mm-30) REVERT: H 209 ASP cc_start: 0.9127 (t0) cc_final: 0.8058 (t0) REVERT: H 227 HIS cc_start: 0.9115 (t70) cc_final: 0.8646 (t70) REVERT: H 284 LEU cc_start: 0.9293 (mt) cc_final: 0.8820 (pt) REVERT: H 291 GLN cc_start: 0.8555 (pp30) cc_final: 0.7965 (pp30) REVERT: H 292 GLN cc_start: 0.8790 (tt0) cc_final: 0.8510 (tt0) REVERT: H 304 ASP cc_start: 0.9272 (t70) cc_final: 0.8976 (t0) REVERT: H 307 HIS cc_start: 0.9243 (m-70) cc_final: 0.8694 (m-70) REVERT: H 320 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7619 (mmm160) REVERT: H 325 GLU cc_start: 0.9283 (tt0) cc_final: 0.8934 (tt0) REVERT: H 329 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8831 (mm-40) REVERT: H 367 PHE cc_start: 0.9112 (t80) cc_final: 0.8902 (t80) REVERT: H 383 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8674 (tm-30) REVERT: H 406 MET cc_start: 0.8610 (tpp) cc_final: 0.8336 (tpp) REVERT: H 407 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8555 (mt-10) REVERT: H 421 GLU cc_start: 0.8720 (tp30) cc_final: 0.8410 (tp30) REVERT: I 19 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8745 (tptm) REVERT: I 92 PHE cc_start: 0.9416 (p90) cc_final: 0.9127 (p90) REVERT: I 106 TYR cc_start: 0.9338 (m-80) cc_final: 0.9121 (m-80) REVERT: I 114 ASP cc_start: 0.8927 (m-30) cc_final: 0.8697 (m-30) REVERT: I 117 LEU cc_start: 0.9496 (mm) cc_final: 0.9173 (mm) REVERT: I 121 ARG cc_start: 0.9097 (ttm110) cc_final: 0.8700 (ttm110) REVERT: I 136 THR cc_start: 0.9528 (m) cc_final: 0.9044 (p) REVERT: I 159 TYR cc_start: 0.9262 (m-80) cc_final: 0.8878 (m-80) REVERT: I 164 MET cc_start: 0.8342 (mtp) cc_final: 0.8141 (mtp) REVERT: I 195 ASN cc_start: 0.8581 (m-40) cc_final: 0.8327 (p0) REVERT: I 198 GLU cc_start: 0.8883 (pt0) cc_final: 0.7936 (pt0) REVERT: I 208 TYR cc_start: 0.9007 (m-10) cc_final: 0.8802 (m-80) REVERT: I 209 ASP cc_start: 0.9221 (t0) cc_final: 0.8247 (t0) REVERT: I 291 GLN cc_start: 0.8584 (pp30) cc_final: 0.8228 (pp30) REVERT: I 293 MET cc_start: 0.7756 (mtt) cc_final: 0.7454 (mtt) REVERT: I 295 ASP cc_start: 0.8831 (p0) cc_final: 0.8270 (p0) REVERT: I 304 ASP cc_start: 0.9248 (t70) cc_final: 0.9043 (t0) REVERT: I 307 HIS cc_start: 0.9233 (m-70) cc_final: 0.8828 (m-70) REVERT: I 325 GLU cc_start: 0.9119 (tt0) cc_final: 0.8524 (tt0) REVERT: I 329 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8898 (mm-40) REVERT: I 406 MET cc_start: 0.9167 (tpp) cc_final: 0.8606 (tpp) REVERT: I 421 GLU cc_start: 0.8940 (tp30) cc_final: 0.8643 (tp30) REVERT: I 425 TYR cc_start: 0.8117 (m-10) cc_final: 0.7909 (m-10) REVERT: J 88 HIS cc_start: 0.9068 (t70) cc_final: 0.8485 (t70) REVERT: J 120 ASP cc_start: 0.9299 (t70) cc_final: 0.9082 (t0) REVERT: J 124 LYS cc_start: 0.9537 (mtpp) cc_final: 0.9261 (mtpp) REVERT: J 128 GLN cc_start: 0.7918 (pp30) cc_final: 0.7679 (pp30) REVERT: J 150 THR cc_start: 0.9670 (m) cc_final: 0.9196 (p) REVERT: J 155 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9003 (mt-10) REVERT: J 161 TYR cc_start: 0.8539 (m-10) cc_final: 0.8300 (m-10) REVERT: J 168 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8424 (mt-10) REVERT: J 203 MET cc_start: 0.8550 (mmm) cc_final: 0.8100 (mmm) REVERT: J 293 ASN cc_start: 0.9629 (m-40) cc_final: 0.9324 (m-40) REVERT: J 313 MET cc_start: 0.8108 (mpp) cc_final: 0.7756 (mtm) REVERT: J 341 ILE cc_start: 0.9024 (mp) cc_final: 0.8695 (mp) REVERT: J 396 ASP cc_start: 0.8825 (m-30) cc_final: 0.8619 (m-30) REVERT: J 413 MET cc_start: 0.8142 (mtp) cc_final: 0.7888 (ttm) REVERT: J 417 GLU cc_start: 0.8321 (pt0) cc_final: 0.7819 (pt0) REVERT: K 1 MET cc_start: 0.6789 (tmm) cc_final: 0.6555 (tmm) REVERT: K 36 MET cc_start: 0.8532 (ttm) cc_final: 0.8328 (ttt) REVERT: K 88 HIS cc_start: 0.9064 (t70) cc_final: 0.8591 (t-170) REVERT: K 90 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8371 (mm-30) REVERT: K 112 LYS cc_start: 0.9072 (pttt) cc_final: 0.8718 (pttt) REVERT: K 150 THR cc_start: 0.9615 (m) cc_final: 0.9197 (p) REVERT: K 155 GLU cc_start: 0.9062 (pt0) cc_final: 0.8381 (pp20) REVERT: K 214 ARG cc_start: 0.8920 (tmm160) cc_final: 0.8677 (ttp80) REVERT: K 286 LEU cc_start: 0.9076 (mt) cc_final: 0.8678 (mt) REVERT: K 308 ARG cc_start: 0.9220 (mtm110) cc_final: 0.8910 (mtm-85) REVERT: K 343 PHE cc_start: 0.8720 (m-80) cc_final: 0.8325 (m-80) REVERT: K 417 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8541 (mt-10) REVERT: L 88 HIS cc_start: 0.8838 (t70) cc_final: 0.8399 (t-90) REVERT: L 150 THR cc_start: 0.9591 (m) cc_final: 0.9318 (p) REVERT: L 155 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8513 (mt-10) REVERT: L 290 GLU cc_start: 0.9346 (tt0) cc_final: 0.9044 (mt-10) REVERT: L 313 MET cc_start: 0.8330 (mpp) cc_final: 0.7924 (mtm) REVERT: L 377 MET cc_start: 0.9026 (ttm) cc_final: 0.8699 (ttp) REVERT: L 396 ASP cc_start: 0.8868 (m-30) cc_final: 0.8663 (m-30) REVERT: L 411 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7657 (mt-10) REVERT: L 430 LYS cc_start: 0.9483 (pttp) cc_final: 0.9185 (pttm) REVERT: M 29 HIS cc_start: 0.9335 (t-90) cc_final: 0.8921 (t-90) REVERT: M 57 HIS cc_start: 0.7605 (t-170) cc_final: 0.7362 (t70) REVERT: M 84 LYS cc_start: 0.9422 (ttmt) cc_final: 0.9070 (ttpt) REVERT: M 100 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7662 (mmtp) REVERT: M 109 GLN cc_start: 0.8879 (pt0) cc_final: 0.8649 (pt0) REVERT: N 29 HIS cc_start: 0.9259 (t-90) cc_final: 0.8933 (t-90) REVERT: N 57 HIS cc_start: 0.7858 (t-170) cc_final: 0.7160 (t-170) REVERT: N 60 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7908 (mmtt) REVERT: N 62 LYS cc_start: 0.8457 (mttt) cc_final: 0.8215 (mttp) REVERT: N 84 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8697 (ttpt) REVERT: N 109 GLN cc_start: 0.8715 (pt0) cc_final: 0.8250 (pt0) REVERT: N 118 ASN cc_start: 0.8008 (m-40) cc_final: 0.7633 (m110) outliers start: 6 outliers final: 0 residues processed: 1992 average time/residue: 0.5739 time to fit residues: 1842.2341 Evaluate side-chains 1505 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1502 time to evaluate : 5.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain D residue 298 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 10.0000 chunk 406 optimal weight: 0.1980 chunk 225 optimal weight: 20.0000 chunk 138 optimal weight: 0.0470 chunk 274 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 chunk 420 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 chunk 312 optimal weight: 6.9990 chunk 486 optimal weight: 0.4980 overall best weight: 1.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN D 43 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 245 GLN D 292 GLN D 337 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 227 HIS G 292 GLN G 298 ASN H 256 ASN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 347 ASN I 43 GLN I 165 ASN ** I 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 HIS ** J 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 HIS ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS ** L 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS M 125 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44232 Z= 0.185 Angle : 0.609 10.359 60052 Z= 0.309 Chirality : 0.044 0.238 6552 Planarity : 0.005 0.071 7788 Dihedral : 11.613 169.411 6075 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.11 % Allowed : 14.93 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 5394 helix: 1.08 (0.10), residues: 2526 sheet: 0.27 (0.20), residues: 774 loop : -1.28 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 344 HIS 0.009 0.001 HIS I 57 PHE 0.025 0.001 PHE I 367 TYR 0.024 0.001 TYR D 50 ARG 0.008 0.001 ARG J 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1607 time to evaluate : 5.548 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7817 (ptt) cc_final: 0.7615 (ptt) REVERT: A 18 ASN cc_start: 0.9185 (m110) cc_final: 0.8979 (m110) REVERT: A 152 LEU cc_start: 0.9415 (tp) cc_final: 0.9004 (tp) REVERT: A 211 ASP cc_start: 0.8586 (t70) cc_final: 0.8125 (t0) REVERT: A 286 LEU cc_start: 0.9274 (mt) cc_final: 0.9038 (mt) REVERT: A 317 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9202 (mt) REVERT: A 324 VAL cc_start: 0.9056 (t) cc_final: 0.8761 (p) REVERT: A 335 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9399 (tp) REVERT: A 338 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8875 (mtmt) REVERT: A 377 MET cc_start: 0.9098 (tmm) cc_final: 0.8741 (tmm) REVERT: A 411 GLU cc_start: 0.8542 (tp30) cc_final: 0.8217 (tp30) REVERT: A 414 GLU cc_start: 0.8812 (mp0) cc_final: 0.8369 (mp0) REVERT: A 415 GLU cc_start: 0.9026 (mp0) cc_final: 0.8791 (tt0) REVERT: A 430 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9174 (pttm) REVERT: B 14 ASN cc_start: 0.8905 (m110) cc_final: 0.8630 (m110) REVERT: B 124 CYS cc_start: 0.8932 (m) cc_final: 0.8439 (p) REVERT: B 198 GLU cc_start: 0.8455 (pt0) cc_final: 0.8206 (pt0) REVERT: B 213 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8204 (ttm170) REVERT: B 291 GLN cc_start: 0.8729 (pm20) cc_final: 0.8412 (pm20) REVERT: B 293 MET cc_start: 0.8453 (mmm) cc_final: 0.8116 (mtt) REVERT: B 298 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8543 (t0) REVERT: B 329 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8888 (mm-40) REVERT: B 331 LEU cc_start: 0.9481 (tp) cc_final: 0.9256 (tp) REVERT: B 367 PHE cc_start: 0.9225 (t80) cc_final: 0.8996 (t80) REVERT: B 375 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8017 (pp30) REVERT: B 412 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 50 ASN cc_start: 0.8770 (t0) cc_final: 0.8520 (t0) REVERT: C 76 ASP cc_start: 0.9127 (m-30) cc_final: 0.8821 (m-30) REVERT: C 150 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9249 (m) REVERT: C 256 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8843 (tt0) REVERT: C 280 LYS cc_start: 0.5098 (mmtt) cc_final: 0.3813 (ttpt) REVERT: C 335 ILE cc_start: 0.9577 (mm) cc_final: 0.9227 (tp) REVERT: C 376 CYS cc_start: 0.9090 (t) cc_final: 0.8756 (t) REVERT: C 377 MET cc_start: 0.8817 (ttp) cc_final: 0.7916 (tmm) REVERT: C 378 LEU cc_start: 0.9517 (mt) cc_final: 0.9017 (mt) REVERT: D 19 LYS cc_start: 0.8881 (tptt) cc_final: 0.8261 (tptm) REVERT: D 41 ASP cc_start: 0.8721 (p0) cc_final: 0.7780 (p0) REVERT: D 45 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7829 (mm-30) REVERT: D 124 CYS cc_start: 0.8852 (m) cc_final: 0.8479 (p) REVERT: D 156 ARG cc_start: 0.8981 (ttm-80) cc_final: 0.8617 (ttm170) REVERT: D 195 ASN cc_start: 0.8473 (m-40) cc_final: 0.7988 (m110) REVERT: D 198 GLU cc_start: 0.8664 (pt0) cc_final: 0.8461 (pt0) REVERT: D 213 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8020 (ttm170) REVERT: D 252 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8580 (ttmm) REVERT: D 307 HIS cc_start: 0.9181 (m-70) cc_final: 0.8773 (m-70) REVERT: D 323 MET cc_start: 0.8287 (mmm) cc_final: 0.8084 (mmm) REVERT: D 327 ASP cc_start: 0.9084 (m-30) cc_final: 0.8837 (m-30) REVERT: D 375 GLN cc_start: 0.8583 (pp30) cc_final: 0.7581 (pp30) REVERT: D 379 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8886 (mtmt) REVERT: D 390 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7550 (ptt90) REVERT: D 412 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8595 (tm-30) REVERT: D 417 ASP cc_start: 0.9255 (m-30) cc_final: 0.8893 (m-30) REVERT: D 424 GLN cc_start: 0.9462 (OUTLIER) cc_final: 0.9171 (tm-30) REVERT: E 16 ILE cc_start: 0.9153 (mm) cc_final: 0.8708 (mm) REVERT: E 20 CYS cc_start: 0.8189 (m) cc_final: 0.7885 (m) REVERT: E 76 ASP cc_start: 0.9099 (m-30) cc_final: 0.8806 (m-30) REVERT: E 88 HIS cc_start: 0.8765 (t70) cc_final: 0.8112 (t-170) REVERT: E 90 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 150 THR cc_start: 0.9507 (m) cc_final: 0.9165 (p) REVERT: E 152 LEU cc_start: 0.9328 (tp) cc_final: 0.8843 (tp) REVERT: E 155 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8781 (mt-10) REVERT: E 214 ARG cc_start: 0.9160 (tmm-80) cc_final: 0.8951 (tmm-80) REVERT: E 232 SER cc_start: 0.9469 (p) cc_final: 0.9143 (m) REVERT: E 245 ASP cc_start: 0.8962 (t70) cc_final: 0.8626 (t0) REVERT: E 269 LEU cc_start: 0.8781 (pp) cc_final: 0.8551 (pp) REVERT: E 293 ASN cc_start: 0.9342 (m-40) cc_final: 0.9125 (m110) REVERT: E 301 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8436 (tp40) REVERT: E 357 TYR cc_start: 0.9077 (m-80) cc_final: 0.8830 (m-80) REVERT: E 411 GLU cc_start: 0.8476 (tp30) cc_final: 0.8177 (tp30) REVERT: E 417 GLU cc_start: 0.8103 (pm20) cc_final: 0.7541 (pm20) REVERT: E 430 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9200 (ttpp) REVERT: E 431 ASP cc_start: 0.8315 (m-30) cc_final: 0.7793 (m-30) REVERT: F 41 ASP cc_start: 0.8899 (p0) cc_final: 0.7956 (p0) REVERT: F 45 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7949 (mm-30) REVERT: F 106 TYR cc_start: 0.8983 (m-80) cc_final: 0.8773 (m-10) REVERT: F 170 VAL cc_start: 0.9444 (t) cc_final: 0.9223 (m) REVERT: F 209 ASP cc_start: 0.8562 (t0) cc_final: 0.8195 (t0) REVERT: F 252 LYS cc_start: 0.9252 (mtpp) cc_final: 0.8851 (ttmm) REVERT: F 325 GLU cc_start: 0.9043 (tt0) cc_final: 0.8742 (tt0) REVERT: F 329 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8383 (mm-40) REVERT: F 341 PHE cc_start: 0.9030 (m-80) cc_final: 0.8123 (m-80) REVERT: F 348 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7344 (p0) REVERT: F 375 GLN cc_start: 0.8309 (pp30) cc_final: 0.7331 (pp30) REVERT: F 376 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8089 (mt-10) REVERT: F 379 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8775 (mtmt) REVERT: F 403 MET cc_start: 0.7914 (mtp) cc_final: 0.7657 (mtp) REVERT: F 423 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8578 (tp-100) REVERT: G 3 GLU cc_start: 0.8332 (mp0) cc_final: 0.7877 (mp0) REVERT: G 164 MET cc_start: 0.8799 (ttm) cc_final: 0.7930 (mtp) REVERT: G 198 GLU cc_start: 0.8857 (pt0) cc_final: 0.8550 (pt0) REVERT: G 200 TYR cc_start: 0.9081 (m-10) cc_final: 0.8557 (m-80) REVERT: G 284 LEU cc_start: 0.9074 (mt) cc_final: 0.8433 (pp) REVERT: G 292 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: G 329 GLN cc_start: 0.8850 (mm110) cc_final: 0.8402 (mm-40) REVERT: G 362 LYS cc_start: 0.8875 (tmmt) cc_final: 0.8055 (tmmt) REVERT: G 406 MET cc_start: 0.8939 (tpt) cc_final: 0.8356 (tpt) REVERT: G 407 GLU cc_start: 0.8378 (pt0) cc_final: 0.7706 (pt0) REVERT: G 410 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8723 (mt-10) REVERT: G 412 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8581 (tp30) REVERT: G 421 GLU cc_start: 0.8760 (tp30) cc_final: 0.8387 (tp30) REVERT: H 194 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7705 (mm-30) REVERT: H 198 GLU cc_start: 0.8611 (pt0) cc_final: 0.8302 (pt0) REVERT: H 209 ASP cc_start: 0.9164 (t0) cc_final: 0.8724 (t0) REVERT: H 291 GLN cc_start: 0.8542 (pp30) cc_final: 0.8295 (pp30) REVERT: H 298 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8839 (t0) REVERT: H 304 ASP cc_start: 0.9194 (t70) cc_final: 0.8920 (t0) REVERT: H 307 HIS cc_start: 0.9434 (m-70) cc_final: 0.8876 (m-70) REVERT: H 406 MET cc_start: 0.8688 (tpp) cc_final: 0.8365 (tpp) REVERT: I 83 HIS cc_start: 0.8794 (m90) cc_final: 0.8298 (m90) REVERT: I 86 ARG cc_start: 0.8746 (tpp80) cc_final: 0.8514 (ttm-80) REVERT: I 114 ASP cc_start: 0.8943 (m-30) cc_final: 0.8728 (m-30) REVERT: I 195 ASN cc_start: 0.8693 (m-40) cc_final: 0.8338 (p0) REVERT: I 198 GLU cc_start: 0.8786 (pt0) cc_final: 0.8425 (pt0) REVERT: I 209 ASP cc_start: 0.9258 (t0) cc_final: 0.8793 (t70) REVERT: I 213 ARG cc_start: 0.9137 (ttm110) cc_final: 0.8249 (ttp-110) REVERT: I 284 LEU cc_start: 0.8927 (pt) cc_final: 0.8581 (pt) REVERT: I 293 MET cc_start: 0.7640 (mtt) cc_final: 0.7148 (mtt) REVERT: I 295 ASP cc_start: 0.9039 (p0) cc_final: 0.8653 (p0) REVERT: I 299 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: I 325 GLU cc_start: 0.9098 (tt0) cc_final: 0.8571 (tt0) REVERT: I 329 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8823 (mm-40) REVERT: I 379 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8879 (mttt) REVERT: I 417 ASP cc_start: 0.9348 (m-30) cc_final: 0.9143 (m-30) REVERT: I 421 GLU cc_start: 0.8872 (tp30) cc_final: 0.8662 (tp30) REVERT: I 423 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8829 (tp-100) REVERT: I 425 TYR cc_start: 0.7945 (m-10) cc_final: 0.7716 (m-10) REVERT: J 88 HIS cc_start: 0.8755 (t70) cc_final: 0.8205 (t70) REVERT: J 90 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8647 (mm-30) REVERT: J 120 ASP cc_start: 0.9305 (t70) cc_final: 0.9071 (t0) REVERT: J 124 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9283 (mtpp) REVERT: J 128 GLN cc_start: 0.7980 (pp30) cc_final: 0.7698 (pp30) REVERT: J 136 LEU cc_start: 0.9526 (mt) cc_final: 0.9302 (mp) REVERT: J 155 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9078 (mt-10) REVERT: J 168 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8369 (mt-10) REVERT: J 293 ASN cc_start: 0.9663 (m-40) cc_final: 0.9348 (m-40) REVERT: J 308 ARG cc_start: 0.9394 (mtm110) cc_final: 0.9122 (mtm-85) REVERT: J 313 MET cc_start: 0.8112 (mpp) cc_final: 0.7789 (mtm) REVERT: J 377 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8595 (ttm) REVERT: J 396 ASP cc_start: 0.8812 (m-30) cc_final: 0.8577 (m-30) REVERT: K 88 HIS cc_start: 0.9054 (t70) cc_final: 0.8219 (t70) REVERT: K 90 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8307 (mm-30) REVERT: K 108 TYR cc_start: 0.8952 (m-80) cc_final: 0.8608 (m-10) REVERT: K 155 GLU cc_start: 0.9050 (pt0) cc_final: 0.8678 (pp20) REVERT: K 214 ARG cc_start: 0.8849 (tmm160) cc_final: 0.8604 (ttp80) REVERT: K 300 ASN cc_start: 0.8793 (t160) cc_final: 0.8571 (t0) REVERT: K 308 ARG cc_start: 0.9194 (mtm110) cc_final: 0.8965 (mtm-85) REVERT: K 336 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8673 (mmmm) REVERT: K 388 TRP cc_start: 0.9047 (m100) cc_final: 0.8796 (m100) REVERT: K 392 ASP cc_start: 0.8939 (m-30) cc_final: 0.8694 (m-30) REVERT: K 414 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8531 (mm-30) REVERT: L 150 THR cc_start: 0.9372 (m) cc_final: 0.9062 (p) REVERT: L 155 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8881 (mt-10) REVERT: L 156 ARG cc_start: 0.9009 (mmp80) cc_final: 0.8677 (mmp80) REVERT: L 214 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7973 (ttp80) REVERT: L 290 GLU cc_start: 0.9371 (tt0) cc_final: 0.9063 (mt-10) REVERT: L 293 ASN cc_start: 0.9479 (m-40) cc_final: 0.9226 (p0) REVERT: L 313 MET cc_start: 0.8345 (mpp) cc_final: 0.7935 (mtm) REVERT: L 377 MET cc_start: 0.9028 (ttm) cc_final: 0.8798 (ttp) REVERT: L 396 ASP cc_start: 0.8848 (m-30) cc_final: 0.8647 (m-30) REVERT: M 14 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8040 (p0) REVERT: M 29 HIS cc_start: 0.9358 (t-90) cc_final: 0.8922 (t-90) REVERT: M 84 LYS cc_start: 0.9417 (ttmt) cc_final: 0.9046 (ttpt) REVERT: M 118 ASN cc_start: 0.7705 (m-40) cc_final: 0.7495 (m110) REVERT: N 29 HIS cc_start: 0.9305 (t-90) cc_final: 0.8896 (t-90) REVERT: N 57 HIS cc_start: 0.7924 (t-170) cc_final: 0.6849 (t-170) REVERT: N 62 LYS cc_start: 0.8443 (mttt) cc_final: 0.8154 (mttp) REVERT: N 84 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8719 (ttpt) REVERT: N 100 LYS cc_start: 0.7553 (mmmm) cc_final: 0.7061 (mmtp) REVERT: N 118 ASN cc_start: 0.8234 (m-40) cc_final: 0.7940 (m-40) outliers start: 98 outliers final: 55 residues processed: 1647 average time/residue: 0.5784 time to fit residues: 1535.9498 Evaluate side-chains 1502 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1433 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 420 GLU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain I residue 81 PHE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 55 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 405 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 487 optimal weight: 0.0670 chunk 526 optimal weight: 10.0000 chunk 434 optimal weight: 0.0270 chunk 483 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 391 optimal weight: 8.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 165 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN G 227 HIS G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 227 HIS H 256 ASN H 292 GLN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN I 245 GLN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN J 8 HIS J 139 HIS K 101 ASN ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 HIS ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 HIS N 102 GLN N 109 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44232 Z= 0.185 Angle : 0.582 9.945 60052 Z= 0.293 Chirality : 0.043 0.196 6552 Planarity : 0.004 0.065 7788 Dihedral : 11.476 169.694 6073 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.93 % Allowed : 17.41 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 5394 helix: 1.21 (0.11), residues: 2488 sheet: 0.49 (0.19), residues: 786 loop : -1.08 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 344 HIS 0.011 0.001 HIS F 190 PHE 0.021 0.001 PHE I 92 TYR 0.022 0.001 TYR E 172 ARG 0.012 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1674 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1538 time to evaluate : 5.074 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7762 (mp0) cc_final: 0.7528 (mp0) REVERT: A 211 ASP cc_start: 0.8631 (t70) cc_final: 0.8117 (t0) REVERT: A 218 ASP cc_start: 0.8731 (m-30) cc_final: 0.8308 (m-30) REVERT: A 280 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7673 (mtmm) REVERT: A 324 VAL cc_start: 0.9068 (t) cc_final: 0.8768 (p) REVERT: A 335 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9389 (tp) REVERT: A 377 MET cc_start: 0.9105 (tmm) cc_final: 0.8572 (tmm) REVERT: A 430 LYS cc_start: 0.9453 (ttpt) cc_final: 0.9165 (pttm) REVERT: B 124 CYS cc_start: 0.8899 (m) cc_final: 0.8464 (p) REVERT: B 201 CYS cc_start: 0.9154 (m) cc_final: 0.8901 (m) REVERT: B 213 ARG cc_start: 0.8619 (ttm110) cc_final: 0.8271 (ttp80) REVERT: B 282 ARG cc_start: 0.7659 (ptm-80) cc_final: 0.7291 (ptm-80) REVERT: B 293 MET cc_start: 0.8510 (mmm) cc_final: 0.8176 (mtt) REVERT: B 307 HIS cc_start: 0.9228 (m-70) cc_final: 0.8986 (m-70) REVERT: B 329 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8854 (mm-40) REVERT: B 350 LYS cc_start: 0.8715 (tppt) cc_final: 0.8423 (tptm) REVERT: B 367 PHE cc_start: 0.9244 (t80) cc_final: 0.8982 (t80) REVERT: B 375 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7327 (pp30) REVERT: B 379 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8696 (mtmt) REVERT: B 425 TYR cc_start: 0.8561 (m-10) cc_final: 0.8343 (m-10) REVERT: C 3 GLU cc_start: 0.7885 (mp0) cc_final: 0.7310 (mp0) REVERT: C 76 ASP cc_start: 0.9139 (m-30) cc_final: 0.8837 (m-30) REVERT: C 168 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7481 (mt-10) REVERT: C 207 GLU cc_start: 0.8496 (tt0) cc_final: 0.8163 (mt-10) REVERT: C 218 ASP cc_start: 0.9244 (m-30) cc_final: 0.8995 (m-30) REVERT: C 275 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9180 (m) REVERT: C 279 GLU cc_start: 0.8524 (pp20) cc_final: 0.8071 (pp20) REVERT: C 280 LYS cc_start: 0.3982 (mmtt) cc_final: 0.3192 (mmtt) REVERT: C 377 MET cc_start: 0.8907 (ttp) cc_final: 0.7816 (tmm) REVERT: C 378 LEU cc_start: 0.9528 (mt) cc_final: 0.9130 (mt) REVERT: D 19 LYS cc_start: 0.8758 (tptt) cc_final: 0.8529 (tptm) REVERT: D 41 ASP cc_start: 0.8773 (p0) cc_final: 0.8520 (p0) REVERT: D 124 CYS cc_start: 0.8837 (m) cc_final: 0.8491 (p) REVERT: D 156 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8546 (ttm170) REVERT: D 213 ARG cc_start: 0.8644 (ttm110) cc_final: 0.8437 (mtm110) REVERT: D 252 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8533 (ttmm) REVERT: D 307 HIS cc_start: 0.9231 (m-70) cc_final: 0.8791 (m-70) REVERT: D 327 ASP cc_start: 0.9087 (m-30) cc_final: 0.8861 (m-30) REVERT: D 350 LYS cc_start: 0.8697 (tptm) cc_final: 0.8184 (tppt) REVERT: D 375 GLN cc_start: 0.8553 (pp30) cc_final: 0.7414 (pp30) REVERT: D 379 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8844 (mtmt) REVERT: D 390 ARG cc_start: 0.7870 (ptt-90) cc_final: 0.7406 (ptt90) REVERT: D 424 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9233 (tm-30) REVERT: E 76 ASP cc_start: 0.9092 (m-30) cc_final: 0.8767 (m-30) REVERT: E 88 HIS cc_start: 0.8720 (t70) cc_final: 0.8263 (t70) REVERT: E 90 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8373 (mm-30) REVERT: E 150 THR cc_start: 0.9441 (m) cc_final: 0.9121 (p) REVERT: E 152 LEU cc_start: 0.9365 (tp) cc_final: 0.8809 (tp) REVERT: E 155 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8790 (mt-10) REVERT: E 199 ASP cc_start: 0.8181 (m-30) cc_final: 0.7947 (m-30) REVERT: E 232 SER cc_start: 0.9490 (p) cc_final: 0.8890 (m) REVERT: E 245 ASP cc_start: 0.8912 (t70) cc_final: 0.8558 (t0) REVERT: E 269 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8548 (pp) REVERT: E 290 GLU cc_start: 0.8711 (pt0) cc_final: 0.8294 (pt0) REVERT: E 301 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8497 (tp40) REVERT: E 357 TYR cc_start: 0.9101 (m-80) cc_final: 0.8836 (m-80) REVERT: E 377 MET cc_start: 0.8896 (ttp) cc_final: 0.7897 (tmm) REVERT: E 417 GLU cc_start: 0.8003 (pm20) cc_final: 0.7719 (pm20) REVERT: E 430 LYS cc_start: 0.9494 (ttpt) cc_final: 0.9205 (ttpp) REVERT: E 431 ASP cc_start: 0.8294 (m-30) cc_final: 0.7797 (m-30) REVERT: F 41 ASP cc_start: 0.8891 (p0) cc_final: 0.8564 (p0) REVERT: F 86 ARG cc_start: 0.5429 (mmt180) cc_final: 0.4833 (tpt170) REVERT: F 106 TYR cc_start: 0.8847 (m-80) cc_final: 0.8594 (m-10) REVERT: F 170 VAL cc_start: 0.9441 (t) cc_final: 0.9213 (m) REVERT: F 198 GLU cc_start: 0.7733 (pp20) cc_final: 0.7316 (pp20) REVERT: F 209 ASP cc_start: 0.8590 (t0) cc_final: 0.8261 (t0) REVERT: F 252 LYS cc_start: 0.9268 (mtpp) cc_final: 0.8996 (ttmm) REVERT: F 266 PHE cc_start: 0.8649 (m-10) cc_final: 0.8404 (m-10) REVERT: F 325 GLU cc_start: 0.9063 (tt0) cc_final: 0.8808 (tt0) REVERT: F 329 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8578 (mm-40) REVERT: F 341 PHE cc_start: 0.9030 (m-80) cc_final: 0.8792 (m-80) REVERT: F 375 GLN cc_start: 0.8319 (pp30) cc_final: 0.7279 (pp30) REVERT: F 376 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7964 (mt-10) REVERT: F 379 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8829 (mtmt) REVERT: F 406 MET cc_start: 0.8590 (tmm) cc_final: 0.8229 (tmm) REVERT: F 423 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8562 (tp-100) REVERT: G 164 MET cc_start: 0.8765 (ttm) cc_final: 0.7894 (mtp) REVERT: G 200 TYR cc_start: 0.9055 (m-10) cc_final: 0.8633 (m-80) REVERT: G 282 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7025 (ptm-80) REVERT: G 284 LEU cc_start: 0.9018 (mt) cc_final: 0.8501 (mt) REVERT: G 299 MET cc_start: 0.9178 (tpp) cc_final: 0.8962 (tpp) REVERT: G 321 MET cc_start: 0.8947 (ptp) cc_final: 0.8594 (ptp) REVERT: G 406 MET cc_start: 0.8826 (tpt) cc_final: 0.8152 (tpt) REVERT: G 407 GLU cc_start: 0.8371 (pt0) cc_final: 0.7534 (pt0) REVERT: G 410 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8636 (mt-10) REVERT: G 421 GLU cc_start: 0.8726 (tp30) cc_final: 0.8354 (tp30) REVERT: G 425 TYR cc_start: 0.8177 (m-10) cc_final: 0.7485 (m-10) REVERT: H 53 GLU cc_start: 0.8488 (tp30) cc_final: 0.8269 (tp30) REVERT: H 69 GLU cc_start: 0.8211 (pp20) cc_final: 0.7963 (pp20) REVERT: H 194 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7628 (mm-30) REVERT: H 203 ASP cc_start: 0.7483 (t70) cc_final: 0.7204 (t70) REVERT: H 213 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8633 (tmm-80) REVERT: H 292 GLN cc_start: 0.9038 (tt0) cc_final: 0.8770 (tt0) REVERT: H 304 ASP cc_start: 0.9145 (t70) cc_final: 0.8809 (t0) REVERT: H 307 HIS cc_start: 0.9495 (m-70) cc_final: 0.8964 (m-70) REVERT: H 331 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9222 (tp) REVERT: H 406 MET cc_start: 