Starting phenix.real_space_refine on Fri Feb 23 07:25:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h38_34455/02_2024/8h38_34455.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 245 5.16 5 C 23674 2.51 5 N 6367 2.21 5 O 7016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 466": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 412": "OD1" <-> "OD2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 157": "OE1" <-> "OE2" Residue "I PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L GLU 278": "OE1" <-> "OE2" Residue "L PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L ASP 760": "OD1" <-> "OD2" Residue "L TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37306 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3296 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3430 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 407} Chain: "C" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3235 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 13, 'TRANS': 393} Chain: "D" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3251 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 396} Chain: "E" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2452 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain: "F" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2279 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain: "G" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1692 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain breaks: 1 Chain: "I" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4505 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 535} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5866 Classifications: {'peptide': 720} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4557 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 22, 'TRANS': 541} Chain breaks: 2 Chain: "R" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "N" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 591 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36171 SG CYS R 42 101.009 98.525 55.565 1.00135.97 S ATOM 36190 SG CYS R 45 102.148 95.106 54.339 1.00137.74 S ATOM 36485 SG CYS R 83 98.573 95.602 55.722 1.00118.07 S ATOM 36414 SG CYS R 75 101.155 109.936 61.737 1.00115.91 S ATOM 36581 SG CYS R 94 100.344 106.504 63.224 1.00129.19 S ATOM 36257 SG CYS R 53 96.883 93.650 52.414 1.00143.05 S ATOM 36280 SG CYS R 56 94.584 92.901 49.482 1.00146.03 S ATOM 36364 SG CYS R 68 96.443 96.034 49.713 1.00133.77 S Time building chain proxies: 18.33, per 1000 atoms: 0.49 Number of scatterers: 37306 At special positions: 0 Unit cell: (156.6, 202.536, 183.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 245 16.00 O 7016 8.00 N 6367 7.00 C 23674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.32 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " pdb=" ZN R4001 " pdb="ZN ZN R4001 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 42 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 45 " pdb="ZN ZN R4001 " - pdb=" SG CYS R 83 " pdb=" ZN R4002 " pdb="ZN ZN R4002 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R4002 " - pdb=" SG CYS R 75 " pdb="ZN ZN R4002 " - pdb=" SG CYS R 94 " pdb=" ZN R4003 " pdb="ZN ZN R4003 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 53 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 56 " pdb="ZN ZN R4003 " - pdb=" SG CYS R 68 " Number of angles added : 6 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8890 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 28 sheets defined 60.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 83 through 91 removed outlier: 3.791A pdb=" N TYR A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 128 through 146 removed outlier: 3.719A pdb=" N GLU A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 192 Processing helix chain 'A' and resid 193 through 212 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.651A pdb=" N TYR A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 removed outlier: 3.541A pdb=" N THR A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.269A pdb=" N LYS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.730A pdb=" N SER A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.616A pdb=" N ASP A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 removed outlier: 4.015A pdb=" N ARG A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 466 through 498 removed outlier: 3.760A pdb=" N THR A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N ASN B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 4.116A pdb=" N GLY B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 85 through 100 removed outlier: 3.903A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 124 through 142 removed outlier: 3.783A pdb=" N ALA B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.509A pdb=" N ARG B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.998A pdb=" N LYS B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 3.738A pdb=" N GLU B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.800A pdb=" N HIS B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.614A pdb=" N ALA B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 321 removed outlier: 4.408A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.909A pdb=" N MET B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 367 removed outlier: 4.393A pdb=" N GLU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 420 through 443 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 52 through 68 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 96 through 115 removed outlier: 3.548A pdb=" N PHE C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 3.578A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.652A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 removed outlier: 3.830A pdb=" N TYR C 161 " --> pdb=" O PRO C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.854A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.737A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.575A pdb=" N LYS C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 400 removed outlier: 3.822A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 removed outlier: 3.840A pdb=" N VAL C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 removed outlier: 3.572A pdb=" N ASN D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.503A pdb=" N LEU D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.619A pdb=" N GLN D 41 " --> pdb=" O SER D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 100 through 117 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.539A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.691A pdb=" N ASP D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 176 removed outlier: 3.581A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.707A pdb=" N TYR D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.745A pdb=" N GLN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 258' Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.636A pdb=" N PHE D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 315 removed outlier: 3.594A pdb=" N LEU D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 44 through 48 Processing helix chain 'E' and resid 58 through 72 Processing helix chain 'E' and resid 112 through 128 removed outlier: 3.937A pdb=" N TYR E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 207 through 218 removed outlier: 4.664A pdb=" N GLU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 247 removed outlier: 3.651A pdb=" N VAL E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 284 removed outlier: 4.482A pdb=" N THR E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 330 removed outlier: 3.740A pdb=" N ASP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 62 removed outlier: 3.607A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.512A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 209 Processing helix chain 'F' and resid 217 through 248 Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.565A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.626A pdb=" N GLN G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 57 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 73 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.568A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.652A pdb=" N LEU G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 138 Processing helix chain 'G' and resid 165 through 220 removed outlier: 4.333A pdb=" N ASN G 169 " --> pdb=" O LYS G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 26 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.633A pdb=" N LYS H 65 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 84 removed outlier: 3.811A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 3.769A pdb=" N HIS H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 150 removed outlier: 3.528A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 209 removed outlier: 3.759A pdb=" N ASN H 209 " --> pdb=" O ALA H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 27 removed outlier: 3.731A pdb=" N LEU I 17 " --> pdb=" O TYR I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.581A pdb=" N LEU I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 62 removed outlier: 3.529A pdb=" N SER I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 100 through 112 Processing helix chain 'I' and resid 113 through 127 Processing helix chain 'I' and resid 132 through 143 Processing helix chain 'I' and resid 145 through 164 removed outlier: 3.673A pdb=" N THR I 161 " --> pdb=" O GLU I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'I' and resid 173 through 183 Processing helix chain 'I' and resid 191 through 203 removed outlier: 3.817A pdb=" N ARG I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 217 removed outlier: 3.873A pdb=" N TYR I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER I 214 " --> pdb=" O SER I 210 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER I 215 " --> pdb=" O GLN I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 220 No H-bonds generated for 'chain 'I' and resid 218 through 220' Processing helix chain 'I' and resid 221 through 225 Processing helix chain 'I' and resid 228 through 236 removed outlier: 4.117A pdb=" N GLN I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY I 236 " --> pdb=" O ALA I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 250 Processing helix chain 'L' and resid 26 through 46 removed outlier: 3.634A pdb=" N VAL L 30 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 67 removed outlier: 4.091A pdb=" N LEU L 57 " --> pdb=" O SER L 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 88 Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 100 through 135 removed outlier: 4.246A pdb=" N MET L 118 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL L 129 " --> pdb=" O TYR L 125 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN L 133 " --> pdb=" O VAL L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 156 through 175 removed outlier: 3.717A pdb=" N GLY L 175 " --> pdb=" O ARG L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 195 removed outlier: 3.928A pdb=" N LEU L 195 " --> pdb=" O MET L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 228 removed outlier: 3.650A pdb=" N GLU L 203 " --> pdb=" O SER L 199 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) Proline residue: L 208 - end of helix removed outlier: 3.889A pdb=" N ALA L 226 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 252 Processing helix chain 'L' and resid 257 through 280 removed outlier: 3.589A pdb=" N LYS L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 263 " --> pdb=" O PRO L 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU L 278 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET L 279 " --> pdb=" O THR L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 290 Processing helix chain 'L' and resid 292 through 304 Processing helix chain 'L' and resid 308 through 329 removed outlier: 4.004A pdb=" N THR L 312 " --> pdb=" O ASN L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 359 Processing helix chain 'L' and resid 363 through 378 removed outlier: 3.647A pdb=" N LEU L 378 " --> pdb=" O PHE L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 398 removed outlier: 3.612A pdb=" N LYS L 398 " --> pdb=" O ASP L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 421 removed outlier: 3.606A pdb=" N MET L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL L 417 " --> pdb=" O ASP L 413 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE L 421 " --> pdb=" O VAL L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 424 through 441 removed outlier: 3.677A pdb=" N PHE L 428 " --> pdb=" O GLU L 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU L 436 " --> pdb=" O TYR L 432 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA L 437 " --> pdb=" O LYS L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 462 Processing helix chain 'L' and resid 464 through 494 removed outlier: 4.007A pdb=" N LYS L 469 " --> pdb=" O GLN L 465 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 542 Processing helix chain 'L' and resid 598 through 608 Processing helix chain 'L' and resid 612 through 619 Processing helix chain 'L' and resid 625 through 632 Processing helix chain 'L' and resid 664 through 668 Processing helix chain 'L' and resid 687 through 714 removed outlier: 3.706A pdb=" N THR L 691 " --> pdb=" O GLU L 687 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU L 702 " --> pdb=" O ASP L 698 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS L 712 " --> pdb=" O VAL L 708 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER L 713 " --> pdb=" O ARG L 709 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 726 Processing helix chain 'L' and resid 727 through 730 Processing helix chain 'L' and resid 737 through 744 removed outlier: 3.852A pdb=" N ILE L 741 " --> pdb=" O SER L 737 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS L 743 " --> pdb=" O VAL L 739 " (cutoff:3.500A) Processing helix chain 'L' and resid 746 through 751 removed outlier: 3.530A pdb=" N ILE L 749 " --> pdb=" O GLU L 746 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU L 750 " --> pdb=" O GLY L 747 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 27 Processing helix chain 'M' and resid 45 through 53 removed outlier: 3.660A