0.8626 (tpp) cc_final: 0.8292 (tpp) REVERT: H 407 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8233 (mt-10) REVERT: H 421 GLU cc_start: 0.8641 (tp30) cc_final: 0.8039 (tp30) REVERT: I 59 TYR cc_start: 0.9004 (m-80) cc_final: 0.8801 (m-80) REVERT: I 194 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7841 (mp0) REVERT: I 198 GLU cc_start: 0.8770 (pt0) cc_final: 0.8337 (pt0) REVERT: I 203 ASP cc_start: 0.7546 (t70) cc_final: 0.7324 (t70) REVERT: I 209 ASP cc_start: 0.9220 (t0) cc_final: 0.8987 (t0) REVERT: I 213 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8400 (ttp80) REVERT: I 291 GLN cc_start: 0.8579 (pp30) cc_final: 0.8049 (pp30) REVERT: I 304 ASP cc_start: 0.9209 (t0) cc_final: 0.8953 (t70) REVERT: I 325 GLU cc_start: 0.9105 (tt0) cc_final: 0.8611 (tt0) REVERT: I 329 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8778 (mm-40) REVERT: I 417 ASP cc_start: 0.9364 (m-30) cc_final: 0.8916 (m-30) REVERT: I 423 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8726 (tp-100) REVERT: J 88 HIS cc_start: 0.8751 (t70) cc_final: 0.8175 (t70) REVERT: J 90 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8615 (mm-30) REVERT: J 120 ASP cc_start: 0.9321 (t70) cc_final: 0.9086 (t0) REVERT: J 124 LYS cc_start: 0.9538 (mtpp) cc_final: 0.9271 (mtpp) REVERT: J 128 GLN cc_start: 0.7945 (pp30) cc_final: 0.7660 (pp30) REVERT: J 150 THR cc_start: 0.9129 (m) cc_final: 0.8910 (p) REVERT: J 155 GLU cc_start: 0.9482 (mt-10) cc_final: 0.8972 (mt-10) REVERT: J 168 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8353 (mt-10) REVERT: J 205 ASP cc_start: 0.8539 (t70) cc_final: 0.8318 (t0) REVERT: J 214 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7403 (ttp80) REVERT: J 290 GLU cc_start: 0.9323 (pt0) cc_final: 0.8956 (pt0) REVERT: J 293 ASN cc_start: 0.9650 (m-40) cc_final: 0.9367 (m-40) REVERT: J 308 ARG cc_start: 0.9425 (mtm110) cc_final: 0.9151 (mtm-85) REVERT: J 313 MET cc_start: 0.8089 (mpp) cc_final: 0.7746 (mtm) REVERT: J 377 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (ttm) REVERT: J 388 TRP cc_start: 0.9088 (m100) cc_final: 0.8735 (m100) REVERT: J 396 ASP cc_start: 0.8795 (m-30) cc_final: 0.8549 (m-30) REVERT: J 413 MET cc_start: 0.8530 (mtp) cc_final: 0.8008 (ttm) REVERT: K 1 MET cc_start: 0.6461 (tmm) cc_final: 0.6209 (tmm) REVERT: K 88 HIS cc_start: 0.9094 (t70) cc_final: 0.8403 (t70) REVERT: K 90 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8480 (mm-30) REVERT: K 108 TYR cc_start: 0.8894 (m-80) cc_final: 0.8585 (m-10) REVERT: K 155 GLU cc_start: 0.9216 (pt0) cc_final: 0.8750 (pp20) REVERT: K 214 ARG cc_start: 0.8847 (tmm160) cc_final: 0.8573 (ttp80) REVERT: K 290 GLU cc_start: 0.9377 (pt0) cc_final: 0.8993 (pp20) REVERT: K 293 ASN cc_start: 0.9523 (m-40) cc_final: 0.9251 (p0) REVERT: K 300 ASN cc_start: 0.8815 (t160) cc_final: 0.8573 (t0) REVERT: K 308 ARG cc_start: 0.9236 (mtm110) cc_final: 0.9028 (mtm-85) REVERT: K 311 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8919 (tppt) REVERT: K 313 MET cc_start: 0.8959 (mtm) cc_final: 0.8263 (mtm) REVERT: K 336 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8770 (mmmm) REVERT: K 388 TRP cc_start: 0.9079 (m100) cc_final: 0.8878 (m100) REVERT: L 22 GLU cc_start: 0.9201 (pt0) cc_final: 0.8963 (pt0) REVERT: L 155 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8792 (mt-10) REVERT: L 156 ARG cc_start: 0.9072 (mmp80) cc_final: 0.8783 (mmp80) REVERT: L 177 VAL cc_start: 0.9049 (p) cc_final: 0.8589 (m) REVERT: L 214 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8161 (ttp80) REVERT: L 290 GLU cc_start: 0.9369 (tt0) cc_final: 0.9059 (mt-10) REVERT: L 293 ASN cc_start: 0.9485 (m-40) cc_final: 0.9153 (p0) REVERT: L 308 ARG cc_start: 0.9208 (mtm-85) cc_final: 0.8918 (mtm-85) REVERT: L 313 MET cc_start: 0.8424 (mpp) cc_final: 0.8050 (mtm) REVERT: L 413 MET cc_start: 0.8715 (ttm) cc_final: 0.8320 (ttm) REVERT: L 430 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9187 (pttm) REVERT: M 14 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7998 (p0) REVERT: M 29 HIS cc_start: 0.9352 (t-90) cc_final: 0.8874 (t-90) REVERT: M 57 HIS cc_start: 0.7819 (t-170) cc_final: 0.7045 (t70) REVERT: M 84 LYS cc_start: 0.9385 (ttmt) cc_final: 0.9004 (ttpt) REVERT: M 112 LYS cc_start: 0.9135 (tptp) cc_final: 0.8642 (tppt) REVERT: M 118 ASN cc_start: 0.7846 (m-40) cc_final: 0.7501 (m110) REVERT: N 29 HIS cc_start: 0.9329 (t-90) cc_final: 0.8875 (t-90) REVERT: N 57 HIS cc_start: 0.8016 (t-170) cc_final: 0.7497 (t70) REVERT: N 84 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8746 (ttpt) outliers start: 136 outliers final: 75 residues processed: 1589 average time/residue: 0.5563 time to fit residues: 1426.6624 Evaluate side-chains 1471 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1388 time to evaluate : 4.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 213 ARG Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 292 GLN Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 83 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 489 optimal weight: 5.9990 chunk 518 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 463 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 298 ASN B 307 HIS ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 337 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 298 ASN ** F 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 HIS ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 370 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 247 ASN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 44232 Z= 0.333 Angle : 0.634 10.341 60052 Z= 0.324 Chirality : 0.045 0.207 6552 Planarity : 0.004 0.069 7788 Dihedral : 11.726 174.741 6071 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.63 % Favored : 97.33 % Rotamer: Outliers : 4.11 % Allowed : 18.48 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.12), residues: 5394 helix: 1.28 (0.11), residues: 2464 sheet: 0.50 (0.19), residues: 798 loop : -1.08 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 344 HIS 0.036 0.001 HIS G 227 PHE 0.024 0.002 PHE I 92 TYR 0.023 0.002 TYR F 183 ARG 0.014 0.001 ARG H 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1431 time to evaluate : 5.243 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 207 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 211 ASP cc_start: 0.8720 (t70) cc_final: 0.8201 (t0) REVERT: A 218 ASP cc_start: 0.9032 (m-30) cc_final: 0.8596 (m-30) REVERT: A 300 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8392 (t0) REVERT: A 324 VAL cc_start: 0.9240 (t) cc_final: 0.8922 (p) REVERT: A 335 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9469 (tp) REVERT: A 361 THR cc_start: 0.9362 (m) cc_final: 0.8915 (t) REVERT: A 377 MET cc_start: 0.9122 (tmm) cc_final: 0.8570 (tmm) REVERT: A 392 ASP cc_start: 0.9095 (m-30) cc_final: 0.8838 (m-30) REVERT: A 425 MET cc_start: 0.9161 (tpp) cc_final: 0.8726 (mpp) REVERT: A 430 LYS cc_start: 0.9502 (ttpt) cc_final: 0.9241 (pttm) REVERT: B 124 CYS cc_start: 0.8892 (m) cc_final: 0.8449 (p) REVERT: B 161 ASP cc_start: 0.8855 (p0) cc_final: 0.8468 (p0) REVERT: B 201 CYS cc_start: 0.9276 (m) cc_final: 0.9053 (m) REVERT: B 209 ASP cc_start: 0.8679 (t0) cc_final: 0.8009 (t0) REVERT: B 213 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8274 (mtm110) REVERT: B 252 LYS cc_start: 0.9318 (mttm) cc_final: 0.8912 (mttm) REVERT: B 329 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8868 (mm-40) REVERT: B 375 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7785 (pp30) REVERT: B 379 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8771 (mtmt) REVERT: C 76 ASP cc_start: 0.9132 (m-30) cc_final: 0.8871 (m-30) REVERT: C 168 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7621 (mt-10) REVERT: C 215 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8302 (mtm-85) REVERT: C 218 ASP cc_start: 0.9360 (m-30) cc_final: 0.8862 (m-30) REVERT: C 256 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8895 (tt0) REVERT: C 275 VAL cc_start: 0.9445 (OUTLIER) cc_final: 0.9232 (m) REVERT: C 280 LYS cc_start: 0.3763 (mmtt) cc_final: 0.3271 (mtmm) REVERT: C 304 LYS cc_start: 0.9243 (tppt) cc_final: 0.8959 (tppt) REVERT: C 377 MET cc_start: 0.9006 (ttp) cc_final: 0.7335 (tmm) REVERT: C 378 LEU cc_start: 0.9575 (mt) cc_final: 0.9136 (mt) REVERT: C 433 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9053 (mm-30) REVERT: D 19 LYS cc_start: 0.8855 (tptt) cc_final: 0.8619 (tptp) REVERT: D 41 ASP cc_start: 0.8850 (p0) cc_final: 0.8535 (p0) REVERT: D 124 CYS cc_start: 0.8883 (m) cc_final: 0.8601 (p) REVERT: D 211 CYS cc_start: 0.9227 (m) cc_final: 0.9023 (m) REVERT: D 213 ARG cc_start: 0.8662 (ttm110) cc_final: 0.8429 (mtm110) REVERT: D 252 LYS cc_start: 0.9175 (mtpp) cc_final: 0.8679 (ttmm) REVERT: D 291 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (pm20) REVERT: D 307 HIS cc_start: 0.9288 (m-70) cc_final: 0.8863 (m-70) REVERT: D 327 ASP cc_start: 0.9061 (m-30) cc_final: 0.8755 (m-30) REVERT: D 375 GLN cc_start: 0.8443 (pp30) cc_final: 0.7304 (pp30) REVERT: D 379 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8754 (mtmt) REVERT: D 390 ARG cc_start: 0.7853 (ptt-90) cc_final: 0.7536 (ptt90) REVERT: D 424 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9178 (tm-30) REVERT: E 76 ASP cc_start: 0.9164 (m-30) cc_final: 0.8796 (m-30) REVERT: E 88 HIS cc_start: 0.9058 (t70) cc_final: 0.8467 (t-170) REVERT: E 90 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8448 (mm-30) REVERT: E 150 THR cc_start: 0.9361 (m) cc_final: 0.9129 (m) REVERT: E 155 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8802 (mt-10) REVERT: E 245 ASP cc_start: 0.8839 (t70) cc_final: 0.8323 (t0) REVERT: E 301 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8706 (mm-40) REVERT: E 357 TYR cc_start: 0.9181 (m-80) cc_final: 0.8879 (m-80) REVERT: E 361 THR cc_start: 0.9294 (m) cc_final: 0.8967 (t) REVERT: E 377 MET cc_start: 0.9023 (ttp) cc_final: 0.8107 (tmm) REVERT: E 413 MET cc_start: 0.8850 (tpp) cc_final: 0.8453 (tpp) REVERT: E 430 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9268 (ttpp) REVERT: E 431 ASP cc_start: 0.8425 (m-30) cc_final: 0.7939 (m-30) REVERT: E 438 ASP cc_start: 0.8730 (t0) cc_final: 0.8252 (t0) REVERT: F 41 ASP cc_start: 0.8939 (p0) cc_final: 0.8593 (p0) REVERT: F 86 ARG cc_start: 0.4992 (mmt180) cc_final: 0.4200 (tpt170) REVERT: F 106 TYR cc_start: 0.8934 (m-80) cc_final: 0.8692 (m-10) REVERT: F 198 GLU cc_start: 0.7863 (pp20) cc_final: 0.7587 (pp20) REVERT: F 207 LEU cc_start: 0.9695 (mt) cc_final: 0.9376 (mp) REVERT: F 252 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8712 (mtpp) REVERT: F 266 PHE cc_start: 0.8948 (m-10) cc_final: 0.8735 (m-10) REVERT: F 291 GLN cc_start: 0.8819 (pp30) cc_final: 0.8531 (pp30) REVERT: F 292 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: F 375 GLN cc_start: 0.8522 (pp30) cc_final: 0.7432 (pp30) REVERT: F 376 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7960 (mt-10) REVERT: F 379 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8801 (mtmt) REVERT: F 423 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8601 (tp-100) REVERT: G 164 MET cc_start: 0.8768 (ttm) cc_final: 0.8176 (mtp) REVERT: G 198 GLU cc_start: 0.9237 (pt0) cc_final: 0.8773 (pt0) REVERT: G 266 PHE cc_start: 0.9023 (m-10) cc_final: 0.8620 (m-10) REVERT: G 282 ARG cc_start: 0.7468 (ttp80) cc_final: 0.6940 (ptm-80) REVERT: G 284 LEU cc_start: 0.9113 (mt) cc_final: 0.8725 (mt) REVERT: G 299 MET cc_start: 0.9147 (tpp) cc_final: 0.8908 (tpp) REVERT: G 321 MET cc_start: 0.9072 (ptp) cc_final: 0.8713 (ptp) REVERT: G 406 MET cc_start: 0.8771 (tpt) cc_final: 0.8494 (tpt) REVERT: G 407 GLU cc_start: 0.8856 (pt0) cc_final: 0.8656 (pt0) REVERT: H 194 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7797 (mm-30) REVERT: H 198 GLU cc_start: 0.8492 (pt0) cc_final: 0.8261 (pt0) REVERT: H 200 TYR cc_start: 0.9133 (m-80) cc_final: 0.8656 (m-10) REVERT: H 203 ASP cc_start: 0.7644 (t70) cc_final: 0.7278 (t70) REVERT: H 213 ARG cc_start: 0.8986 (ttm110) cc_final: 0.8513 (ttp80) REVERT: H 282 ARG cc_start: 0.8024 (ptm-80) cc_final: 0.7789 (ptm-80) REVERT: H 298 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.9017 (t0) REVERT: H 307 HIS cc_start: 0.9542 (m-70) cc_final: 0.9258 (m-70) REVERT: H 331 LEU cc_start: 0.9490 (tp) cc_final: 0.9275 (tp) REVERT: H 406 MET cc_start: 0.8747 (tpp) cc_final: 0.8479 (tpp) REVERT: H 421 GLU cc_start: 0.8762 (tp30) cc_final: 0.8273 (tp30) REVERT: I 198 GLU cc_start: 0.8866 (pt0) cc_final: 0.8112 (pt0) REVERT: I 203 ASP cc_start: 0.7576 (t70) cc_final: 0.7161 (t0) REVERT: I 209 ASP cc_start: 0.9231 (t0) cc_final: 0.8916 (t0) REVERT: I 291 GLN cc_start: 0.8789 (pp30) cc_final: 0.8537 (pp30) REVERT: I 325 GLU cc_start: 0.9175 (tt0) cc_final: 0.8856 (tt0) REVERT: I 329 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8729 (mm110) REVERT: I 362 LYS cc_start: 0.8882 (tmmt) cc_final: 0.8633 (ttpp) REVERT: I 379 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8807 (mtmm) REVERT: I 406 MET cc_start: 0.8990 (tpt) cc_final: 0.8692 (tpt) REVERT: I 423 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8583 (tm-30) REVERT: I 427 ASP cc_start: 0.8240 (p0) cc_final: 0.7634 (p0) REVERT: J 88 HIS cc_start: 0.8887 (t70) cc_final: 0.8233 (t70) REVERT: J 90 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8682 (mm-30) REVERT: J 128 GLN cc_start: 0.8067 (pp30) cc_final: 0.7818 (pp30) REVERT: J 155 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9128 (mt-10) REVERT: J 156 ARG cc_start: 0.9088 (mmp80) cc_final: 0.8757 (mmp80) REVERT: J 168 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8283 (mt-10) REVERT: J 172 TYR cc_start: 0.8400 (t80) cc_final: 0.8170 (t80) REVERT: J 214 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7438 (ttp80) REVERT: J 293 ASN cc_start: 0.9642 (m-40) cc_final: 0.9356 (m-40) REVERT: J 308 ARG cc_start: 0.9488 (mtm110) cc_final: 0.9176 (mtm-85) REVERT: J 313 MET cc_start: 0.8128 (mpp) cc_final: 0.7748 (mtm) REVERT: J 318 LEU cc_start: 0.9401 (mt) cc_final: 0.9182 (mp) REVERT: J 388 TRP cc_start: 0.9126 (m100) cc_final: 0.8577 (m100) REVERT: J 396 ASP cc_start: 0.8802 (m-30) cc_final: 0.8586 (m-30) REVERT: K 88 HIS cc_start: 0.9303 (t70) cc_final: 0.8440 (t70) REVERT: K 90 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8588 (mm-30) REVERT: K 108 TYR cc_start: 0.8880 (m-80) cc_final: 0.8601 (m-10) REVERT: K 155 GLU cc_start: 0.9260 (pt0) cc_final: 0.8770 (pp20) REVERT: K 156 ARG cc_start: 0.9179 (mmp80) cc_final: 0.8952 (mmm160) REVERT: K 214 ARG cc_start: 0.8973 (tmm160) cc_final: 0.8619 (ttp80) REVERT: K 290 GLU cc_start: 0.9381 (pt0) cc_final: 0.9168 (pt0) REVERT: K 300 ASN cc_start: 0.8912 (t160) cc_final: 0.8529 (t0) REVERT: K 308 ARG cc_start: 0.9276 (mtm110) cc_final: 0.8945 (mtm-85) REVERT: K 313 MET cc_start: 0.8988 (mtm) cc_final: 0.8509 (mtm) REVERT: L 155 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8768 (mt-10) REVERT: L 156 ARG cc_start: 0.9128 (mmp80) cc_final: 0.8824 (mmp80) REVERT: L 163 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6990 (mmpt) REVERT: L 214 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8069 (ttp80) REVERT: L 290 GLU cc_start: 0.9376 (tt0) cc_final: 0.9174 (tt0) REVERT: L 293 ASN cc_start: 0.9494 (m-40) cc_final: 0.9225 (p0) REVERT: L 313 MET cc_start: 0.8439 (mpp) cc_final: 0.8090 (mtm) REVERT: L 361 THR cc_start: 0.8697 (m) cc_final: 0.8242 (p) REVERT: L 388 TRP cc_start: 0.9211 (m100) cc_final: 0.8987 (m100) REVERT: L 413 MET cc_start: 0.8751 (ttm) cc_final: 0.8399 (ttm) REVERT: L 425 MET cc_start: 0.9212 (tpp) cc_final: 0.8707 (tpt) REVERT: L 430 LYS cc_start: 0.9445 (ptmm) cc_final: 0.9242 (pttm) REVERT: M 20 MET cc_start: 0.9145 (mtt) cc_final: 0.8887 (mtp) REVERT: M 29 HIS cc_start: 0.9368 (t-90) cc_final: 0.8850 (t-90) REVERT: M 57 HIS cc_start: 0.8227 (t-170) cc_final: 0.7528 (t70) REVERT: M 84 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9027 (ttpt) REVERT: M 118 ASN cc_start: 0.7731 (m-40) cc_final: 0.7514 (m110) REVERT: N 29 HIS cc_start: 0.9337 (t-90) cc_final: 0.8861 (t-90) REVERT: N 57 HIS cc_start: 0.8304 (t-170) cc_final: 0.7711 (t70) REVERT: N 60 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7861 (mmtt) REVERT: N 84 LYS cc_start: 0.9255 (ttmt) cc_final: 0.8722 (ttpt) REVERT: N 104 ASN cc_start: 0.8526 (m-40) cc_final: 0.8221 (m110) REVERT: N 127 LEU cc_start: 0.8802 (mm) cc_final: 0.8488 (mm) outliers start: 191 outliers final: 123 residues processed: 1518 average time/residue: 0.5724 time to fit residues: 1400.8128 Evaluate side-chains 1462 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1330 time to evaluate : 5.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 GLN Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 118 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 385 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 442 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 465 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 HIS C 300 ASN C 301 GLN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 99 ASN D 204 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 GLN E 41 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN F 298 ASN F 370 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 292 GLN H 298 ASN ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS I 227 HIS I 247 ASN ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 192 HIS ** L 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN N 14 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 44232 Z= 0.450 Angle : 0.685 10.249 60052 Z= 0.352 Chirality : 0.046 0.172 6552 Planarity : 0.005 0.060 7788 Dihedral : 11.981 177.272 6071 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 5.03 % Allowed : 19.26 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 5394 helix: 1.14 (0.11), residues: 2434 sheet: 0.56 (0.19), residues: 774 loop : -1.03 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.012 0.001 HIS G 227 PHE 0.029 0.002 PHE I 260 TYR 0.024 0.002 TYR B 183 ARG 0.007 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1355 time to evaluate : 4.708 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 207 GLU cc_start: 0.8657 (tt0) cc_final: 0.8303 (mt-10) REVERT: A 211 ASP cc_start: 0.8861 (t70) cc_final: 0.8183 (t70) REVERT: A 215 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8461 (ttp80) REVERT: A 300 ASN cc_start: 0.8766 (t0) cc_final: 0.8471 (t0) REVERT: A 324 VAL cc_start: 0.9373 (t) cc_final: 0.9112 (t) REVERT: A 361 THR cc_start: 0.9414 (m) cc_final: 0.8995 (t) REVERT: A 377 MET cc_start: 0.9093 (tmm) cc_final: 0.8445 (tmm) REVERT: A 425 MET cc_start: 0.9172 (tpp) cc_final: 0.8778 (mpp) REVERT: A 430 LYS cc_start: 0.9533 (ttpt) cc_final: 0.9260 (pttm) REVERT: B 111 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 161 ASP cc_start: 0.9073 (p0) cc_final: 0.8703 (p0) REVERT: B 188 SER cc_start: 0.9413 (OUTLIER) cc_final: 0.9085 (p) REVERT: B 209 ASP cc_start: 0.8592 (t0) cc_final: 0.8329 (t0) REVERT: B 240 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8826 (tt) REVERT: B 252 LYS cc_start: 0.9267 (mttm) cc_final: 0.8854 (mttm) REVERT: B 375 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7802 (pp30) REVERT: B 379 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8810 (mtmt) REVERT: C 22 GLU cc_start: 0.8889 (tt0) cc_final: 0.8616 (pt0) REVERT: C 76 ASP cc_start: 0.9103 (m-30) cc_final: 0.8813 (m-30) REVERT: C 218 ASP cc_start: 0.9363 (m-30) cc_final: 0.8966 (m-30) REVERT: C 256 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: C 280 LYS cc_start: 0.4109 (mmtt) cc_final: 0.3440 (ttpt) REVERT: C 300 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8775 (t0) REVERT: C 304 LYS cc_start: 0.9224 (tppt) cc_final: 0.8872 (tppt) REVERT: C 319 TYR cc_start: 0.9127 (m-80) cc_final: 0.8828 (m-80) REVERT: C 376 CYS cc_start: 0.9174 (t) cc_final: 0.8831 (t) REVERT: C 377 MET cc_start: 0.8985 (ttp) cc_final: 0.8020 (tmm) REVERT: C 378 LEU cc_start: 0.9547 (mt) cc_final: 0.8981 (mt) REVERT: D 41 ASP cc_start: 0.8942 (p0) cc_final: 0.8591 (p0) REVERT: D 124 CYS cc_start: 0.8937 (m) cc_final: 0.8549 (p) REVERT: D 198 GLU cc_start: 0.8485 (pt0) cc_final: 0.8167 (pt0) REVERT: D 205 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8024 (mt-10) REVERT: D 252 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8575 (ttmm) REVERT: D 323 MET cc_start: 0.8567 (mmp) cc_final: 0.8199 (mmp) REVERT: D 327 ASP cc_start: 0.9081 (m-30) cc_final: 0.8797 (m-30) REVERT: D 375 GLN cc_start: 0.8572 (pp30) cc_final: 0.7547 (pp30) REVERT: D 379 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8807 (mtmt) REVERT: D 424 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9147 (tm-30) REVERT: D 425 TYR cc_start: 0.8788 (m-10) cc_final: 0.8492 (m-10) REVERT: E 22 GLU cc_start: 0.9027 (pt0) cc_final: 0.8680 (pt0) REVERT: E 76 ASP cc_start: 0.9140 (m-30) cc_final: 0.8761 (m-30) REVERT: E 155 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 230 LEU cc_start: 0.9607 (mp) cc_final: 0.9399 (mp) REVERT: E 346 TRP cc_start: 0.9214 (p-90) cc_final: 0.8957 (p-90) REVERT: E 349 THR cc_start: 0.8795 (p) cc_final: 0.8535 (p) REVERT: E 361 THR cc_start: 0.9342 (m) cc_final: 0.9010 (t) REVERT: E 377 MET cc_start: 0.9100 (ttp) cc_final: 0.8844 (tmm) REVERT: E 425 MET cc_start: 0.9249 (mmm) cc_final: 0.8984 (mmp) REVERT: E 430 LYS cc_start: 0.9555 (ttpt) cc_final: 0.9218 (pttm) REVERT: E 431 ASP cc_start: 0.8471 (m-30) cc_final: 0.8197 (m-30) REVERT: F 41 ASP cc_start: 0.8971 (p0) cc_final: 0.8591 (p0) REVERT: F 50 TYR cc_start: 0.9067 (m-80) cc_final: 0.8686 (m-80) REVERT: F 86 ARG cc_start: 0.4819 (mmt180) cc_final: 0.4000 (tpt170) REVERT: F 291 GLN cc_start: 0.8869 (pp30) cc_final: 0.8589 (pp30) REVERT: F 292 GLN cc_start: 0.8895 (tt0) cc_final: 0.8625 (tt0) REVERT: F 293 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: F 375 GLN cc_start: 0.8767 (pp30) cc_final: 0.8403 (pp30) REVERT: F 423 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8569 (tp-100) REVERT: G 164 MET cc_start: 0.8699 (ttm) cc_final: 0.8058 (mtp) REVERT: G 197 ASP cc_start: 0.8959 (m-30) cc_final: 0.8530 (m-30) REVERT: G 198 GLU cc_start: 0.9229 (pt0) cc_final: 0.8755 (pt0) REVERT: G 209 ASP cc_start: 0.9048 (t70) cc_final: 0.8837 (t70) REVERT: G 213 ARG cc_start: 0.8769 (ttp80) cc_final: 0.7839 (tmm-80) REVERT: G 266 PHE cc_start: 0.9154 (m-10) cc_final: 0.8787 (m-10) REVERT: G 282 ARG cc_start: 0.7410 (ttp80) cc_final: 0.6948 (ptm-80) REVERT: G 284 LEU cc_start: 0.9115 (mt) cc_final: 0.8736 (mt) REVERT: G 298 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9086 (t0) REVERT: G 299 MET cc_start: 0.9091 (tpp) cc_final: 0.8850 (tpp) REVERT: G 321 MET cc_start: 0.9043 (ptp) cc_final: 0.8692 (ptp) REVERT: G 325 GLU cc_start: 0.9147 (tt0) cc_final: 0.8849 (tt0) REVERT: H 194 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7912 (mm-30) REVERT: H 203 ASP cc_start: 0.7737 (t70) cc_final: 0.7060 (t70) REVERT: H 205 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: H 303 CYS cc_start: 0.8391 (p) cc_final: 0.8158 (p) REVERT: H 375 GLN cc_start: 0.9090 (pt0) cc_final: 0.8625 (pp30) REVERT: H 406 MET cc_start: 0.8766 (tpp) cc_final: 0.8449 (tpp) REVERT: H 421 GLU cc_start: 0.8883 (tp30) cc_final: 0.8393 (tp30) REVERT: H 425 TYR cc_start: 0.8376 (m-80) cc_final: 0.7693 (m-10) REVERT: I 51 TYR cc_start: 0.9113 (m-80) cc_final: 0.8794 (m-80) REVERT: I 197 ASP cc_start: 0.8907 (m-30) cc_final: 0.8604 (m-30) REVERT: I 198 GLU cc_start: 0.9053 (pt0) cc_final: 0.8264 (pt0) REVERT: I 209 ASP cc_start: 0.9188 (t0) cc_final: 0.8478 (t0) REVERT: I 213 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8161 (ttm110) REVERT: I 291 GLN cc_start: 0.8937 (pp30) cc_final: 0.8697 (pp30) REVERT: I 325 GLU cc_start: 0.9199 (tt0) cc_final: 0.8794 (tt0) REVERT: I 329 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8770 (mm110) REVERT: I 362 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8538 (ttpp) REVERT: I 406 MET cc_start: 0.9027 (tpt) cc_final: 0.7551 (tpp) REVERT: I 410 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8451 (mm-30) REVERT: I 423 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8640 (tm-30) REVERT: I 427 ASP cc_start: 0.8355 (p0) cc_final: 0.7723 (p0) REVERT: J 88 HIS cc_start: 0.8983 (t70) cc_final: 0.8323 (t70) REVERT: J 90 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8867 (mm-30) REVERT: J 155 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9077 (mt-10) REVERT: J 168 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8183 (mt-10) REVERT: J 172 TYR cc_start: 0.8518 (t80) cc_final: 0.8311 (t80) REVERT: J 214 ARG cc_start: 0.8735 (ttp80) cc_final: 0.7865 (ttp80) REVERT: J 293 ASN cc_start: 0.9643 (m-40) cc_final: 0.9364 (m-40) REVERT: J 308 ARG cc_start: 0.9483 (mtm110) cc_final: 0.9192 (mtm-85) REVERT: J 313 MET cc_start: 0.8129 (mpp) cc_final: 0.7718 (mtm) REVERT: J 318 LEU cc_start: 0.9352 (mt) cc_final: 0.9140 (mp) REVERT: J 388 TRP cc_start: 0.9182 (m100) cc_final: 0.8615 (m100) REVERT: J 413 MET cc_start: 0.9008 (mtp) cc_final: 0.8772 (ttm) REVERT: K 108 TYR cc_start: 0.8800 (m-80) cc_final: 0.8593 (m-10) REVERT: K 155 GLU cc_start: 0.9271 (pt0) cc_final: 0.8716 (pp20) REVERT: K 156 ARG cc_start: 0.9257 (mmp80) cc_final: 0.8954 (mmm160) REVERT: K 205 ASP cc_start: 0.8291 (t0) cc_final: 0.8060 (t0) REVERT: K 214 ARG cc_start: 0.9044 (tmm160) cc_final: 0.8730 (ttp80) REVERT: K 218 ASP cc_start: 0.9495 (m-30) cc_final: 0.9259 (m-30) REVERT: K 290 GLU cc_start: 0.9459 (pt0) cc_final: 0.9210 (pt0) REVERT: K 300 ASN cc_start: 0.8983 (t160) cc_final: 0.8659 (t0) REVERT: K 313 MET cc_start: 0.9010 (mtm) cc_final: 0.8680 (mtm) REVERT: L 155 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8910 (mt-10) REVERT: L 214 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8325 (ttp80) REVERT: L 218 ASP cc_start: 0.9460 (m-30) cc_final: 0.9203 (m-30) REVERT: L 308 ARG cc_start: 0.9184 (mtm-85) cc_final: 0.8820 (mtm-85) REVERT: L 313 MET cc_start: 0.8433 (mpp) cc_final: 0.8149 (mtm) REVERT: L 388 TRP cc_start: 0.9298 (m100) cc_final: 0.8927 (m100) REVERT: L 413 MET cc_start: 0.8750 (ttm) cc_final: 0.8386 (ttm) REVERT: L 430 LYS cc_start: 0.9489 (ptmm) cc_final: 0.9265 (pttm) REVERT: L 433 GLU cc_start: 0.9153 (tp30) cc_final: 0.8943 (tp30) REVERT: M 14 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7490 (p0) REVERT: M 29 HIS cc_start: 0.9387 (t-90) cc_final: 0.8841 (t-90) REVERT: M 57 HIS cc_start: 0.8348 (t-170) cc_final: 0.7473 (t70) REVERT: M 60 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7734 (mmtt) REVERT: M 84 LYS cc_start: 0.9401 (ttmt) cc_final: 0.9028 (ttpt) REVERT: N 29 HIS cc_start: 0.9379 (t-90) cc_final: 0.8912 (t-90) REVERT: N 57 HIS cc_start: 0.8250 (t-170) cc_final: 0.7437 (t70) REVERT: N 100 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7536 (mmtp) REVERT: N 104 ASN cc_start: 0.8563 (m-40) cc_final: 0.8143 (m110) outliers start: 234 outliers final: 165 residues processed: 1468 average time/residue: 0.6174 time to fit residues: 1468.2124 Evaluate side-chains 1474 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1299 time to evaluate : 5.