pdb=" N ALA M 50 " --> pdb=" O LYS M 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS M 52 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 100 through 112 Processing helix chain 'M' and resid 113 through 128 Processing helix chain 'M' and resid 132 through 143 Processing helix chain 'M' and resid 145 through 164 removed outlier: 3.535A pdb=" N HIS M 158 " --> pdb=" O ARG M 154 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 161 " --> pdb=" O GLU M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 170 Processing helix chain 'M' and resid 173 through 183 Processing helix chain 'M' and resid 191 through 204 removed outlier: 3.744A pdb=" N ARG M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 208 removed outlier: 5.803A pdb=" N SER M 208 " --> pdb=" O ASN M 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 205 through 208' Processing helix chain 'M' and resid 209 through 217 removed outlier: 3.849A pdb=" N SER M 214 " --> pdb=" O SER M 210 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER M 215 " --> pdb=" O GLN M 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 218 through 220 No H-bonds generated for 'chain 'M' and resid 218 through 220' Processing helix chain 'M' and resid 230 through 237 Processing helix chain 'M' and resid 244 through 250 removed outlier: 3.524A pdb=" N TYR M 250 " --> pdb=" O VAL M 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'N' and resid 22 through 34 removed outlier: 3.955A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 27 " --> pdb=" O VAL N 23 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'B' and resid 402 through 403 removed outlier: 5.678A pdb=" N ILE B 402 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 419 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 418 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 315 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 453 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 317 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 370 removed outlier: 3.802A pdb=" N ILE B 369 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 358 through 359 removed outlier: 6.574A pdb=" N LYS G 144 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL G 154 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP G 146 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU G 152 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 221 through 223 removed outlier: 4.292A pdb=" N ASN E 182 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N VAL E 166 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE E 134 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 132 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET E 81 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP E 136 " --> pdb=" O GLY E 79 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY E 79 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.535A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU F 77 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 41 " --> pdb=" O THR F 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA7, first strand: chain 'I' and resid 40 through 44 removed outlier: 3.605A pdb=" N ILE I 33 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 72 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 580 through 586 removed outlier: 3.537A pdb=" N ARG I 580 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU I 266 " --> pdb=" O LEU I 586 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE I 270 " --> pdb=" O TYR I 288 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR I 288 " --> pdb=" O ILE I 270 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE I 272 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL I 286 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 285 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU I 592 " --> pdb=" O LYS I 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 309 through 312 removed outlier: 3.713A pdb=" N GLY I 309 " --> pdb=" O ALA I 321 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 321 " --> pdb=" O GLY I 309 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 311 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 319 " --> pdb=" O VAL I 311 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE I 318 " --> pdb=" O PHE I 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.710A pdb=" N SER I 374 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU I 408 " --> pdb=" O ASP I 403 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 423 through 427 removed outlier: 3.564A pdb=" N TYR I 440 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER I 448 " --> pdb=" O PHE I 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 463 through 467 removed outlier: 4.174A pdb=" N SER I 463 " --> pdb=" O ILE I 474 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE I 474 " --> pdb=" O SER I 463 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP I 503 " --> pdb=" O GLU I 508 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU I 508 " --> pdb=" O ASP I 503 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 527 through 530 removed outlier: 3.549A pdb=" N VAL I 528 " --> pdb=" O CYS I 535 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS I 535 " --> pdb=" O VAL I 528 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LEU I 534 " --> pdb=" O TYR I 554 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET I 538 " --> pdb=" O VAL I 550 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 550 " --> pdb=" O MET I 538 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 540 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS I 548 " --> pdb=" O GLU I 540 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR I 549 " --> pdb=" O HIS I 566 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS I 566 " --> pdb=" O TYR I 549 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR I 551 " --> pdb=" O ARG I 564 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG I 564 " --> pdb=" O THR I 551 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 502 through 503 removed outlier: 3.503A pdb=" N ASP L 502 " --> pdb=" O LYS R 25 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP L 558 " --> pdb=" O LYS R 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 506 through 509 removed outlier: 5.962A pdb=" N ARG L 506 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP R 33 " --> pdb=" O ARG L 506 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU L 508 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU R 32 " --> pdb=" O THR L 549 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA R 34 " --> pdb=" O GLN L 547 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN L 547 " --> pdb=" O ALA R 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 645 through 646 Processing sheet with id=AB8, first strand: chain 'M' and resid 40 through 44 removed outlier: 3.705A pdb=" N ILE M 33 " --> pdb=" O CYS M 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL M 72 " --> pdb=" O VAL M 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 295 through 297 removed outlier: 3.519A pdb=" N GLU M 266 " --> pdb=" O LEU M 586 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 586 " --> pdb=" O GLU M 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 274 through 275 Processing sheet with id=AC2, first strand: chain 'M' and resid 309 through 312 removed outlier: 3.602A pdb=" N GLY M 309 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA M 321 " --> pdb=" O GLY M 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL M 311 " --> pdb=" O TYR M 319 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE M 318 " --> pdb=" O PHE M 353 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE M 350 " --> pdb=" O LYS M 363 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR M 359 " --> pdb=" O ASP M 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 324 through 325 Processing sheet with id=AC4, first strand: chain 'M' and resid 374 through 378 removed outlier: 3.816A pdb=" N SER M 374 " --> pdb=" O ILE M 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU M 400 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 423 through 427 removed outlier: 3.608A pdb=" N VAL M 433 " --> pdb=" O TYR M 440 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR M 440 " --> pdb=" O VAL M 433 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER M 448 " --> pdb=" O PHE M 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 463 through 467 removed outlier: 3.909A pdb=" N SER M 463 " --> pdb=" O ILE M 474 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 465 " --> pdb=" O PHE M 472 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE M 472 " --> pdb=" O ALA M 465 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU M 508 " --> pdb=" O ASP M 503 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 527 through 530 removed outlier: 4.752A pdb=" N LEU M 534 " --> pdb=" O TYR M 554 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M 550 " --> pdb=" O MET M 538 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR M 549 " --> pdb=" O HIS M 566 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N HIS M 566 " --> pdb=" O TYR M 549 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR M 551 " --> pdb=" O ARG M 564 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG M 564 " --> pdb=" O THR M 551 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG M 560 " --> pdb=" O ASP M 555 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 78 through 80 Processing sheet with id=AC9, first strand: chain 'N' and resid 13 through 16 removed outlier: 8.844A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 44 through 45 2146 hydrogen bonds defined for protein. 6282 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: 14.46 Time building geometry restraints manager: 15.38 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: 7466 1.33 - 1.45: 8734 1.45 - 1.57: 21425 1.57 - 1.69: 1 1.69 - 1.81: 390 Bond restraints: 38016 Sorted by residual: bond pdb=" C CYS F 264 " pdb=" O CYS F 264 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.17e-02 7.31e+03 4.43e+01 bond pdb=" N TYR A 75 " pdb=" CA TYR A 75 " ideal model delta sigma weight residual 1.458 1.486 -0.028 6.30e-03 2.52e+04 1.94e+01 bond pdb=" C HIS F 254 " pdb=" O HIS F 254 " ideal model delta sigma weight residual 1.235 1.285 -0.049 1.26e-02 6.30e+03 1.53e+01 bond pdb=" N LYS B 364 " pdb=" CA LYS B 364 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" N ILE N 36 " pdb=" CA ILE N 36 " ideal model delta sigma weight residual 1.461 1.494 -0.034 9.10e-03 1.21e+04 1.37e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.97: 675 105.97 - 113.07: 20591 113.07 - 120.18: 13620 120.18 - 127.28: 16151 127.28 - 134.39: 329 Bond angle restraints: 51366 Sorted by residual: angle pdb=" C THR C 245 " pdb=" CA THR C 245 " pdb=" CB THR C 245 " ideal model delta sigma weight residual 115.79 107.29 8.50 1.19e+00 7.06e-01 5.10e+01 angle pdb=" C SER E 95 " pdb=" N PHE E 96 " pdb=" CA PHE E 96 " ideal model delta sigma weight residual 121.94 113.00 8.94 1.76e+00 3.23e-01 2.58e+01 angle pdb=" N LYS E 125 " pdb=" CA LYS E 125 " pdb=" C LYS E 125 " ideal model delta sigma weight residual 111.71 105.93 5.78 1.15e+00 7.56e-01 2.53e+01 angle pdb=" N PRO F 268 " pdb=" CA PRO F 268 " pdb=" CB PRO F 268 " ideal model delta sigma weight residual 102.35 105.89 -3.54 7.10e-01 1.98e+00 2.49e+01 angle pdb=" C PRO M 254 " pdb=" N LYS M 255 " pdb=" CA LYS M 255 " ideal model delta sigma weight residual 122.74 129.47 -6.73 1.44e+00 4.82e-01 2.18e+01 ... (remaining 51361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 21372 18.06 - 36.11: 1427 36.11 - 54.17: 262 54.17 - 72.22: 92 72.22 - 90.28: 22 Dihedral angle restraints: 23175 sinusoidal: 9471 harmonic: 13704 Sorted by residual: dihedral pdb=" C ASP L 685 " pdb=" N ASP L 685 " pdb=" CA ASP L 685 " pdb=" CB ASP L 685 " ideal model delta harmonic sigma weight residual -122.60 -137.93 15.33 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" CA LYS M 255 " pdb=" C LYS M 255 " pdb=" N PHE M 256 " pdb=" CA PHE M 256 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" N ASP L 685 " pdb=" C ASP L 685 " pdb=" CA ASP L 685 " pdb=" CB ASP L 685 " ideal model delta harmonic sigma weight residual 122.80 137.33 -14.53 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 23172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 5529 0.107 - 0.214: 206 0.214 - 0.321: 12 0.321 - 0.428: 1 0.428 - 0.535: 1 Chirality restraints: 5749 Sorted by residual: chirality pdb=" CA ASP L 685 " pdb=" N ASP L 685 " pdb=" C ASP L 685 " pdb=" CB ASP L 685 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA TYR E 143 " pdb=" N TYR E 143 " pdb=" C TYR E 143 " pdb=" CB TYR E 143 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA GLU E 115 " pdb=" N GLU E 115 " pdb=" C GLU E 115 " pdb=" CB GLU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 5746 not shown) Planarity restraints: 6583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 286 " 0.085 5.00e-02 4.00e+02 1.30e-01 2.68e+01 pdb=" N PRO D 287 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 226 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C VAL E 226 " -0.078 2.00e-02 2.50e+03 pdb=" O VAL E 226 " 0.029 2.00e-02 2.50e+03 pdb=" N SER E 227 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 254 " 0.054 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 255 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 255 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 255 " 0.046 5.00e-02 4.00e+02 ... (remaining 6580 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 248 2.57 - 3.15: 30671 3.15 - 3.73: 60853 3.73 - 4.32: 80961 4.32 - 4.90: 131742 Nonbonded interactions: 304475 Sorted by model distance: nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.986 2.230 nonbonded pdb=" OG SER I 275 " pdb=" O ASP I 574 " model vdw 2.210 2.440 nonbonded pdb=" OG SER M 389 " pdb=" OG1 THR M 398 " model vdw 2.217 2.440 nonbonded pdb=" O GLY L 463 " pdb=" OG1 THR L 467 " model vdw 2.219 2.440 nonbonded pdb=" O PRO C 255 " pdb=" ND2 ASN M 544 " model vdw 2.224 2.520 ... (remaining 304470 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 'I' and resid 7 through 598) selection = (chain 'M' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 325 or resid 344 through 477 or resid 496 through 598)) } 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: 0.850 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: 0.030 Extract box with map and model: 4.480 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 100.710 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.160 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: 111.