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 293 MET Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 227 HIS Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 196 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 304 ASP Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 423 GLU Chi-restraints excluded: chain M residue 14 ASN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 109 GLN Chi-restraints excluded: chain M residue 127 LEU Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 0.0270 chunk 466 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 518 optimal weight: 7.9990 chunk 430 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** G 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 57 HIS ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 285 GLN ** L 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 44232 Z= 0.339 Angle : 0.649 11.875 60052 Z= 0.330 Chirality : 0.045 0.180 6552 Planarity : 0.004 0.049 7788 Dihedral : 11.919 174.004 6071 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 4.37 % Allowed : 20.80 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 5394 helix: 1.19 (0.11), residues: 2434 sheet: 0.59 (0.19), residues: 774 loop : -0.98 (0.14), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.023 0.001 HIS G 227 PHE 0.023 0.002 PHE N 115 TYR 0.018 0.002 TYR H 183 ARG 0.007 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1369 time to evaluate : 4.831 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8497 (mmmt) REVERT: A 207 GLU cc_start: 0.8669 (tt0) cc_final: 0.8340 (mt-10) REVERT: A 211 ASP cc_start: 0.8838 (t70) cc_final: 0.8515 (t70) REVERT: A 300 ASN cc_start: 0.8805 (t0) cc_final: 0.8487 (t0) REVERT: A 361 THR cc_start: 0.9409 (m) cc_final: 0.8991 (t) REVERT: A 377 MET cc_start: 0.9055 (tmm) cc_final: 0.8421 (tmm) REVERT: A 425 MET cc_start: 0.9123 (tpp) cc_final: 0.8511 (mpp) REVERT: A 430 LYS cc_start: 0.9526 (ttpt) cc_final: 0.9244 (pttm) REVERT: B 111 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 161 ASP cc_start: 0.9105 (p0) cc_final: 0.8692 (p0) REVERT: B 203 ASP cc_start: 0.8300 (t0) cc_final: 0.7966 (t0) REVERT: B 209 ASP cc_start: 0.8666 (t0) cc_final: 0.8359 (t0) REVERT: B 240 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8778 (tt) REVERT: B 252 LYS cc_start: 0.9247 (mttm) cc_final: 0.8831 (mttm) REVERT: B 307 HIS cc_start: 0.9360 (m-70) cc_final: 0.9005 (m90) REVERT: B 375 GLN cc_start: 0.8900 (pp30) cc_final: 0.7841 (pp30) REVERT: B 379 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8819 (mtmt) REVERT: B 423 GLN cc_start: 0.9085 (tp40) cc_final: 0.8879 (tp40) REVERT: C 22 GLU cc_start: 0.8855 (tt0) cc_final: 0.8597 (pt0) REVERT: C 76 ASP cc_start: 0.9074 (m-30) cc_final: 0.8804 (m-30) REVERT: C 187 SER cc_start: 0.9445 (m) cc_final: 0.9234 (p) REVERT: C 218 ASP cc_start: 0.9360 (m-30) cc_final: 0.9030 (m-30) REVERT: C 256 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8878 (tt0) REVERT: C 280 LYS cc_start: 0.3894 (mmtt) cc_final: 0.3515 (ttpt) REVERT: C 304 LYS cc_start: 0.9221 (tppt) cc_final: 0.8792 (tppt) REVERT: C 319 TYR cc_start: 0.9117 (m-80) cc_final: 0.8828 (m-80) REVERT: C 376 CYS cc_start: 0.9144 (t) cc_final: 0.8789 (t) REVERT: C 377 MET cc_start: 0.8920 (ttp) cc_final: 0.8060 (tmm) REVERT: C 378 LEU cc_start: 0.9560 (mt) cc_final: 0.9015 (mt) REVERT: D 41 ASP cc_start: 0.8999 (p0) cc_final: 0.8687 (p0) REVERT: D 124 CYS cc_start: 0.9045 (m) cc_final: 0.8646 (p) REVERT: D 154 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9278 (mmmm) REVERT: D 198 GLU cc_start: 0.8519 (pt0) cc_final: 0.8156 (pt0) REVERT: D 203 ASP cc_start: 0.8417 (t0) cc_final: 0.8214 (t70) REVERT: D 252 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8558 (ttmm) REVERT: D 323 MET cc_start: 0.8619 (mmp) cc_final: 0.8309 (mmp) REVERT: D 327 ASP cc_start: 0.9111 (m-30) cc_final: 0.8834 (m-30) REVERT: D 375 GLN cc_start: 0.8496 (pp30) cc_final: 0.7995 (pp30) REVERT: D 424 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9193 (tm-30) REVERT: D 425 TYR cc_start: 0.8778 (m-10) cc_final: 0.8473 (m-10) REVERT: E 22 GLU cc_start: 0.9008 (pt0) cc_final: 0.8778 (pt0) REVERT: E 76 ASP cc_start: 0.9124 (m-30) cc_final: 0.8744 (m-30) REVERT: E 88 HIS cc_start: 0.8957 (t70) cc_final: 0.8575 (t70) REVERT: E 123 ARG cc_start: 0.8827 (ttp-110) cc_final: 0.8568 (ttm-80) REVERT: E 155 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8761 (mt-10) REVERT: E 230 LEU cc_start: 0.9635 (mp) cc_final: 0.9396 (mp) REVERT: E 280 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8496 (mtmm) REVERT: E 346 TRP cc_start: 0.9183 (p-90) cc_final: 0.8933 (p-90) REVERT: E 349 THR cc_start: 0.8784 (p) cc_final: 0.8540 (p) REVERT: E 361 THR cc_start: 0.9341 (m) cc_final: 0.9012 (t) REVERT: E 377 MET cc_start: 0.9025 (ttp) cc_final: 0.8221 (tmm) REVERT: E 413 MET cc_start: 0.8850 (tpp) cc_final: 0.8560 (tpp) REVERT: E 430 LYS cc_start: 0.9547 (ttpt) cc_final: 0.9238 (pttm) REVERT: E 433 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8710 (mm-30) REVERT: E 438 ASP cc_start: 0.8646 (t0) cc_final: 0.8443 (t0) REVERT: F 41 ASP cc_start: 0.8991 (p0) cc_final: 0.8583 (p0) REVERT: F 50 TYR cc_start: 0.9083 (m-80) cc_final: 0.8735 (m-80) REVERT: F 86 ARG cc_start: 0.4973 (mmt180) cc_final: 0.3846 (tpt170) REVERT: F 266 PHE cc_start: 0.8958 (m-10) cc_final: 0.8619 (m-10) REVERT: F 291 GLN cc_start: 0.8897 (pp30) cc_final: 0.8610 (pp30) REVERT: F 292 GLN cc_start: 0.9086 (tt0) cc_final: 0.8741 (tt0) REVERT: F 293 MET cc_start: 0.8294 (mtt) cc_final: 0.8002 (mtt) REVERT: F 323 MET cc_start: 0.8864 (mmm) cc_final: 0.8635 (mmm) REVERT: F 329 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8663 (mm-40) REVERT: F 375 GLN cc_start: 0.8805 (pp30) cc_final: 0.8447 (pp30) REVERT: F 423 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8688 (tp-100) REVERT: G 164 MET cc_start: 0.8595 (ttm) cc_final: 0.8067 (mtp) REVERT: G 197 ASP cc_start: 0.9016 (m-30) cc_final: 0.8523 (m-30) REVERT: G 198 GLU cc_start: 0.9253 (pt0) cc_final: 0.8734 (pt0) REVERT: G 203 ASP cc_start: 0.7844 (t70) cc_final: 0.7456 (t70) REVERT: G 209 ASP cc_start: 0.9032 (t70) cc_final: 0.8507 (t70) REVERT: G 213 ARG cc_start: 0.8688 (ttp80) cc_final: 0.7944 (ttp80) REVERT: G 266 PHE cc_start: 0.9157 (m-10) cc_final: 0.8811 (m-10) REVERT: G 282 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7017 (ptm-80) REVERT: G 284 LEU cc_start: 0.9082 (mt) cc_final: 0.8771 (mt) REVERT: G 321 MET cc_start: 0.9044 (ptp) cc_final: 0.8690 (ptp) REVERT: G 325 GLU cc_start: 0.9055 (tt0) cc_final: 0.8815 (tt0) REVERT: G 423 GLN cc_start: 0.8924 (tp40) cc_final: 0.8700 (tm-30) REVERT: H 74 ASP cc_start: 0.9064 (m-30) cc_final: 0.8851 (m-30) REVERT: H 194 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7867 (mm-30) REVERT: H 205 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: H 303 CYS cc_start: 0.8367 (p) cc_final: 0.8084 (p) REVERT: H 330 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.9079 (mmm) REVERT: H 331 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9274 (tp) REVERT: H 375 GLN cc_start: 0.9095 (pt0) cc_final: 0.8675 (pp30) REVERT: H 406 MET cc_start: 0.8723 (tpp) cc_final: 0.7307 (tpp) REVERT: H 410 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8148 (mm-30) REVERT: I 51 TYR cc_start: 0.9062 (m-80) cc_final: 0.8700 (m-80) REVERT: I 197 ASP cc_start: 0.8860 (m-30) cc_final: 0.8590 (m-30) REVERT: I 198 GLU cc_start: 0.8983 (pt0) cc_final: 0.8523 (pt0) REVERT: I 203 ASP cc_start: 0.7866 (t0) cc_final: 0.7568 (t70) REVERT: I 213 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8268 (tmm-80) REVERT: I 291 GLN cc_start: 0.8918 (pp30) cc_final: 0.8657 (pp30) REVERT: I 325 GLU cc_start: 0.9031 (tt0) cc_final: 0.8814 (tt0) REVERT: I 329 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8757 (mm110) REVERT: I 362 LYS cc_start: 0.8918 (tmmt) cc_final: 0.8465 (tmmt) REVERT: I 406 MET cc_start: 0.9067 (tpt) cc_final: 0.7510 (tpp) REVERT: I 410 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8434 (mm-30) REVERT: I 423 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8731 (tm-30) REVERT: I 427 ASP cc_start: 0.8368 (p0) cc_final: 0.7701 (p0) REVERT: J 88 HIS cc_start: 0.9036 (t70) cc_final: 0.8396 (t70) REVERT: J 90 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8917 (mm-30) REVERT: J 155 GLU cc_start: 0.9473 (mt-10) cc_final: 0.9022 (mt-10) REVERT: J 156 ARG cc_start: 0.9042 (mmp80) cc_final: 0.8807 (mmp80) REVERT: J 163 LYS cc_start: 0.7471 (mmpt) cc_final: 0.7265 (mmpt) REVERT: J 168 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8150 (mt-10) REVERT: J 172 TYR cc_start: 0.8493 (t80) cc_final: 0.8157 (t80) REVERT: J 214 ARG cc_start: 0.8750 (ttp80) cc_final: 0.7908 (ttp80) REVERT: J 293 ASN cc_start: 0.9621 (m-40) cc_final: 0.9340 (m-40) REVERT: J 313 MET cc_start: 0.8167 (mpp) cc_final: 0.7796 (mtm) REVERT: J 413 MET cc_start: 0.8971 (mtp) cc_final: 0.8740 (ttm) REVERT: K 155 GLU cc_start: 0.9274 (pt0) cc_final: 0.8582 (pp20) REVERT: K 156 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8780 (mmp80) REVERT: K 214 ARG cc_start: 0.9083 (tmm160) cc_final: 0.8733 (ttp80) REVERT: K 218 ASP cc_start: 0.9480 (m-30) cc_final: 0.9257 (m-30) REVERT: K 300 ASN cc_start: 0.9029 (t160) cc_final: 0.8613 (t0) REVERT: K 313 MET cc_start: 0.9004 (mtm) cc_final: 0.8699 (mtm) REVERT: K 388 TRP cc_start: 0.9196 (m100) cc_final: 0.8771 (m100) REVERT: L 155 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8988 (mt-10) REVERT: L 156 ARG cc_start: 0.9155 (mmp80) cc_final: 0.8953 (mmp80) REVERT: L 214 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8299 (ttp80) REVERT: L 218 ASP cc_start: 0.9473 (m-30) cc_final: 0.9210 (m-30) REVERT: L 293 ASN cc_start: 0.9468 (m-40) cc_final: 0.9264 (m110) REVERT: L 304 LYS cc_start: 0.9455 (tppt) cc_final: 0.9070 (tppt) REVERT: L 308 ARG cc_start: 0.9191 (mtm-85) cc_final: 0.8802 (mtm-85) REVERT: L 313 MET cc_start: 0.8364 (mpp) cc_final: 0.8111 (mtm) REVERT: L 388 TRP cc_start: 0.9302 (m100) cc_final: 0.8954 (m100) REVERT: L 413 MET cc_start: 0.8780 (ttm) cc_final: 0.8431 (ttm) REVERT: M 14 ASN cc_start: 0.7918 (p0) cc_final: 0.7592 (p0) REVERT: M 29 HIS cc_start: 0.9397 (t-90) cc_final: 0.8820 (t-90) REVERT: M 57 HIS cc_start: 0.8259 (t-170) cc_final: 0.7660 (t70) REVERT: M 84 LYS cc_start: 0.9377 (ttmt) cc_final: 0.8980 (ttpt) REVERT: N 29 HIS cc_start: 0.9385 (t-90) cc_final: 0.8696 (t-90) REVERT: N 57 HIS cc_start: 0.8453 (t-170) cc_final: 0.7611 (t70) REVERT: N 100 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7541 (mmtp) REVERT: N 104 ASN cc_start: 0.8588 (m-40) cc_final: 0.8067 (m110) outliers start: 203 outliers final: 154 residues processed: 1469 average time/residue: 0.5776 time to fit residues: 1360.6178 Evaluate side-chains 1468 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1307 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 167 PHE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 392 LYS Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 330 MET Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 114 ASP Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 19 ASP Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 436 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 516 optimal weight: 0.0770 chunk 323 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 298 ASN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN D 204 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS G 292 GLN G 298 ASN G 307 HIS G 384 GLN G 416 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 126 ASN H 204 ASN H 307 HIS I 57 HIS I 89 ASN ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 ASN M 104 ASN ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44232 Z= 0.197 Angle : 0.625 13.416 60052 Z= 0.315 Chirality : 0.044 0.222 6552 Planarity : 0.004 0.051 7788 Dihedral : 11.680 178.279 6068 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 3.72 % Allowed : 22.42 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5394 helix: 1.26 (0.11), residues: 2416 sheet: 0.61 (0.19), residues: 798 loop : -0.88 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 344 HIS 0.008 0.001 HIS K 309 PHE 0.031 0.001 PHE N 115 TYR 0.014 0.001 TYR F 222 ARG 0.015 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1427 time to evaluate : 5.583 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8650 (tt0) cc_final: 0.8308 (mt-10) REVERT: A 211 ASP cc_start: 0.8867 (t70) cc_final: 0.8264 (t70) REVERT: A 215 ARG cc_start: 0.8638 (ttp-170) cc_final: 0.8375 (ttp-170) REVERT: A 280 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8052 (mtmm) REVERT: A 300 ASN cc_start: 0.8878 (t0) cc_final: 0.8414 (t0) REVERT: A 361 THR cc_start: 0.9381 (m) cc_final: 0.8971 (t) REVERT: A 377 MET cc_start: 0.9033 (tmm) cc_final: 0.8363 (tmm) REVERT: A 425 MET cc_start: 0.9080 (tpp) cc_final: 0.8535 (mpp) REVERT: A 430 LYS cc_start: 0.9509 (ttpt) cc_final: 0.9235 (pttm) REVERT: B 161 ASP cc_start: 0.9021 (p0) cc_final: 0.8542 (p0) REVERT: B 203 ASP cc_start: 0.8266 (t0) cc_final: 0.8062 (t0) REVERT: B 252 LYS cc_start: 0.9266 (mttm) cc_final: 0.8828 (mttm) REVERT: B 282 ARG cc_start: 0.7376 (ptm-80) cc_final: 0.7147 (ptm-80) REVERT: B 307 HIS cc_start: 0.9358 (m-70) cc_final: 0.9157 (m-70) REVERT: B 329 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8822 (mm-40) REVERT: B 375 GLN cc_start: 0.8850 (pp30) cc_final: 0.7797 (pp30) REVERT: B 379 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8790 (mtmt) REVERT: C 22 GLU cc_start: 0.8818 (tt0) cc_final: 0.8596 (pt0) REVERT: C 76 ASP cc_start: 0.9070 (m-30) cc_final: 0.8812 (m-30) REVERT: C 168 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7382 (mt-10) REVERT: C 187 SER cc_start: 0.9400 (m) cc_final: 0.9189 (p) REVERT: C 214 ARG cc_start: 0.9250 (tmm-80) cc_final: 0.8876 (tmm-80) REVERT: C 218 ASP cc_start: 0.9349 (m-30) cc_final: 0.9146 (m-30) REVERT: C 256 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: C 280 LYS cc_start: 0.4632 (mmtt) cc_final: 0.3935 (ttpt) REVERT: C 293 ASN cc_start: 0.9432 (m110) cc_final: 0.9166 (p0) REVERT: C 304 LYS cc_start: 0.9158 (tppt) cc_final: 0.8674 (tppt) REVERT: C 377 MET cc_start: 0.8842 (ttp) cc_final: 0.7721 (tmm) REVERT: C 378 LEU cc_start: 0.9547 (mt) cc_final: 0.9184 (mt) REVERT: D 41 ASP cc_start: 0.9005 (p0) cc_final: 0.8693 (p0) REVERT: D 198 GLU cc_start: 0.8578 (pt0) cc_final: 0.8369 (pt0) REVERT: D 202 