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 38016 Z= 0.264 Angle : 0.696 10.225 51366 Z= 0.450 Chirality : 0.046 0.535 5749 Planarity : 0.004 0.130 6583 Dihedral : 13.050 90.279 14285 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.48 % Favored : 92.84 % Rotamer: Outliers : 2.22 % Allowed : 1.56 % Favored : 96.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4597 helix: 1.18 (0.10), residues: 2607 sheet: -1.05 (0.24), residues: 430 loop : -2.11 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 246 HIS 0.007 0.001 HIS E 49 PHE 0.025 0.001 PHE M 160 TYR 0.021 0.001 TYR E 143 ARG 0.004 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1323 time to evaluate : 4.167 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: 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: 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 83 ASP cc_start: 0.6533 (t0) cc_final: 0.6109 (t0) REVERT: A 97 ILE cc_start: 0.7226 (mt) cc_final: 0.6993 (mt) REVERT: A 102 PHE cc_start: 0.5963 (t80) cc_final: 0.5277 (t80) REVERT: A 117 MET cc_start: 0.8413 (mtt) cc_final: 0.6954 (mtt) REVERT: A 130 MET cc_start: 0.6863 (mmp) cc_final: 0.6344 (mmp) REVERT: A 132 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 234 VAL cc_start: 0.8361 (t) cc_final: 0.8008 (t) REVERT: A 235 ILE cc_start: 0.8568 (mt) cc_final: 0.7827 (mt) REVERT: A 237 MET cc_start: 0.6095 (ttp) cc_final: 0.5560 (ttp) REVERT: A 293 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6864 (mm-30) REVERT: A 332 CYS cc_start: 0.7038 (m) cc_final: 0.6358 (p) REVERT: A 342 LEU cc_start: 0.7246 (mt) cc_final: 0.7036 (mt) REVERT: A 364 ASP cc_start: 0.8159 (m-30) cc_final: 0.7206 (m-30) REVERT: A 365 ILE cc_start: 0.7902 (mt) cc_final: 0.7693 (mm) REVERT: A 388 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5346 (pp) REVERT: A 389 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6582 (mt) REVERT: A 437 GLU cc_start: 0.6473 (tt0) cc_final: 0.5913 (tm-30) REVERT: A 438 ASP cc_start: 0.6009 (m-30) cc_final: 0.4917 (m-30) REVERT: A 472 PHE cc_start: 0.5424 (m-80) cc_final: 0.4769 (m-10) REVERT: B 78 ILE cc_start: 0.8186 (mt) cc_final: 0.7367 (tp) REVERT: B 88 MET cc_start: 0.7645 (tmm) cc_final: 0.5626 (tmm) REVERT: B 89 MET cc_start: 0.7136 (ttm) cc_final: 0.6537 (mmm) REVERT: B 96 LEU cc_start: 0.7799 (mt) cc_final: 0.7267 (mt) REVERT: B 109 GLU cc_start: 0.7309 (pt0) cc_final: 0.6008 (pp20) REVERT: B 112 ILE cc_start: 0.8371 (mm) cc_final: 0.7899 (pt) REVERT: B 117 ASP cc_start: 0.7870 (m-30) cc_final: 0.7628 (m-30) REVERT: B 128 LEU cc_start: 0.8061 (mm) cc_final: 0.7751 (mt) REVERT: B 137 GLU cc_start: 0.6882 (pt0) cc_final: 0.6491 (tm-30) REVERT: B 150 LYS cc_start: 0.9025 (mttp) cc_final: 0.8523 (mmtm) REVERT: B 179 CYS cc_start: 0.7310 (m) cc_final: 0.7034 (p) REVERT: B 190 LYS cc_start: 0.7229 (mmpt) cc_final: 0.6996 (mtmm) REVERT: B 194 LEU cc_start: 0.7778 (mt) cc_final: 0.6852 (mt) REVERT: B 196 GLU cc_start: 0.6798 (mp0) cc_final: 0.6557 (mp0) REVERT: B 214 LEU cc_start: 0.8068 (mt) cc_final: 0.7507 (mt) REVERT: B 215 LYS cc_start: 0.7010 (pttm) cc_final: 0.6302 (pttm) REVERT: B 218 TYR cc_start: 0.7787 (t80) cc_final: 0.7367 (t80) REVERT: B 237 ILE cc_start: 0.8211 (mt) cc_final: 0.6715 (tp) REVERT: B 240 CYS cc_start: 0.7639 (t) cc_final: 0.6921 (p) REVERT: B 244 MET cc_start: 0.7518 (ttp) cc_final: 0.7218 (mmp) REVERT: B 260 GLU cc_start: 0.8479 (mt-10) cc_final: 0.6777 (mm-30) REVERT: B 262 PHE cc_start: 0.7220 (t80) cc_final: 0.5731 (t80) REVERT: B 263 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8282 (mtmm) REVERT: B 265 TYR cc_start: 0.7466 (m-10) cc_final: 0.7073 (m-80) REVERT: B 266 ASP cc_start: 0.7588 (m-30) cc_final: 0.7240 (m-30) REVERT: B 267 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6756 (pt0) REVERT: B 277 LEU cc_start: 0.8482 (tp) cc_final: 0.8225 (tp) REVERT: B 284 ASN cc_start: 0.7577 (t0) cc_final: 0.7206 (t0) REVERT: B 285 MET cc_start: 0.8215 (mtm) cc_final: 0.7616 (ptm) REVERT: B 304 ASN cc_start: 0.8403 (m-40) cc_final: 0.7158 (p0) REVERT: B 312 THR cc_start: 0.8886 (m) cc_final: 0.8528 (p) REVERT: B 315 VAL cc_start: 0.9410 (t) cc_final: 0.9060 (t) REVERT: B 326 PHE cc_start: 0.7504 (t80) cc_final: 0.6940 (t80) REVERT: B 328 LYS cc_start: 0.9200 (tttt) cc_final: 0.8464 (ttpp) REVERT: B 329 ILE cc_start: 0.8676 (mt) cc_final: 0.7720 (mm) REVERT: B 330 LEU cc_start: 0.9217 (mt) cc_final: 0.8761 (mt) REVERT: B 331 LYS cc_start: 0.8851 (mttt) cc_final: 0.8004 (mmtm) REVERT: B 345 GLU cc_start: 0.8019 (tt0) cc_final: 0.6711 (tm-30) REVERT: B 346 HIS cc_start: 0.8003 (m-70) cc_final: 0.6997 (m-70) REVERT: B 348 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7839 (mp0) REVERT: B 349 GLU cc_start: 0.8309 (tt0) cc_final: 0.7531 (mp0) REVERT: B 352 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: B 354 ILE cc_start: 0.8336 (tt) cc_final: 0.8019 (pt) REVERT: B 355 ARG cc_start: 0.8516 (mtt180) cc_final: 0.8082 (mtt90) REVERT: B 357 GLN cc_start: 0.8369 (mt0) cc_final: 0.7867 (mm-40) REVERT: B 363 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6213 (mt) REVERT: B 364 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8554 (mtmm) REVERT: B 384 ASP cc_start: 0.7973 (m-30) cc_final: 0.7144 (m-30) REVERT: B 386 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 388 LEU cc_start: 0.8637 (mp) cc_final: 0.8373 (mm) REVERT: B 390 VAL cc_start: 0.9207 (t) cc_final: 0.8777 (p) REVERT: B 395 ASP cc_start: 0.7990 (m-30) cc_final: 0.7329 (m-30) REVERT: C 25 CYS cc_start: 0.7661 (m) cc_final: 0.7267 (p) REVERT: C 59 LEU cc_start: 0.7634 (tp) cc_final: 0.7400 (tt) REVERT: C 92 HIS cc_start: 0.6291 (m90) cc_final: 0.5691 (m-70) REVERT: C 104 CYS cc_start: 0.7883 (m) cc_final: 0.6852 (p) REVERT: C 156 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7377 (ttpp) REVERT: C 190 MET cc_start: 0.7246 (mtp) cc_final: 0.6831 (mtp) REVERT: C 224 TYR cc_start: 0.7143 (t80) cc_final: 0.6797 (t80) REVERT: C 225 LYS cc_start: 0.6923 (mttt) cc_final: 0.6599 (mmtt) REVERT: C 262 GLU cc_start: 0.8694 (tt0) cc_final: 0.8238 (tt0) REVERT: C 274 GLU cc_start: 0.7887 (tt0) cc_final: 0.7648 (tt0) REVERT: C 282 HIS cc_start: 0.5531 (m-70) cc_final: 0.5054 (m-70) REVERT: C 337 TYR cc_start: 0.7842 (m-80) cc_final: 0.6847 (m-80) REVERT: C 344 ASP cc_start: 0.7990 (m-30) cc_final: 0.7343 (m-30) REVERT: C 346 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7344 (mp0) REVERT: C 348 PHE cc_start: 0.7282 (m-80) cc_final: 0.6956 (m-80) REVERT: C 357 MET cc_start: 0.4989 (mmm) cc_final: 0.4466 (mmm) REVERT: C 359 SER cc_start: 0.7137 (m) cc_final: 0.6859 (t) REVERT: C 380 MET cc_start: 0.7144 (ttp) cc_final: 0.6569 (mmt) REVERT: D 66 LEU cc_start: 0.8083 (mt) cc_final: 0.7711 (mt) REVERT: D 68 ASP cc_start: 0.7963 (m-30) cc_final: 0.7632 (m-30) REVERT: D 127 LEU cc_start: 0.9538 (tp) cc_final: 0.8947 (tp) REVERT: D 139 TYR cc_start: 0.5810 (m-80) cc_final: 