ILE cc_start: 0.9366 (mt) cc_final: 0.9156 (tp) REVERT: D 203 ASP cc_start: 0.8379 (t0) cc_final: 0.8175 (t70) REVERT: D 323 MET cc_start: 0.8600 (mmp) cc_final: 0.8348 (mmp) REVERT: D 324 LYS cc_start: 0.9280 (ptmm) cc_final: 0.9005 (ptmm) REVERT: D 327 ASP cc_start: 0.9131 (m-30) cc_final: 0.8862 (m-30) REVERT: D 424 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9212 (tm-30) REVERT: D 425 TYR cc_start: 0.8732 (m-10) cc_final: 0.8458 (m-10) REVERT: E 22 GLU cc_start: 0.8991 (pt0) cc_final: 0.8766 (pt0) REVERT: E 76 ASP cc_start: 0.9114 (m-30) cc_final: 0.8733 (m-30) REVERT: E 88 HIS cc_start: 0.8863 (t70) cc_final: 0.8442 (t70) REVERT: E 155 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8757 (mt-10) REVERT: E 203 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8213 (mmm) REVERT: E 230 LEU cc_start: 0.9638 (mp) cc_final: 0.9415 (mp) REVERT: E 280 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8433 (mtmm) REVERT: E 346 TRP cc_start: 0.9088 (p-90) cc_final: 0.8882 (p-90) REVERT: E 349 THR cc_start: 0.8633 (p) cc_final: 0.8359 (p) REVERT: E 361 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9000 (t) REVERT: E 377 MET cc_start: 0.8920 (ttp) cc_final: 0.8196 (tmm) REVERT: E 413 MET cc_start: 0.8803 (tpp) cc_final: 0.8432 (tpp) REVERT: E 430 LYS cc_start: 0.9532 (ttpt) cc_final: 0.9217 (pttm) REVERT: E 433 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8675 (mm-30) REVERT: F 41 ASP cc_start: 0.9023 (p0) cc_final: 0.8659 (p0) REVERT: F 50 TYR cc_start: 0.8981 (m-80) cc_final: 0.8738 (m-80) REVERT: F 86 ARG cc_start: 0.5029 (mmt180) cc_final: 0.3908 (tpt170) REVERT: F 252 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8705 (mtpp) REVERT: F 291 GLN cc_start: 0.8880 (pp30) cc_final: 0.8602 (pp30) REVERT: F 292 GLN cc_start: 0.9058 (tt0) cc_final: 0.8726 (tt0) REVERT: F 293 MET cc_start: 0.8240 (mtt) cc_final: 0.7919 (mtt) REVERT: F 323 MET cc_start: 0.8832 (mmm) cc_final: 0.8594 (mmm) REVERT: F 329 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8598 (mm-40) REVERT: F 375 GLN cc_start: 0.8879 (pp30) cc_final: 0.8447 (pp30) REVERT: G 19 LYS cc_start: 0.8933 (tptt) cc_final: 0.8559 (tptt) REVERT: G 77 ARG cc_start: 0.9054 (ttm110) cc_final: 0.8768 (ttm110) REVERT: G 164 MET cc_start: 0.8523 (ttm) cc_final: 0.8081 (mtp) REVERT: G 198 GLU cc_start: 0.9230 (pt0) cc_final: 0.8738 (pt0) REVERT: G 203 ASP cc_start: 0.7899 (t70) cc_final: 0.7492 (t70) REVERT: G 209 ASP cc_start: 0.9007 (t70) cc_final: 0.8774 (t70) REVERT: G 266 PHE cc_start: 0.9039 (m-10) cc_final: 0.8775 (m-10) REVERT: G 284 LEU cc_start: 0.9104 (mt) cc_final: 0.8834 (mt) REVERT: G 298 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8943 (t0) REVERT: G 299 MET cc_start: 0.8989 (tpp) cc_final: 0.8362 (mpp) REVERT: G 321 MET cc_start: 0.9045 (ptp) cc_final: 0.8679 (ptp) REVERT: G 406 MET cc_start: 0.9257 (tpt) cc_final: 0.8565 (tpt) REVERT: G 410 GLU cc_start: 0.8825 (mm-30) cc_final: 0.7875 (mm-30) REVERT: H 45 GLU cc_start: 0.8726 (pt0) cc_final: 0.8245 (pm20) REVERT: H 74 ASP cc_start: 0.9053 (m-30) cc_final: 0.8822 (m-30) REVERT: H 156 ARG cc_start: 0.9108 (ttt90) cc_final: 0.8816 (tpp-160) REVERT: H 194 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7797 (mm-30) REVERT: H 200 TYR cc_start: 0.8904 (m-80) cc_final: 0.8399 (m-80) REVERT: H 205 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: H 303 CYS cc_start: 0.8366 (p) cc_final: 0.8027 (p) REVERT: H 375 GLN cc_start: 0.9084 (pt0) cc_final: 0.8702 (pp30) REVERT: H 406 MET cc_start: 0.8688 (tpp) cc_final: 0.8321 (tpp) REVERT: H 410 GLU cc_start: 0.8653 (mt-10) cc_final: 0.7813 (mt-10) REVERT: H 423 GLN cc_start: 0.8932 (tp40) cc_final: 0.8379 (tp-100) REVERT: I 198 GLU cc_start: 0.8836 (pt0) cc_final: 0.8271 (pt0) REVERT: I 203 ASP cc_start: 0.7857 (t0) cc_final: 0.6695 (t70) REVERT: I 213 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8237 (tmm-80) REVERT: I 288 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8640 (mt-10) REVERT: I 315 THR cc_start: 0.9732 (m) cc_final: 0.9207 (p) REVERT: I 325 GLU cc_start: 0.9012 (tt0) cc_final: 0.8751 (tt0) REVERT: I 329 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8675 (mm-40) REVERT: I 362 LYS cc_start: 0.8922 (tmmt) cc_final: 0.8508 (tmmt) REVERT: I 406 MET cc_start: 0.8990 (tpt) cc_final: 0.8323 (tpp) REVERT: I 423 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8728 (tm-30) REVERT: I 427 ASP cc_start: 0.8341 (p0) cc_final: 0.7589 (p0) REVERT: J 88 HIS cc_start: 0.8978 (t70) cc_final: 0.8337 (t70) REVERT: J 90 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8894 (mm-30) REVERT: J 155 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9010 (mt-10) REVERT: J 156 ARG cc_start: 0.9074 (mmp80) cc_final: 0.8788 (mmp80) REVERT: J 168 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8105 (mt-10) REVERT: J 290 GLU cc_start: 0.9201 (pt0) cc_final: 0.8802 (pp20) REVERT: J 293 ASN cc_start: 0.9605 (m-40) cc_final: 0.9312 (m-40) REVERT: J 308 ARG cc_start: 0.9373 (mtm-85) cc_final: 0.8980 (mtm-85) REVERT: J 313 MET cc_start: 0.8026 (mpp) cc_final: 0.7698 (mtm) REVERT: J 413 MET cc_start: 0.8918 (mtp) cc_final: 0.8618 (ttm) REVERT: J 425 MET cc_start: 0.9154 (tpp) cc_final: 0.8681 (tpt) REVERT: K 155 GLU cc_start: 0.9260 (pt0) cc_final: 0.8566 (pp20) REVERT: K 156 ARG cc_start: 0.9282 (mmp80) cc_final: 0.8814 (mmp80) REVERT: K 163 LYS cc_start: 0.6934 (mmpt) cc_final: 0.6660 (mmpt) REVERT: K 172 TYR cc_start: 0.8454 (t80) cc_final: 0.7691 (t80) REVERT: K 214 ARG cc_start: 0.9059 (tmm160) cc_final: 0.8726 (ttp80) REVERT: K 218 ASP cc_start: 0.9474 (m-30) cc_final: 0.9250 (m-30) REVERT: K 280 LYS cc_start: 0.9002 (mttm) cc_final: 0.8395 (tptt) REVERT: K 296 PHE cc_start: 0.9106 (m-80) cc_final: 0.8839 (m-80) REVERT: K 300 ASN cc_start: 0.9016 (t160) cc_final: 0.8609 (t0) REVERT: K 420 GLU cc_start: 0.8764 (pt0) cc_final: 0.8388 (pt0) REVERT: L 155 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8956 (mt-10) REVERT: L 156 ARG cc_start: 0.9177 (mmp80) cc_final: 0.8937 (mmp80) REVERT: L 172 TYR cc_start: 0.8390 (t80) cc_final: 0.7618 (t80) REVERT: L 183 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8028 (mt-10) REVERT: L 214 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8215 (ttp80) REVERT: L 215 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8844 (ttp-110) REVERT: L 218 ASP cc_start: 0.9451 (m-30) cc_final: 0.9177 (m-30) REVERT: L 290 GLU cc_start: 0.9352 (pt0) cc_final: 0.8999 (pp20) REVERT: L 304 LYS cc_start: 0.9477 (tppt) cc_final: 0.9049 (tppt) REVERT: L 308 ARG cc_start: 0.9168 (mtm-85) cc_final: 0.8767 (mtm-85) REVERT: L 388 TRP cc_start: 0.9314 (m100) cc_final: 0.8666 (m100) REVERT: L 413 MET cc_start: 0.8739 (ttm) cc_final: 0.8413 (ttm) REVERT: L 425 MET cc_start: 0.9109 (tpp) cc_final: 0.8822 (tpt) REVERT: M 14 ASN cc_start: 0.7774 (p0) cc_final: 0.7451 (p0) REVERT: M 29 HIS cc_start: 0.9373 (t-90) cc_final: 0.8749 (t-90) REVERT: M 57 HIS cc_start: 0.8536 (t-170) cc_final: 0.7962 (t70) REVERT: M 84 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8963 (ttpt) REVERT: N 29 HIS cc_start: 0.9319 (t-90) cc_final: 0.8787 (t-90) REVERT: N 57 HIS cc_start: 0.8508 (t-170) cc_final: 0.7824 (t70) REVERT: N 103 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7866 (t70) REVERT: N 104 ASN cc_start: 0.8589 (m-40) cc_final: 0.7943 (m110) outliers start: 173 outliers final: 127 residues processed: 1512 average time/residue: 0.5804 time to fit residues: 1413.7985 Evaluate side-chains 1497 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1362 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 308 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 406 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 292 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 ASN G 384 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 44232 Z= 0.262 Angle : 0.642 13.835 60052 Z= 0.324 Chirality : 0.045 0.219 6552 Planarity : 0.004 0.080 7788 Dihedral : 11.676 178.996 6068 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 3.74 % Allowed : 22.98 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 5394 helix: 1.20 (0.11), residues: 2422 sheet: 0.82 (0.20), residues: 762 loop : -0.88 (0.14), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 344 HIS 0.007 0.001 HIS C 88 PHE 0.030 0.001 PHE D 367 TYR 0.025 0.001 TYR D 222 ARG 0.008 0.001 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1369 time to evaluate : 5.595 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8792 (pt0) cc_final: 0.8573 (pt0) REVERT: A 207 GLU cc_start: 0.8648 (tt0) cc_final: 0.8335 (mt-10) REVERT: A 211 ASP cc_start: 0.8887 (t70) cc_final: 0.8418 (t70) REVERT: A 300 ASN cc_start: 0.8899 (t0) cc_final: 0.8445 (t0) REVERT: A 361 THR cc_start: 0.9374 (m) cc_final: 0.8965 (t) REVERT: A 377 MET cc_start: 0.9035 (tmm) cc_final: 0.8392 (tmm) REVERT: A 425 MET cc_start: 0.9093 (tpp) cc_final: 0.8532 (mpp) REVERT: A 430 LYS cc_start: 0.9513 (ttpt) cc_final: 0.9225 (pttm) REVERT: B 111 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 147 MET cc_start: 0.9087 (mmm) cc_final: 0.8836 (tpp) REVERT: B 161 ASP cc_start: 0.9056 (p0) cc_final: 0.8513 (p0) REVERT: B 240 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 252 LYS cc_start: 0.9257 (mttm) cc_final: 0.8822 (mttm) REVERT: B 288 GLU cc_start: 0.8581 (tt0) cc_final: 0.8369 (tt0) REVERT: B 329 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8814 (mm-40) REVERT: B 375 GLN cc_start: 0.8827 (pp30) cc_final: 0.7787 (pp30) REVERT: B 379 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8791 (mtmt) REVERT: B 423 GLN cc_start: 0.9208 (tp40) cc_final: 0.8830 (tp40) REVERT: C 76 ASP cc_start: 0.9078 (m-30) cc_final: 0.8815 (m-30) REVERT: C 214 ARG cc_start: 0.9227 (tmm-80) cc_final: 0.8891 (tmm-80) REVERT: C 218 ASP cc_start: 0.9354 (m-30) cc_final: 0.9133 (m-30) REVERT: C 256 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8901 (tt0) REVERT: C 280 LYS cc_start: 0.4470 (mmtt) cc_final: 0.3422 (mmmt) REVERT: C 304 LYS cc_start: 0.9191 (tppt) cc_final: 0.8686 (tppt) REVERT: C 377 MET cc_start: 0.8861 (ttp) cc_final: 0.8161 (tmm) REVERT: C 378 LEU cc_start: 0.9550 (mt) cc_final: 0.9068 (mt) REVERT: C 420 GLU cc_start: 0.8893 (pt0) cc_final: 0.8553 (pm20) REVERT: D 41 ASP cc_start: 0.9006 (p0) cc_final: 0.8693 (p0) REVERT: D 124 CYS cc_start: 0.8894 (m) cc_final: 0.8640 (p) REVERT: D 202 ILE cc_start: 0.9387 (mt) cc_final: 0.9156 (tp) REVERT: D 323 MET cc_start: 0.8635 (mmp) cc_final: 0.8384 (mmp) REVERT: D 324 LYS cc_start: 0.9294 (ptmm) cc_final: 0.9070 (ptmm) REVERT: D 327 ASP cc_start: 0.9151 (m-30) cc_final: 0.8886 (m-30) REVERT: D 375 GLN cc_start: 0.8428 (pp30) cc_final: 0.7192 (pp30) REVERT: D 379 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8589 (mtmt) REVERT: D 424 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.9185 (tm-30) REVERT: D 425 TYR cc_start: 0.8715 (m-10) cc_final: 0.8427 (m-10) REVERT: E 22 GLU cc_start: 0.8999 (pt0) cc_final: 0.8769 (pt0) REVERT: E 76 ASP cc_start: 0.9127 (m-30) cc_final: 0.8731 (m-30) REVERT: E 88 HIS cc_start: 0.8873 (t70) cc_final: 0.8473 (t70) REVERT: E 155 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8756 (mt-10) REVERT: E 214 ARG cc_start: 0.9374 (tmm-80) cc_final: 0.8754 (tmm-80) REVERT: E 230 LEU cc_start: 0.9650 (mp) cc_final: 0.9430 (mp) REVERT: E 280 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8411 (mtmm) REVERT: E 361 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8990 (t) REVERT: E 377 MET cc_start: 0.8971 (ttp) cc_final: 0.8155 (tmm) REVERT: E 425 MET cc_start: 0.9074 (mmm) cc_final: 0.8362 (mmm) REVERT: E 430 LYS cc_start: 0.9524 (ttpt) cc_final: 0.9190 (pttm) REVERT: E 433 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8688 (mm-30) REVERT: E 438 ASP cc_start: 0.8743 (t0) cc_final: 0.8397 (t0) REVERT: F 41 ASP cc_start: 0.9042 (p0) cc_final: 0.8684 (p0) REVERT: F 50 TYR cc_start: 0.8999 (m-80) cc_final: 0.8786 (m-80) REVERT: F 86 ARG cc_start: 0.5045 (mmt180) cc_final: 0.3930 (tpt170) REVERT: F 291 GLN cc_start: 0.8870 (pp30) cc_final: 0.8595 (pp30) REVERT: F 292 GLN cc_start: 0.9087 (tt0) cc_final: 0.8740 (tt0) REVERT: F 293 MET cc_start: 0.8267 (mtt) cc_final: 0.7938 (mtt) REVERT: F 323 MET cc_start: 0.8837 (mmm) cc_final: 0.8614 (mmm) REVERT: F 329 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8639 (mm-40) REVERT: F 375 GLN cc_start: 0.8868 (pp30) cc_final: 0.8434 (pp30) REVERT: G 77 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8750 (ttm110) REVERT: G 198 GLU cc_start: 0.9173 (pt0) cc_final: 0.8679 (pt0) REVERT: G 203 ASP cc_start: 0.7866 (t70) cc_final: 0.7441 (t70) REVERT: G 209 ASP cc_start: 0.9041 (t70) cc_final: 0.8813 (t70) REVERT: G 266 PHE cc_start: 0.9048 (m-10) cc_final: 0.8783 (m-10) REVERT: G 282 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7342 (ttp80) REVERT: G 298 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8819 (t0) REVERT: G 299 MET cc_start: 0.8848 (tpp) cc_final: 0.8166 (mpp) REVERT: G 321 MET cc_start: 0.9070 (ptp) cc_final: 0.8716 (ptp) REVERT: G 350 LYS cc_start: 0.9263 (tptp) cc_final: 0.8636 (tppt) REVERT: G 410 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8494 (mm-30) REVERT: H 156 ARG cc_start: 0.9065 (ttt90) cc_final: 0.8845 (tpp-160) REVERT: H 194 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7846 (mm-30) REVERT: H 200 TYR cc_start: 0.8949 (m-80) cc_final: 0.8481 (m-80) REVERT: H 203 ASP cc_start: 0.7849 (t0) cc_final: 0.7343 (t70) REVERT: H 205 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: H 303 CYS cc_start: 0.8264 (p) cc_final: 0.8040 (p) REVERT: H 406 MET cc_start: 0.8668 (tpp) cc_final: 0.7233 (tpp) REVERT: H 410 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8153 (mm-30) REVERT: H 423 GLN cc_start: 0.8908 (tp40) cc_final: 0.8656 (tp-100) REVERT: I 194 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7590 (mm-30) REVERT: I 198 GLU cc_start: 0.8794 (pt0) cc_final: 0.7814 (pt0) REVERT: I 203 ASP cc_start: 0.8088 (t0) cc_final: 0.7728 (t70) REVERT: I 211 CYS cc_start: 0.9565 (m) cc_final: 0.9298 (m) REVERT: I 213 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8246 (tmm-80) REVERT: I 315 THR cc_start: 0.9695 (m) cc_final: 0.9261 (p) REVERT: I 325 GLU cc_start: 0.9051 (tt0) cc_final: 0.8754 (tt0) REVERT: I 329 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8729 (mm-40) REVERT: I 350 LYS cc_start: 0.9169 (tppt) cc_final: 0.8538 (tppt) REVERT: I 362 LYS cc_start: 0.8929 (tmmt) cc_final: 0.8470 (tmmt) REVERT: I 406 MET cc_start: 0.9020 (tpt) cc_final: 0.7377 (tpp) REVERT: I 410 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8366 (mm-30) REVERT: I 423 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8818 (tm-30) REVERT: I 427 ASP cc_start: 0.8384 (p0) cc_final: 0.7761 (p0) REVERT: J 88 HIS cc_start: 0.8970 (t70) cc_final: 0.8325 (t70) REVERT: J 155 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9047 (mt-10) REVERT: J 168 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8085 (mt-10) REVERT: J 290 GLU cc_start: 0.9210 (pt0) cc_final: 0.8859 (pp20) REVERT: J 293 ASN cc_start: 0.9604 (m-40) cc_final: 0.9319 (m-40) REVERT: J 308 ARG cc_start: 0.9326 (mtm-85) cc_final: 0.8996 (mtm-85) REVERT: J 313 MET cc_start: 0.7992 (mpp) cc_final: 0.7676 (mtm) REVERT: J 413 MET cc_start: 0.8970 (mtp) cc_final: 0.8740 (ttm) REVERT: K 155 GLU cc_start: 0.9256 (pt0) cc_final: 0.8561 (pp20) REVERT: K 156 ARG cc_start: 0.9280 (mmp80) cc_final: 0.8800 (mmp80) REVERT: K 163 LYS cc_start: 0.7049 (mmpt) cc_final: 0.6803 (mmpt) REVERT: K 172 TYR cc_start: 0.8501 (t80) cc_final: 0.7807 (t80) REVERT: K 214 ARG cc_start: 0.9091 (tmm160) cc_final: 0.8760 (ttp80) REVERT: K 218 ASP cc_start: 0.9462 (m-30) cc_final: 0.9255 (m-30) REVERT: K 296 PHE cc_start: 0.9091 (m-80) cc_final: 0.8795 (m-80) REVERT: K 300 ASN cc_start: 0.9078 (t160) cc_final: 0.8729 (t0) REVERT: K 308 ARG cc_start: 0.9008 (mtm-85) cc_final: 0.8762 (mtm-85) REVERT: K 388 TRP cc_start: 0.9141 (m100) cc_final: 0.8304 (m100) REVERT: K 420 GLU cc_start: 0.8777 (pt0) cc_final: 0.8418 (pt0) REVERT: L 1 MET cc_start: 0.5915 (tmm) cc_final: 0.5624 (tpt) REVERT: L 76 ASP cc_start: 0.9394 (m-30) cc_final: 0.9108 (m-30) REVERT: L 155 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8916 (mt-10) REVERT: L 156 ARG cc_start: 0.9183 (mmp80) cc_final: 0.8923 (mmp80) REVERT: L 172 TYR cc_start: 0.8405 (t80) cc_final: 0.7680 (t80) REVERT: L 183 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8008 (mt-10) REVERT: L 214 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8179 (ttp80) REVERT: L 218 ASP cc_start: 0.9446 (m-30) cc_final: 0.9170 (m-30) REVERT: L 290 GLU cc_start: 0.9413 (pt0) cc_final: 0.8937 (pp20) REVERT: L 293 ASN cc_start: 0.9534 (m110) cc_final: 0.9320 (p0) REVERT: L 304 LYS cc_start: 0.9481 (tppt) cc_final: 0.9034 (tppt) REVERT: L 308 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8766 (mtm-85) REVERT: L 313 MET cc_start: 0.8755 (mtm) cc_final: 0.7862 (mtm) REVERT: L 388 TRP cc_start: 0.9320 (m100) cc_final: 0.8751 (m100) REVERT: L 413 MET cc_start: 0.8737 (ttm) cc_final: 0.8381 (ttm) REVERT: L 425 MET cc_start: 0.9217 (tpp) cc_final: 0.8849 (tpt) REVERT: M 14 ASN cc_start: 0.7759 (p0) cc_final: 0.7529 (p0) REVERT: M 29 HIS cc_start: 0.9372 (t-90) cc_final: 0.8736 (t-90) REVERT: M 57 HIS cc_start: 0.8608 (t-170) cc_final: 0.7905 (t70) REVERT: M 84 LYS cc_start: 0.9395 (ttmt) cc_final: 0.9001 (ttpt) REVERT: N 29 HIS cc_start: 0.9334 (t-90) cc_final: 0.8845 (t-90) REVERT: N 57 HIS cc_start: 0.8486 (t-170) cc_final: 0.7913 (t70) REVERT: N 100 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7445 (mmtp) REVERT: N 103 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7831 (t70) REVERT: N 104 ASN cc_start: 0.8512 (m-40) cc_final: 0.7858 (m110) outliers start: 174 outliers final: 140 residues processed: 1454 average time/residue: 0.5951 time to fit residues: 1394.0869 Evaluate side-chains 1497 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1349 time to evaluate : 5.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 404 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 6.9990 chunk 494 optimal weight: 0.9990 chunk 451 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 435 optimal weight: 2.9990 chunk 455 optimal weight: 20.0000 chunk 479 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS D 165 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN G 384 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 204 ASN H 329 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 HIS ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 44232 Z= 0.241 Angle : 0.650 13.785 60052 Z= 0.327 Chirality : 0.045 0.235 6552 Planarity : 0.005 0.075 7788 Dihedral : 11.629 178.144 6068 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 3.57 % Allowed : 23.39 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 5394 helix: 1.18 (0.11), residues: 2416 sheet: 0.80 (0.20), residues: 720 loop : -0.77 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 344 HIS 0.007 0.001 HIS C 88 PHE 0.029 0.001 PHE M 114 TYR 0.025 0.001 TYR D 222 ARG 0.012 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1389 time to evaluate : 4.878 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8781 (pt0) cc_final: 0.8569 (pt0) REVERT: A 207 GLU cc_start: 0.8647 (tt0) cc_final: 0.8319 (mt-10) REVERT: A 211 ASP cc_start: 0.8871 (t70) cc_final: 0.8431 (t70) REVERT: A 300 ASN cc_start: 0.8910 (t0) cc_final: 0.8436 (t0) REVERT: A 361 THR cc_start: 0.9346 (m) cc_final: 0.8943 (t) REVERT: A 377 MET cc_start: 0.9033 (tmm) cc_final: 0.8386 (tmm) REVERT: A 425 MET cc_start: 0.9080 (tpp) cc_final: 0.8528 (mpp) REVERT: A 430 LYS cc_start: 0.9504 (ttpt) cc_final: 0.9192 (pttm) REVERT: B 111 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 147 MET cc_start: 0.9104 (mmm) cc_final: 0.8839 (tpp) REVERT: B 161 ASP cc_start: 0.9079 (p0) cc_final: 0.8519 (p0) REVERT: B 213 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8335 (mtm110) REVERT: B 252 LYS cc_start: 0.9247 (mttm) cc_final: 0.8790 (mttm) REVERT: B 288 GLU cc_start: 0.8585 (tt0) cc_final: 0.8373 (tt0) REVERT: B 307 HIS cc_start: 0.9369 (m-70) cc_final: 0.9109 (m90) REVERT: B 323 MET cc_start: 0.8790 (mmp) cc_final: 0.8534 (mmm) REVERT: B 329 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8803 (mm-40) REVERT: B 375 GLN cc_start: 0.8842 (pp30) cc_final: 0.7876 (pp30) REVERT: B 379 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8800 (mtmt) REVERT: B 423 GLN cc_start: 0.9212 (tp40) cc_final: 0.8830 (tp40) REVERT: C 76 ASP cc_start: 0.9081 (m-30) cc_final: 0.8800 (m-30) REVERT: C 218 ASP cc_start: 0.9328 (m-30) cc_final: 0.9108 (m-30) REVERT: C 256 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: C 280 LYS cc_start: 0.4449 (mmtt) cc_final: 0.3402 (mmmt) REVERT: C 293 ASN cc_start: 0.9433 (m110) cc_final: 0.9180 (p0) REVERT: C 304 LYS cc_start: 0.9200 (tppt) cc_final: 0.8662 (tppt) REVERT: C 377 MET cc_start: 0.8852 (ttp) cc_final: 0.8170 (tmm) REVERT: C 378 LEU cc_start: 0.9548 (mt) cc_final: 0.9078 (mt) REVERT: D 41 ASP cc_start: 0.9048 (p0) cc_final: 0.8780 (p0) REVERT: D 124 CYS cc_start: 0.8876 (m) cc_final: 0.8629 (p) REVERT: D 202 ILE cc_start: 0.9369 (mt) cc_final: 0.9151 (tp) REVERT: D 307 HIS cc_start: 0.9390 (m-70) cc_final: 0.9074 (m-70) REVERT: D 323 MET cc_start: 0.8645 (mmp) cc_final: 0.8415 (mmp) REVERT: D 324 LYS cc_start: 0.9287 (ptmm) cc_final: 0.9067 (ptmm) REVERT: D 327 ASP cc_start: 0.9170 (m-30) cc_final: 0.8902 (m-30) REVERT: D 375 GLN cc_start: 0.8495 (pp30) cc_final: 0.7331 (pp30) REVERT: D 379 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8634 (mtmt) REVERT: D 424 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.9244 (tm-30) REVERT: D 425 TYR cc_start: 0.8687 (m-10) cc_final: 0.8330 (m-10) REVERT: E 1 MET cc_start: 0.7577 (pmm) cc_final: 0.7340 (pmm) REVERT: E 22 GLU cc_start: 0.9008 (pt0) cc_final: 0.8743 (pt0) REVERT: E 76 ASP cc_start: 0.9119 (m-30) cc_final: 0.8724 (m-30) REVERT: E 88 HIS cc_start: 0.8854 (t70) cc_final: 0.8451 (t70) REVERT: E 155 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8750 (mt-10) REVERT: E 203 MET cc_start: 0.8529 (mmm) cc_final: 0.8222 (mmm) REVERT: E 214 ARG cc_start: 0.9380 (tmm-80) cc_final: 0.8758 (tmm-80) REVERT: E 230 LEU cc_start: 0.9645 (mp) cc_final: 0.9424 (mp) REVERT: E 280 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8501 (mtmm) REVERT: E 361 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.8998 (t) REVERT: E 377 MET cc_start: 0.8944 (ttp) cc_final: 0.8175 (tmm) REVERT: E 415 GLU cc_start: 0.9148 (mp0) cc_final: 0.8534 (mt-10) REVERT: E 430 LYS cc_start: 0.9532 (ttpt) cc_final: 0.9171 (pttm) REVERT: E 433 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8702 (mm-30) REVERT: E 438 ASP cc_start: 0.8660 (t0) cc_final: 0.8328 (t0) REVERT: F 41 ASP cc_start: 0.9080 (p0) cc_final: 0.8741 (p0) REVERT: F 50 TYR cc_start: 0.9076 (m-80) cc_final: 0.8823 (m-80) REVERT: F 86 ARG cc_start: 0.5061 (mmt180) cc_final: 0.3662 (tpt170) REVERT: F 291 GLN cc_start: 0.8880 (pp30) cc_final: 0.8593 (pp30) REVERT: F 292 GLN cc_start: 0.9071 (tt0) cc_final: 0.8741 (tt0) REVERT: F 293 MET cc_start: 0.8251 (mtt) cc_final: 0.7908 (mtt) REVERT: F 320 ARG cc_start: 0.8493 (mmp80) cc_final: 0.8216 (mmp80) REVERT: F 323 MET cc_start: 0.8801 (mmm) cc_final: 0.8580 (mmm) REVERT: F 329 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8626 (mm-40) REVERT: F 375 GLN cc_start: 0.8907 (pp30) cc_final: 0.8450 (pp30) REVERT: G 198 GLU cc_start: 0.9074 (pt0) cc_final: 0.8548 (pt0) REVERT: G 203 ASP cc_start: 0.7899 (t70) cc_final: 0.7449 (t70) REVERT: G 209 ASP cc_start: 0.9037 (t70) cc_final: 0.8809 (t70) REVERT: G 266 PHE cc_start: 0.9032 (m-10) cc_final: 0.8725 (m-10) REVERT: G 282 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7025 (ptm-80) REVERT: G 298 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8794 (t0) REVERT: G 299 MET cc_start: 0.8785 (tpp) cc_final: 0.7922 (mpp) REVERT: G 320 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8284 (mmm160) REVERT: G 321 MET cc_start: 0.9070 (ptp) cc_final: 0.8705 (ptp) REVERT: G 410 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8468 (mm-30) REVERT: H 26 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8691 (m-30) REVERT: H 45 GLU cc_start: 0.8729 (pt0) cc_final: 0.8419 (mp0) REVERT: H 53 GLU cc_start: 0.8523 (tp30) cc_final: 0.8294 (tp30) REVERT: H 74 ASP cc_start: 0.9054 (m-30) cc_final: 0.8818 (m-30) REVERT: H 194 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7822 (mm-30) REVERT: H 200 TYR cc_start: 0.8912 (m-80) cc_final: 0.8542 (m-80) REVERT: H 203 ASP cc_start: 0.7878 (t0) cc_final: 0.7548 (t0) REVERT: H 205 GLU cc_start: 0.8711 (tp30) cc_final: 0.8387 (mt-10) REVERT: H 303 CYS cc_start: 0.8331 (p) cc_final: 0.8118 (p) REVERT: H 362 LYS cc_start: 0.8521 (pptt) cc_final: 0.8225 (pptt) REVERT: H 406 MET cc_start: 0.8621 (tpp) cc_final: 0.8260 (tpp) REVERT: H 423 GLN cc_start: 0.8891 (tp40) cc_final: 0.8640 (tp-100) REVERT: I 194 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7678 (mm-30) REVERT: I 203 ASP cc_start: 0.8122 (t0) cc_final: 0.7722 (t70) REVERT: I 211 CYS cc_start: 0.9587 (m) cc_final: 0.9268 (m) REVERT: I 288 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8751 (mt-10) REVERT: I 291 GLN cc_start: 0.8840 (pp30) cc_final: 0.8570 (pp30) REVERT: I 315 THR cc_start: 0.9690 (m) cc_final: 0.9260 (p) REVERT: I 329 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8675 (mm-40) REVERT: I 362 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8537 (tmmt) REVERT: I 406 MET cc_start: 0.9017 (tpt) cc_final: 0.8310 (tpp) REVERT: I 423 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8771 (tm-30) REVERT: I 427 ASP cc_start: 0.8359 (p0) cc_final: 0.7577 (p0) REVERT: J 88 HIS cc_start: 0.8676 (t70) cc_final: 0.8269 (t70) REVERT: J 155 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8968 (mt-10) REVERT: J 156 ARG cc_start: 0.9087 (mmp80) cc_final: 0.8781 (mmp80) REVERT: J 168 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8108 (mt-10) REVERT: J 290 GLU cc_start: 0.9200 (pt0) cc_final: 0.8863 (pp20) REVERT: J 293 ASN cc_start: 0.9602 (m-40) cc_final: 0.9323 (m-40) REVERT: J 308 ARG cc_start: 0.9344 (mtm-85) cc_final: 0.8991 (mtm-85) REVERT: J 313 MET cc_start: 0.7949 (mpp) cc_final: 0.7646 (mtm) REVERT: J 413 MET cc_start: 0.8978 (mtp) cc_final: 0.8693 (ttm) REVERT: J 425 MET cc_start: 0.9050 (tpp) cc_final: 0.8687 (tpt) REVERT: K 155 GLU cc_start: 0.9250 (pt0) cc_final: 0.8555 (pp20) REVERT: K 156 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8810 (mmp80) REVERT: K 163 LYS cc_start: 0.7108 (mmpt) cc_final: 0.6853 (mmpt) REVERT: K 172 TYR cc_start: 0.8495 (t80) cc_final: 0.7751 (t80) REVERT: K 214 ARG cc_start: 0.9150 (tmm160) cc_final: 0.8842 (ttp80) REVERT: K 300 ASN cc_start: 0.9115 (t160) cc_final: 0.8771 (t0) REVERT: K 420 GLU cc_start: 0.8790 (pt0) cc_final: 0.8439 (pt0) REVERT: L 1 MET cc_start: 0.5800 (tmm) cc_final: 0.5513 (tpt) REVERT: L 76 ASP cc_start: 0.9385 (m-30) cc_final: 0.9089 (m-30) REVERT: L 155 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8947 (mt-10) REVERT: L 156 ARG cc_start: 0.9197 (mmp80) cc_final: 0.8938 (mmp80) REVERT: L 172 TYR cc_start: 0.8410 (t80) cc_final: 0.7721 (t80) REVERT: L 183 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7952 (mt-10) REVERT: L 214 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8240 (ttp80) REVERT: L 218 ASP cc_start: 0.9448 (m-30) cc_final: 0.9206 (m-30) REVERT: L 290 GLU cc_start: 0.9373 (pt0) cc_final: 0.9036 (pp20) REVERT: L 293 ASN cc_start: 0.9538 (m110) cc_final: 0.9329 (p0) REVERT: L 304 LYS cc_start: 0.9479 (tppt) cc_final: 0.9107 (tppt) REVERT: L 308 ARG cc_start: 0.9138 (mtm-85) cc_final: 0.8781 (mtm-85) REVERT: L 313 MET cc_start: 0.8774 (mtm) cc_final: 0.7888 (mtm) REVERT: L 388 TRP cc_start: 0.9334 (m100) cc_final: 0.8811 (m100) REVERT: L 413 MET cc_start: 0.8711 (ttm) cc_final: 0.8379 (ttm) REVERT: L 425 MET cc_start: 0.9265 (tpp) cc_final: 0.8717 (tpt) REVERT: L 430 LYS cc_start: 0.9513 (ptmm) cc_final: 0.9271 (pttm) REVERT: M 29 HIS cc_start: 0.9363 (t-90) cc_final: 0.8735 (t-90) REVERT: M 57 HIS cc_start: 0.8530 (t-170) cc_final: 0.8016 (t70) REVERT: M 84 LYS cc_start: 0.9400 (ttmt) cc_final: 0.9037 (ttpt) REVERT: N 29 HIS cc_start: 0.9340 (t-90) cc_final: 0.8809 (t-90) REVERT: N 57 HIS cc_start: 0.8483 (t-170) cc_final: 0.8213 (t70) REVERT: N 100 LYS cc_start: 0.8021 (mmmm) cc_final: 0.7381 (mmtp) REVERT: N 103 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7827 (t70) REVERT: N 104 ASN cc_start: 0.8486 (m-40) cc_final: 0.7813 (m110) outliers start: 166 outliers final: 139 residues processed: 1466 average time/residue: 0.5955 time to fit residues: 1401.0509 Evaluate side-chains 1496 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1350 time to evaluate : 5.