0.5517 (m-80) REVERT: D 140 ASN cc_start: 0.8703 (t0) cc_final: 0.8447 (t0) REVERT: D 143 TYR cc_start: 0.7107 (t80) cc_final: 0.6845 (t80) REVERT: D 155 TYR cc_start: 0.8662 (m-80) cc_final: 0.8363 (m-80) REVERT: D 173 LEU cc_start: 0.6912 (mt) cc_final: 0.5704 (mt) REVERT: D 196 ASP cc_start: 0.7866 (t0) cc_final: 0.7654 (t0) REVERT: D 227 LYS cc_start: 0.8461 (tttt) cc_final: 0.7247 (tptt) REVERT: D 228 HIS cc_start: 0.4438 (m-70) cc_final: 0.3973 (m-70) REVERT: D 231 HIS cc_start: 0.7131 (m170) cc_final: 0.6840 (m170) REVERT: D 246 LEU cc_start: 0.8367 (mt) cc_final: 0.8008 (tp) REVERT: D 267 MET cc_start: 0.7711 (tpp) cc_final: 0.7465 (tmm) REVERT: D 271 ARG cc_start: 0.7002 (mtm-85) cc_final: 0.6644 (mmt180) REVERT: D 272 ILE cc_start: 0.6985 (mm) cc_final: 0.6763 (pt) REVERT: D 284 MET cc_start: 0.7692 (mtt) cc_final: 0.7391 (mtt) REVERT: D 306 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7411 (mm-30) REVERT: D 307 HIS cc_start: 0.6883 (t70) cc_final: 0.6264 (t70) REVERT: D 308 ASN cc_start: 0.7639 (m-40) cc_final: 0.7008 (p0) REVERT: D 310 LEU cc_start: 0.9115 (mt) cc_final: 0.8197 (mm) REVERT: D 311 SER cc_start: 0.8366 (m) cc_final: 0.7857 (p) REVERT: D 318 ASN cc_start: 0.8904 (p0) cc_final: 0.8182 (p0) REVERT: D 328 LEU cc_start: 0.9364 (mt) cc_final: 0.9142 (mt) REVERT: D 340 SER cc_start: 0.8865 (t) cc_final: 0.8375 (p) REVERT: D 343 ILE cc_start: 0.8646 (mt) cc_final: 0.8356 (mm) REVERT: D 347 ARG cc_start: 0.6305 (mtm110) cc_final: 0.5828 (mtm110) REVERT: D 362 GLU cc_start: 0.5443 (mt-10) cc_final: 0.4932 (mt-10) REVERT: D 369 THR cc_start: 0.6501 (m) cc_final: 0.5602 (p) REVERT: D 372 LYS cc_start: 0.8901 (mttt) cc_final: 0.8637 (mttt) REVERT: D 383 ASN cc_start: 0.8787 (m-40) cc_final: 0.8426 (m110) REVERT: E 82 LEU cc_start: 0.7119 (mt) cc_final: 0.6343 (mm) REVERT: E 94 ASP cc_start: 0.4300 (OUTLIER) cc_final: 0.3409 (m-30) REVERT: E 117 MET cc_start: 0.7827 (tmt) cc_final: 0.7324 (tmm) REVERT: E 122 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: E 129 ARG cc_start: 0.2610 (OUTLIER) cc_final: 0.2063 (mtt180) REVERT: E 231 SER cc_start: 0.6527 (OUTLIER) cc_final: 0.5887 (p) REVERT: E 286 MET cc_start: -0.0696 (tpt) cc_final: -0.1793 (tpt) REVERT: E 321 GLN cc_start: 0.7404 (tm-30) cc_final: 0.7144 (tm-30) REVERT: E 322 VAL cc_start: 0.8377 (t) cc_final: 0.7399 (p) REVERT: F 157 MET cc_start: 0.5262 (mmm) cc_final: 0.4933 (mmm) REVERT: F 181 MET cc_start: -0.5027 (ttm) cc_final: -0.5255 (ttm) REVERT: F 217 VAL cc_start: 0.8154 (m) cc_final: 0.7890 (t) REVERT: F 232 HIS cc_start: 0.7882 (t70) cc_final: 0.7422 (t70) REVERT: F 274 LYS cc_start: 0.7473 (ptmm) cc_final: 0.7116 (mmmm) REVERT: F 275 PHE cc_start: 0.6426 (t80) cc_final: 0.6162 (t80) REVERT: F 284 ASN cc_start: 0.7509 (m-40) cc_final: 0.7265 (t0) REVERT: F 289 MET cc_start: 0.8012 (ttt) cc_final: 0.7158 (mmt) REVERT: F 303 ASN cc_start: 0.7882 (t0) cc_final: 0.7663 (t0) REVERT: F 309 PHE cc_start: 0.7465 (t80) cc_final: 0.7242 (t80) REVERT: G 12 LEU cc_start: 0.7667 (tp) cc_final: 0.7400 (tp) REVERT: G 96 LEU cc_start: 0.8766 (tp) cc_final: 0.8242 (pp) REVERT: G 100 THR cc_start: 0.8344 (m) cc_final: 0.7644 (p) REVERT: G 141 ILE cc_start: 0.7709 (pt) cc_final: 0.7388 (pt) REVERT: G 150 GLN cc_start: 0.6912 (mt0) cc_final: 0.5711 (mp10) REVERT: G 158 ILE cc_start: 0.8343 (pt) cc_final: 0.8016 (mm) REVERT: H 22 ASN cc_start: 0.8014 (m-40) cc_final: 0.7599 (m-40) REVERT: H 45 LEU cc_start: 0.9187 (mt) cc_final: 0.8946 (mm) REVERT: H 74 ILE cc_start: 0.8319 (mt) cc_final: 0.7997 (mm) REVERT: H 77 VAL cc_start: 0.9006 (t) cc_final: 0.8766 (t) REVERT: H 110 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.7952 (ttp-110) REVERT: H 121 VAL cc_start: 0.9086 (t) cc_final: 0.8858 (p) REVERT: H 133 PHE cc_start: 0.7084 (t80) cc_final: 0.6539 (t80) REVERT: H 137 VAL cc_start: 0.8328 (m) cc_final: 0.8114 (p) REVERT: H 145 VAL cc_start: 0.8619 (t) cc_final: 0.8407 (t) REVERT: H 163 LEU cc_start: 0.8192 (mp) cc_final: 0.7867 (mp) REVERT: I 104 LEU cc_start: 0.4595 (tp) cc_final: 0.4074 (tp) REVERT: I 253 MET cc_start: 0.1692 (mpp) cc_final: 0.1408 (mpp) REVERT: I 268 MET cc_start: 0.5877 (mtt) cc_final: 0.5167 (mtt) REVERT: I 366 MET cc_start: 0.1456 (ttt) cc_final: 0.0626 (ttt) REVERT: I 454 MET cc_start: 0.3946 (tpp) cc_final: 0.3404 (tpp) REVERT: L 57 LEU cc_start: 0.7063 (mt) cc_final: 0.6071 (pp) REVERT: L 97 LEU cc_start: 0.8516 (pp) cc_final: 0.8276 (pt) REVERT: L 148 ARG cc_start: 0.7818 (ttp-170) cc_final: 0.7231 (tmm160) REVERT: L 167 ASP cc_start: 0.8802 (t0) cc_final: 0.8406 (t0) REVERT: L 171 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7646 (ptt180) REVERT: L 185 ASN cc_start: 0.8012 (m-40) cc_final: 0.7472 (m-40) REVERT: L 242 ASN cc_start: 0.8297 (m-40) cc_final: 0.7564 (t0) REVERT: L 246 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7347 (tm-30) REVERT: L 276 ILE cc_start: 0.1959 (tp) cc_final: 0.1697 (tp) REVERT: L 284 LEU cc_start: 0.7735 (tp) cc_final: 0.7495 (pp) REVERT: L 346 LEU cc_start: 0.8658 (tp) cc_final: 0.8251 (mt) REVERT: L 366 PHE cc_start: 0.7656 (m-80) cc_final: 0.7001 (m-10) REVERT: L 393 ASP cc_start: 0.6196 (t0) cc_final: 0.5238 (t70) REVERT: L 397 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7337 (mmmt) REVERT: L 419 PHE cc_start: 0.7287 (t80) cc_final: 0.6988 (t80) REVERT: L 435 HIS cc_start: 0.6358 (m90) cc_final: 0.5861 (m90) REVERT: L 448 ASP cc_start: 0.6620 (m-30) cc_final: 0.6349 (t0) REVERT: L 452 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7702 (mmtt) REVERT: L 455 ILE cc_start: 0.8393 (mm) cc_final: 0.7991 (mt) REVERT: L 457 LYS cc_start: 0.8403 (pttp) cc_final: 0.7864 (pptt) REVERT: L 469 LYS cc_start: 0.7888 (tptt) cc_final: 0.6833 (mmmm) REVERT: L 510 THR cc_start: 0.7091 (t) cc_final: 0.6716 (m) REVERT: L 522 CYS cc_start: 0.7796 (t) cc_final: 0.6634 (m) REVERT: L 525 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.7803 (Cg_endo) REVERT: L 526 PRO cc_start: 0.8674 (Cg_endo) cc_final: 0.8449 (Cg_exo) REVERT: L 529 ARG cc_start: 0.8388 (mtt180) cc_final: 0.8132 (mtt180) REVERT: L 535 PHE cc_start: 0.7703 (t80) cc_final: 0.7407 (t80) REVERT: L 554 MET cc_start: 0.7615 (tpp) cc_final: 0.7192 (tpp) REVERT: L 592 LEU cc_start: 0.8377 (mt) cc_final: 0.7648 (mm) REVERT: L 625 ARG cc_start: 0.7241 (mmp-170) cc_final: 0.7035 (mmp-170) REVERT: L 661 VAL cc_start: 0.5434 (p) cc_final: 0.4996 (t) REVERT: L 670 HIS cc_start: 0.8360 (m-70) cc_final: 0.7561 (m-70) REVERT: L 725 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.4796 (tm-30) REVERT: M 96 MET cc_start: 0.5141 (ptp) cc_final: 0.4760 (ptp) REVERT: M 124 LEU cc_start: 0.7959 (mp) cc_final: 0.7663 (mm) REVERT: M 149 LYS cc_start: 0.8636 (tttm) cc_final: 0.7940 (tptp) REVERT: M 361 PHE cc_start: 0.6959 (m-80) cc_final: 0.6640 (m-80) REVERT: M 434 MET cc_start: -0.4401 (tpt) cc_final: -0.5466 (ptp) REVERT: R 25 LYS cc_start: 0.6111 (mptt) cc_final: 0.5820 (mmtp) REVERT: R 91 ARG cc_start: 0.7487 (mtt90) cc_final: 0.7095 (mtt90) REVERT: N 1 MET cc_start: 0.5991 (ptp) cc_final: 0.5671 (ptt) REVERT: N 73 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5520 (mm) outliers start: 91 outliers final: 35 residues processed: 1394 average time/residue: 0.5602 time