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 298 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 329 GLN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 6.9990 chunk 509 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 353 optimal weight: 20.0000 chunk 533 optimal weight: 1.9990 chunk 491 optimal weight: 20.0000 chunk 425 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 89 ASN H 204 ASN H 329 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 165 ASN ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 44232 Z= 0.314 Angle : 0.829 59.159 60052 Z= 0.460 Chirality : 0.047 0.881 6552 Planarity : 0.005 0.139 7788 Dihedral : 11.632 178.112 6068 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 3.42 % Allowed : 23.80 % Favored : 72.78 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 5394 helix: 1.13 (0.11), residues: 2428 sheet: 0.80 (0.20), residues: 720 loop : -0.75 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 344 HIS 0.073 0.001 HIS C 309 PHE 0.027 0.001 PHE D 367 TYR 0.021 0.001 TYR D 222 ARG 0.015 0.001 ARG K 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10788 Ramachandran restraints generated. 5394 Oldfield, 0 Emsley, 5394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1350 time to evaluate : 5.202 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8775 (pt0) cc_final: 0.8557 (pt0) REVERT: A 207 GLU cc_start: 0.8648 (tt0) cc_final: 0.8319 (mt-10) REVERT: A 211 ASP cc_start: 0.8895 (t70) cc_final: 0.8430 (t70) REVERT: A 300 ASN cc_start: 0.8912 (t0) cc_final: 0.8429 (t0) REVERT: A 361 THR cc_start: 0.9344 (m) cc_final: 0.8942 (t) REVERT: A 377 MET cc_start: 0.9034 (tmm) cc_final: 0.8386 (tmm) REVERT: A 425 MET cc_start: 0.9077 (tpp) cc_final: 0.8529 (mpp) REVERT: A 430 LYS cc_start: 0.9504 (ttpt) cc_final: 0.9193 (pttm) REVERT: B 111 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 147 MET cc_start: 0.9101 (mmm) cc_final: 0.8840 (tpp) REVERT: B 161 ASP cc_start: 0.9079 (p0) cc_final: 0.8519 (p0) REVERT: B 213 ARG cc_start: 0.8581 (mtm110) cc_final: 0.8346 (mtm110) REVERT: B 252 LYS cc_start: 0.9237 (mttm) cc_final: 0.8786 (mttm) REVERT: B 288 GLU cc_start: 0.8585 (tt0) cc_final: 0.8374 (tt0) REVERT: B 307 HIS cc_start: 0.9370 (m-70) cc_final: 0.9107 (m90) REVERT: B 329 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8806 (mm-40) REVERT: B 375 GLN cc_start: 0.8840 (pp30) cc_final: 0.7878 (pp30) REVERT: B 379 LYS cc_start: 0.9061 (mtmt) cc_final: 0.8788 (mtmt) REVERT: B 423 GLN cc_start: 0.9215 (tp40) cc_final: 0.8830 (tp40) REVERT: C 76 ASP cc_start: 0.9086 (m-30) cc_final: 0.8804 (m-30) REVERT: C 218 ASP cc_start: 0.9326 (m-30) cc_final: 0.9104 (m-30) REVERT: C 256 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: C 280 LYS cc_start: 0.4444 (mmtt) cc_final: 0.3401 (mmmt) REVERT: C 304 LYS cc_start: 0.9193 (tppt) cc_final: 0.8661 (tppt) REVERT: C 377 MET cc_start: 0.8858 (ttp) cc_final: 0.8167 (tmm) REVERT: C 378 LEU cc_start: 0.9551 (mt) cc_final: 0.9076 (mt) REVERT: D 41 ASP cc_start: 0.9048 (p0) cc_final: 0.8780 (p0) REVERT: D 124 CYS cc_start: 0.8876 (m) cc_final: 0.8621 (p) REVERT: D 202 ILE cc_start: 0.9367 (mt) cc_final: 0.9154 (tp) REVERT: D 307 HIS cc_start: 0.9390 (m-70) cc_final: 0.9074 (m-70) REVERT: D 323 MET cc_start: 0.8645 (mmp) cc_final: 0.8416 (mmp) REVERT: D 324 LYS cc_start: 0.9287 (ptmm) cc_final: 0.9066 (ptmm) REVERT: D 327 ASP cc_start: 0.9170 (m-30) cc_final: 0.8905 (m-30) REVERT: D 375 GLN cc_start: 0.8485 (pp30) cc_final: 0.7324 (pp30) REVERT: D 379 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8634 (mtmt) REVERT: D 424 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.9256 (tm-30) REVERT: D 425 TYR cc_start: 0.8683 (m-10) cc_final: 0.8360 (m-10) REVERT: E 1 MET cc_start: 0.7576 (pmm) cc_final: 0.7340 (pmm) REVERT: E 22 GLU cc_start: 0.9006 (pt0) cc_final: 0.8741 (pt0) REVERT: E 76 ASP cc_start: 0.9131 (m-30) cc_final: 0.8725 (m-30) REVERT: E 88 HIS cc_start: 0.8850 (t70) cc_final: 0.8474 (t70) REVERT: E 155 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8752 (mt-10) REVERT: E 199 ASP cc_start: 0.8531 (m-30) cc_final: 0.8298 (m-30) REVERT: E 203 MET cc_start: 0.8543 (mmm) cc_final: 0.8271 (mmm) REVERT: E 214 ARG cc_start: 0.9381 (tmm-80) cc_final: 0.8758 (tmm-80) REVERT: E 230 LEU cc_start: 0.9646 (mp) cc_final: 0.9435 (mp) REVERT: E 280 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8499 (mtmm) REVERT: E 361 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8998 (t) REVERT: E 377 MET cc_start: 0.8952 (ttp) cc_final: 0.8192 (tmm) REVERT: E 415 GLU cc_start: 0.9154 (mp0) cc_final: 0.8547 (mt-10) REVERT: E 420 GLU cc_start: 0.8459 (mp0) cc_final: 0.8175 (mp0) REVERT: E 430 LYS cc_start: 0.9530 (ttpt) cc_final: 0.9173 (pttm) REVERT: E 433 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8703 (mm-30) REVERT: E 438 ASP cc_start: 0.8697 (t0) cc_final: 0.8344 (t0) REVERT: F 41 ASP cc_start: 0.9079 (p0) cc_final: 0.8741 (p0) REVERT: F 50 TYR cc_start: 0.9092 (m-80) cc_final: 0.8835 (m-80) REVERT: F 86 ARG cc_start: 0.5059 (mmt180) cc_final: 0.3662 (tpt170) REVERT: F 291 GLN cc_start: 0.8897 (pp30) cc_final: 0.8605 (pp30) REVERT: F 292 GLN cc_start: 0.9071 (tt0) cc_final: 0.8741 (tt0) REVERT: F 293 MET cc_start: 0.8239 (mtt) cc_final: 0.7908 (mtt) REVERT: F 320 ARG cc_start: 0.8493 (mmp80) cc_final: 0.8214 (mmp80) REVERT: F 323 MET cc_start: 0.8801 (mmm) cc_final: 0.8580 (mmm) REVERT: F 329 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8624 (mm-40) REVERT: F 341 PHE cc_start: 0.9022 (m-80) cc_final: 0.8334 (t80) REVERT: F 375 GLN cc_start: 0.8906 (pp30) cc_final: 0.8452 (pp30) REVERT: G 198 GLU cc_start: 0.9061 (pt0) cc_final: 0.8547 (pt0) REVERT: G 203 ASP cc_start: 0.7892 (t70) cc_final: 0.7444 (t70) REVERT: G 209 ASP cc_start: 0.9044 (t70) cc_final: 0.8814 (t70) REVERT: G 266 PHE cc_start: 0.9022 (m-10) cc_final: 0.8727 (m-10) REVERT: G 282 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7032 (ptm-80) REVERT: G 299 MET cc_start: 0.8710 (tpp) cc_final: 0.7886 (mpp) REVERT: G 320 ARG cc_start: 0.8529 (mmm160) cc_final: 0.8280 (mmm160) REVERT: G 321 MET cc_start: 0.9070 (ptp) cc_final: 0.8704 (ptp) REVERT: H 26 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8692 (m-30) REVERT: H 53 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8321 (tp30) REVERT: H 74 ASP cc_start: 0.9050 (m-30) cc_final: 0.8816 (m-30) REVERT: H 194 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7824 (mm-30) REVERT: H 200 TYR cc_start: 0.8895 (m-80) cc_final: 0.8545 (m-80) REVERT: H 203 ASP cc_start: 0.7698 (t0) cc_final: 0.7361 (t0) REVERT: H 205 GLU cc_start: 0.8633 (tp30) cc_final: 0.8337 (mt-10) REVERT: H 406 MET cc_start: 0.8624 (tpp) cc_final: 0.7220 (tpp) REVERT: H 410 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8195 (mm-30) REVERT: H 423 GLN cc_start: 0.8890 (tp40) cc_final: 0.8638 (tp-100) REVERT: I 194 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7681 (mm-30) REVERT: I 203 ASP cc_start: 0.8066 (t0) cc_final: 0.7717 (t70) REVERT: I 211 CYS cc_start: 0.9587 (m) cc_final: 0.9272 (m) REVERT: I 288 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8746 (mt-10) REVERT: I 291 GLN cc_start: 0.8841 (pp30) cc_final: 0.8572 (pp30) REVERT: I 315 THR cc_start: 0.9681 (m) cc_final: 0.9262 (p) REVERT: I 329 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8674 (mm-40) REVERT: I 362 LYS cc_start: 0.8953 (tmmt) cc_final: 0.8744 (ttpp) REVERT: I 406 MET cc_start: 0.9018 (tpt) cc_final: 0.8308 (tpp) REVERT: I 423 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8749 (tm-30) REVERT: I 427 ASP cc_start: 0.8358 (p0) cc_final: 0.7630 (p0) REVERT: J 88 HIS cc_start: 0.8667 (t70) cc_final: 0.8281 (t70) REVERT: J 154 MET cc_start: 0.9353 (mmp) cc_final: 0.9063 (mmp) REVERT: J 155 GLU cc_start: 0.9471 (mt-10) cc_final: 0.8964 (mt-10) REVERT: J 156 ARG cc_start: 0.9088 (mmp80) cc_final: 0.8779 (mmp80) REVERT: J 168 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7857 (mt-10) REVERT: J 290 GLU cc_start: 0.9228 (pt0) cc_final: 0.8873 (pp20) REVERT: J 293 ASN cc_start: 0.9602 (m-40) cc_final: 0.9322 (m-40) REVERT: J 308 ARG cc_start: 0.9343 (mtm-85) cc_final: 0.8990 (mtm-85) REVERT: J 313 MET cc_start: 0.7950 (mpp) cc_final: 0.7641 (mtm) REVERT: J 413 MET cc_start: 0.8977 (mtp) cc_final: 0.8693 (ttm) REVERT: J 425 MET cc_start: 0.9070 (tpp) cc_final: 0.8690 (tpt) REVERT: K 155 GLU cc_start: 0.9250 (pt0) cc_final: 0.8554 (pp20) REVERT: K 156 ARG cc_start: 0.9271 (mmp80) cc_final: 0.8810 (mmp80) REVERT: K 163 LYS cc_start: 0.7110 (mmpt) cc_final: 0.6858 (mmpt) REVERT: K 172 TYR cc_start: 0.8504 (t80) cc_final: 0.7748 (t80) REVERT: K 214 ARG cc_start: 0.9149 (tmm160) cc_final: 0.8842 (ttp80) REVERT: K 300 ASN cc_start: 0.9114 (t160) cc_final: 0.8770 (t0) REVERT: K 420 GLU cc_start: 0.8789 (pt0) cc_final: 0.8437 (pt0) REVERT: L 1 MET cc_start: 0.5798 (tmm) cc_final: 0.5479 (tpt) REVERT: L 76 ASP cc_start: 0.9385 (m-30) cc_final: 0.9090 (m-30) REVERT: L 155 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8946 (mt-10) REVERT: L 156 ARG cc_start: 0.9195 (mmp80) cc_final: 0.8938 (mmp80) REVERT: L 172 TYR cc_start: 0.8407 (t80) cc_final: 0.7741 (t80) REVERT: L 183 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7942 (mt-10) REVERT: L 214 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8237 (ttp80) REVERT: L 218 ASP cc_start: 0.9447 (m-30) cc_final: 0.9206 (m-30) REVERT: L 293 ASN cc_start: 0.9538 (m110) cc_final: 0.9333 (p0) REVERT: L 304 LYS cc_start: 0.9478 (tppt) cc_final: 0.9107 (tppt) REVERT: L 308 ARG cc_start: 0.9132 (mtm-85) cc_final: 0.8782 (mtm-85) REVERT: L 313 MET cc_start: 0.8773 (mtm) cc_final: 0.7873 (mtm) REVERT: L 388 TRP cc_start: 0.9336 (m100) cc_final: 0.8808 (m100) REVERT: L 413 MET cc_start: 0.8712 (ttm) cc_final: 0.8382 (ttm) REVERT: L 425 MET cc_start: 0.9265 (tpp) cc_final: 0.8719 (tpt) REVERT: L 430 LYS cc_start: 0.9512 (ptmm) cc_final: 0.9270 (pttm) REVERT: M 29 HIS cc_start: 0.9361 (t-90) cc_final: 0.8734 (t-90) REVERT: M 57 HIS cc_start: 0.8435 (t-170) cc_final: 0.8010 (t70) REVERT: M 84 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9037 (ttpt) REVERT: N 29 HIS cc_start: 0.9336 (t-90) cc_final: 0.8809 (t-90) REVERT: N 57 HIS cc_start: 0.8396 (t-170) cc_final: 0.8183 (t70) REVERT: N 100 LYS cc_start: 0.8021 (mmmm) cc_final: 0.7378 (mmtp) REVERT: N 103 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7826 (t70) REVERT: N 104 ASN cc_start: 0.8485 (m-40) cc_final: 0.7814 (m110) outliers start: 159 outliers final: 149 residues processed: 1424 average time/residue: 0.6110 time to fit residues: 1404.5722 Evaluate side-chains 1496 residues out of total 4656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1340 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 362 LYS Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 329 GLN Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 292 GLN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 328 GLU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 328 GLU Chi-restraints excluded: chain I residue 336 LYS Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 382 THR Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 49 ASP Chi-restraints excluded: chain M residue 55 CYS Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 55 CYS Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 1.9990 chunk 452 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 392 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 118 optimal weight: 0.0570 chunk 425 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 437 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 204 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS ** I 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.090769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071723 restraints weight = 104012.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.074211 restraints weight = 55995.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.075911 restraints weight = 36365.081| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.289 44232 Z= 0.298 Angle : 0.801 59.169 60052 Z= 0.435 Chirality : 0.045 0.633 6552 Planarity : 0.005 0.116 7788 Dihedral : 11.627 178.066 6068 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 3.51 % Allowed : 23.71 % Favored : 72.78 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5394 helix: 1.16 (0.11), residues: 2416 sheet: 0.81 (0.20), residues: 720 loop : -0.77 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 344 HIS 0.087 0.001 HIS C 309 PHE 0.025 0.001 PHE D 367 TYR 0.018 0.001 TYR D 222 ARG 0.014 0.001 ARG K 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18756.99 seconds wall clock time: 336 minutes 38.14 seconds (20198.14 seconds total)