to fit residues: 1218.9350 Evaluate side-chains 1044 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 999 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 358 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 216 ASN A 240 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 321 ASN B 333 ASN B 353 ASN B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C 361 HIS ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 56 ASN D 86 HIS D 109 HIS ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 228 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN E 204 GLN ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 HIS F 232 HIS F 253 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS G 169 ASN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN I 83 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 166 GLN I 187 ASN ** I 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 324 GLN I 357 GLN ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 286 HIS L 362 ASN ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 492 GLN ** L 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 617 GLN L 618 GLN M 76 ASN ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 GLN ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 187 ASN M 219 GLN M 230 GLN M 235 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN R 98 ASN ** R 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 38016 Z= 0.384 Angle : 0.813 11.864 51366 Z= 0.439 Chirality : 0.047 0.259 5749 Planarity : 0.006 0.123 6583 Dihedral : 4.758 32.773 5047 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.18 % Favored : 92.47 % Rotamer: Outliers : 0.22 % Allowed : 5.06 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 4597 helix: 0.62 (0.10), residues: 2678 sheet: -0.82 (0.25), residues: 417 loop : -2.04 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 166 HIS 0.015 0.002 HIS B 399 PHE 0.041 0.003 PHE F 112 TYR 0.032 0.003 TYR M 351 ARG 0.008 0.001 ARG M 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1145 time to evaluate : 4.292 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: 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: 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 83 ASP cc_start: 0.6557 (t0) cc_final: 0.5965 (t0) REVERT: A 106 HIS cc_start: 0.6212 (m-70) cc_final: 0.5917 (m-70) REVERT: A 117 MET cc_start: 0.7771 (mtt) cc_final: 0.7211 (mtt) REVERT: A 130 MET cc_start: 0.7395 (mmp) cc_final: 0.6619 (mmp) REVERT: A 137 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7858 (mmtt) REVERT: A 218 LEU cc_start: 0.8229 (tp) cc_final: 0.7213 (tt) REVERT: A 235 ILE cc_start: 0.8439 (mt) cc_final: 0.8203 (mt) REVERT: A 246 VAL cc_start: 0.8342 (t) cc_final: 0.8042 (t) REVERT: A 254 VAL cc_start: 0.7358 (t) cc_final: 0.7145 (t) REVERT: A 281 ILE cc_start: 0.7600 (mt) cc_final: 0.7076 (mt) REVERT: A 293 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 304 LYS cc_start: 0.8062 (pttm) cc_final: 0.6661 (ptmm) REVERT: A 332 CYS cc_start: 0.8012 (m) cc_final: 0.6539 (p) REVERT: A 342 LEU cc_start: 0.7994 (mt) cc_final: 0.7264 (mt) REVERT: A 365 ILE cc_start: 0.7784 (mt) cc_final: 0.7427 (mt) REVERT: A 369 PHE cc_start: 0.6498 (t80) cc_final: 0.6296 (t80) REVERT: A 392 MET cc_start: 0.3835 (ptt) cc_final: 0.3525 (ptt) REVERT: A 425 MET cc_start: 0.7237 (ptp) cc_final: 0.6907 (ppp) REVERT: A 436 LEU cc_start: 0.7054 (tp) cc_final: 0.5522 (tp) REVERT: A 437 GLU cc_start: 0.6933 (tt0) cc_final: 0.6468 (tm-30) REVERT: A 438 ASP cc_start: 0.6494 (m-30) cc_final: 0.5153 (m-30) REVERT: A 461 TYR cc_start: 0.8092 (m-80) cc_final: 0.7459 (m-10) REVERT: A 476 LEU cc_start: 0.7628 (mt) cc_final: 0.7374 (mm) REVERT: A 489 MET cc_start: 0.6544 (ppp) cc_final: 0.6169 (ppp) REVERT: B 31 ASP cc_start: 0.8156 (t0) cc_final: 0.7924 (t0) REVERT: B 35 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8189 (mm-40) REVERT: B 66 GLU cc_start: 0.7696 (pp20) cc_final: 0.7371 (pp20) REVERT: B 72 LEU cc_start: 0.8671 (mt) cc_final: 0.8277 (mt) REVERT: B 77 LYS cc_start: 0.7575 (mttt) cc_final: 0.6686 (mmmt) REVERT: B 88 MET cc_start: 0.7721 (tmm) cc_final: 0.6764 (tmm) REVERT: B 90 ASN cc_start: 0.7569 (m-40) cc_final: 0.5485 (m110) REVERT: B 93 LYS cc_start: 0.9566 (mttt) cc_final: 0.8088 (mptt) REVERT: B 94 GLN cc_start: 0.8813 (tt0) cc_final: 0.8466 (mp10) REVERT: B 96 LEU cc_start: 0.8050 (mt) cc_final: 0.7662 (mt) REVERT: B 109 GLU cc_start: 0.8204 (pt0) cc_final: 0.6898 (tm-30) REVERT: B 110 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8675 (pttt) REVERT: B 139 LEU cc_start: 0.8993 (mt) cc_final: 0.8241 (mt) REVERT: B 147 LEU cc_start: 0.8730 (tp) cc_final: 0.8218 (tp) REVERT: B 150 LYS cc_start: 0.8934 (mttp) cc_final: 0.8410 (mmtm) REVERT: B 168 LEU cc_start: 0.7890 (tp) cc_final: 0.7607 (tp) REVERT: B 170 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8221 (ptpt) REVERT: B 171 ILE cc_start: 0.8712 (mt) cc_final: 0.8328 (pt) REVERT: B 172 LEU cc_start: 0.8497 (mt) cc_final: 0.8234 (mt) REVERT: B 190 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7439 (mtmt) REVERT: B 194 LEU cc_start: 0.7770 (mt) cc_final: 0.7142 (mt) REVERT: B 196 GLU cc_start: 0.7358 (mp0) cc_final: 0.6423 (mp0) REVERT: B 213 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7409 (mmmm) REVERT: B 218 TYR cc_start: 0.7868 (t80) cc_final: 0.7496 (t80) REVERT: B 233 ILE cc_start: 0.8362 (mt) cc_final: 0.8122 (mt) REVERT: B 237 ILE cc_start: 0.7883 (mt) cc_final: 0.7262 (mm) REVERT: B 239 GLU cc_start: 0.8144 (tt0) cc_final: 0.7711 (tm-30) REVERT: B 240 CYS cc_start: 0.7925 (t) cc_final: 0.6976 (p) REVERT: B 244 MET cc_start: 0.7785 (ttp) cc_final: 0.7457 (mmp) REVERT: B 253 LYS cc_start: 0.7243 (mttt) cc_final: 0.6764 (mtmm) REVERT: B 255 HIS cc_start: 0.8336 (t-90) cc_final: 0.7461 (t-90) REVERT: B 259 PHE cc_start: 0.7283 (t80) cc_final: 0.6934 (t80) REVERT: B 260 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7586 (mm-30) REVERT: B 262 PHE cc_start: 0.8068 (t80) cc_final: 0.7123 (t80) REVERT: B 263 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8336 (ptpp) REVERT: B 265 TYR cc_start: 0.8118 (m-10) cc_final: 0.7340 (m-80) REVERT: B 277 LEU cc_start: 0.8338 (tp) cc_final: 0.7949 (tp) REVERT: B 284 ASN cc_start: 0.7714 (t0) cc_final: 0.7491 (t0) REVERT: B 285 MET cc_start: 0.8611 (mtm) cc_final: 0.7163 (ptm) REVERT: B 287 MET cc_start: 0.7702 (ptp) cc_final: 0.7188 (mmm) REVERT: B 304 ASN cc_start: 0.8530 (m-40) cc_final: 0.8172 (m-40) REVERT: B 312 THR cc_start: 0.8930 (m) cc_final: 0.8631 (p) REVERT: B 313 ASN cc_start: 0.8748 (m110) cc_final: 0.8182 (m-40) REVERT: B 315 VAL cc_start: 0.9125 (t) cc_final: 0.8664 (p) REVERT: B 326 PHE cc_start: 0.7936 (t80) cc_final: 0.7452 (t80) REVERT: B 328 LYS cc_start: 0.9282 (tttt) cc_final: 0.8916 (mtmm) REVERT: B 330 LEU cc_start: 0.9191 (mt) cc_final: 0.8709 (tt) REVERT: B 331 LYS cc_start: 0.9042 (mttt) cc_final: 0.8664 (pttm) REVERT: B 348 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 349 GLU cc_start: 0.8460 (tt0) cc_final: 0.7755 (mp0) REVERT: B 352 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: B 354 ILE cc_start: 0.8719 (tt) cc_final: 0.8442 (pt) REVERT: B 355 ARG cc_start: 0.8887 (mtt180) cc_final: 0.8537 (mtt90) REVERT: B 356 THR cc_start: 0.8918 (m) cc_final: 0.8454 (m) REVERT: B 359 LEU cc_start: 0.9008 (tp) cc_final: 0.8686 (pp) REVERT: B 361 LYS cc_start: 0.9168 (ptmt) cc_final: 0.8723 (pttp) REVERT: B 362 LEU cc_start: 0.8382 (mp) cc_final: 0.8125 (pp) REVERT: B 364 LYS cc_start: 0.9323 (pttm) cc_final: 0.8998 (ptpp) REVERT: B 384 ASP cc_start: 0.8804 (m-30) cc_final: 0.8518 (m-30) REVERT: B 388 LEU cc_start: 0.8932 (mp) cc_final: 0.8524 (mm) REVERT: B 391 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7753 (tp-100) REVERT: B 395 ASP cc_start: 0.8201 (m-30) cc_final: 0.7639 (m-30) REVERT: B 407 GLN cc_start: 0.8452 (mp-120) cc_final: 0.8201 (mm-40) REVERT: C 25 CYS cc_start: 0.8239 (m) cc_final: 0.7798 (t) REVERT: C 82 GLN cc_start: 0.8363 (mt0) cc_final: 0.7283 (mp10) REVERT: C 92 HIS cc_start: 0.6891 (m90) cc_final: 0.5989 (m-70) REVERT: C 104 CYS cc_start: 0.8221 (m) cc_final: 0.7411 (m) REVERT: C 125 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7453 (mttt) REVERT: C 131 MET cc_start: 0.6105 (ppp) cc_final: 0.5878 (ppp) REVERT: C 181 PHE cc_start: 0.5981 (t80) cc_final: 0.5687 (t80) REVERT: C 190 MET cc_start: 0.7657 (mtp) cc_final: 0.7232 (mtp) REVERT: C 191 ILE cc_start: 0.7044 (mt) cc_final: 0.6763 (mt) REVERT: C 202 LEU cc_start: 0.8149 (tp) cc_final: 0.7340 (tp) REVERT: C 227 TYR cc_start: 0.7424 (t80) cc_final: 0.7119 (t80) REVERT: C 292 MET cc_start: 0.0730 (tpp) cc_final: -0.0300 (tpp) REVERT: C 312 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7760 (mmmm) REVERT: C 359 SER cc_start: 0.6571 (m) cc_final: 0.6200 (t) REVERT: C 368 ASN cc_start: 0.7845 (p0) cc_final: 0.7269 (p0) REVERT: C 378 GLN cc_start: 0.9039 (mt0) cc_final: 0.7883 (pp30) REVERT: C 380 MET cc_start: 0.6681 (ttp) cc_final: 0.5843 (mmt) REVERT: D 1 MET cc_start: 0.3208 (mtp) cc_final: 0.2992 (mtp) REVERT: D 65 LEU cc_start: 0.8494 (mt) cc_final: 0.8082 (mt) REVERT: D 66 LEU cc_start: 0.8575 (mt) cc_final: 0.8183 (mt) REVERT: D 68 ASP cc_start: 0.8428 (m-30) cc_final: 0.8014 (m-30) REVERT: D 69 PHE cc_start: 0.7446 (t80) cc_final: 0.7200 (t80) REVERT: D 88 THR cc_start: 0.8493 (m) cc_final: 0.8283 (t) REVERT: D 121 ARG cc_start: 0.8749 (ttm-80) cc_final: 0.8029 (ttt-90) REVERT: D 127 LEU cc_start: 0.9400 (tp) cc_final: 0.8929 (tt) REVERT: D 139 TYR cc_start: 0.6416 (m-80) cc_final: 0.5996 (m-80) REVERT: D 144 LYS cc_start: 0.7928 (mttt) cc_final: 0.7407 (mmtt) REVERT: D 155 TYR cc_start: 0.8623 (m-80) cc_final: 0.8010 (m-80) REVERT: D 167 TYR cc_start: 0.7073 (m-10) cc_final: 0.6692 (m-10) REVERT: D 169 ASN cc_start: 0.7155 (m-40) cc_final: 0.6836 (m-40) REVERT: D 186 HIS cc_start: 0.8307 (m-70) cc_final: 0.7961 (m-70) REVERT: D 227 LYS cc_start: 0.8669 (tttt) cc_final: 0.7271 (tppt) REVERT: D 246 LEU cc_start: 0.8806 (mt) cc_final: 0.8272 (tp) REVERT: D 266 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8717 (pttp) REVERT: D 267 MET cc_start: 0.8224 (tpp) cc_final: 0.7775 (tpt) REVERT: D 271 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.6919 (mmt-90) REVERT: D 284 MET cc_start: 0.7926 (mtt) cc_final: 0.7699 (mtt) REVERT: D 300 LEU cc_start: 0.7132 (tp) cc_final: 0.6772 (tp) REVERT: D 306 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7748 (mm-30) REVERT: D 307 HIS cc_start: 0.6447 (t70) cc_final: 0.5512 (t70) REVERT: D 308 ASN cc_start: 0.7682 (m-40) cc_final: 0.7447 (p0) REVERT: D 310 LEU cc_start: 0.8971 (mt) cc_final: 0.8678 (mm) REVERT: D 318 ASN cc_start: 0.9040 (p0) cc_final: 0.7884 (p0) REVERT: D 360 HIS cc_start: 0.7522 (m-70) cc_final: 0.7047 (m-70) REVERT: D 361 PHE cc_start: 0.6237 (m-80) cc_final: 0.5585 (m-80) REVERT: D 367 LEU cc_start: 0.7188 (tt) cc_final: 0.6742 (tt) REVERT: D 369 THR cc_start: 0.7699 (m) cc_final: 0.6616 (m) REVERT: D 371 ASP cc_start: 0.8373 (m-30) cc_final: 0.8146 (m-30) REVERT: D 378 CYS cc_start: 0.9268 (m) cc_final: 0.8722 (m) REVERT: D 380 GLN cc_start: 0.8021 (mt0) cc_final: 0.7574 (mt0) REVERT: D 383 ASN cc_start: 0.8956 (m-40) cc_final: 0.8171 (m110) REVERT: D 384 LEU cc_start: 0.8954 (tt) cc_final: 0.7376 (tt) REVERT: D 387 LYS cc_start: 0.9036 (mttt) cc_final: 0.8294 (mtmt) REVERT: E 82 LEU cc_start: 0.7103 (mt) cc_final: 0.6891 (mm) REVERT: E 117 MET cc_start: 0.8268 (tmm) cc_final: 0.7847 (tmm) REVERT: E 122 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7725 (mt-10) REVERT: E 136 TRP cc_start: 0.7222 (p-90) cc_final: 0.6725 (p-90) REVERT: E 242 TRP cc_start: 0.5975 (t-100) cc_final: 0.5533 (t-100) REVERT: E 286 MET cc_start: -0.0798 (tpt) cc_final: -0.1898 (tpt) REVERT: E 309 LYS cc_start: 0.5883 (mmtm) cc_final: 0.5664 (mmtt) REVERT: E 313 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7038 (mt-10) REVERT: E 321 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7403 (tm-30) REVERT: E 322 VAL cc_start: 0.8219 (t) cc_final: 0.7555 (p) REVERT: E 328 PHE cc_start: 0.6917 (m-10) cc_final: 0.6702 (m-10) REVERT: F 73 ILE cc_start: 0.7383 (pt) cc_final: 0.6783 (mm) REVERT: F 106 TYR cc_start: 0.7394 (m-80) cc_final: 0.6964 (m-10) REVERT: F 112 PHE cc_start: 0.8176 (p90) cc_final: 0.7608 (p90) REVERT: F 157 MET cc_start: 0.5714 (mmm) cc_final: 0.5477 (mmm) REVERT: F 181 MET cc_start: -0.5012 (ttm) cc_final: -0.5460 (ttm) REVERT: F 232 HIS cc_start: 0.8022 (t-90) cc_final: 0.7620 (t70) REVERT: F 254 HIS cc_start: 0.8431 (m-70) cc_final: 0.8096 (m-70) REVERT: F 275 PHE cc_start: 0.6990 (t80) cc_final: 0.6711 (t80) REVERT: F 288 LEU cc_start: 0.7446 (tp) cc_final: 0.7169 (tt) REVERT: F 289 MET cc_start: 0.8588 (ttt) cc_final: 0.7743 (mmm) REVERT: F 295 ILE cc_start: 0.7766 (mt) cc_final: 0.7441 (mt) REVERT: F 303 ASN cc_start: 0.7965 (t0) cc_final: 0.7748 (t0) REVERT: F 309 PHE cc_start: 0.7701 (t80) cc_final: 0.7176 (t80) REVERT: G 47 LEU cc_start: 0.9243 (tt) cc_final: 0.8978 (mm) REVERT: G 97 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8763 (mmtt) REVERT: G 121 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7095 (tm-30) REVERT: G 130 ASP cc_start: 0.8959 (m-30) cc_final: 0.8595 (m-30) REVERT: G 148 ARG cc_start: 0.8286 (ttt-90) cc_final: 0.7507 (ptm160) REVERT: G 149 ASN cc_start: 0.8745 (m-40) cc_final: 0.7623 (p0) REVERT: G 152 LEU cc_start: 0.7656 (tp) cc_final: 0.7438 (mm) REVERT: G 153 GLU cc_start: 0.7438 (mp0) cc_final: 0.7120 (mp0) REVERT: G 172 LYS cc_start: 0.8848 (tttt) cc_final: 0.8274 (tttt) REVERT: H 22 ASN cc_start: 0.8109 (m-40) cc_final: 0.7839 (m-40) REVERT: H 24 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8402 (tm-30) REVERT: H 96 HIS cc_start: 0.7126 (m90) cc_final: 0.6917 (m90) REVERT: H 110 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.8029 (ttp-110) REVERT: H 133 PHE cc_start: 0.7777 (t80) cc_final: 0.6522 (t80) REVERT: H 137 VAL cc_start: 0.8429 (m) cc_final: 0.8180 (p) REVERT: H 163 LEU cc_start: 0.8447 (mp) cc_final: 0.8123 (mt) REVERT: I 105 TYR cc_start: 0.4087 (t80) cc_final: 0.2861 (t80) REVERT: I 110 PHE cc_start: 0.5265 (t80) cc_final: 0.4978 (t80) REVERT: I 122 GLU cc_start: 0.8085 (pt0) cc_final: 0.7657 (pp20) REVERT: I 190 LYS cc_start: 0.5320 (ptpt) cc_final: 0.5053 (mtmm) REVERT: I 253 MET cc_start: 0.1667 (mpp) cc_final: 0.1438 (mpp) REVERT: I 297 LYS cc_start: 0.8467 (tmtt) cc_final: 0.7911 (tptp) REVERT: I 366 MET cc_start: 0.1517 (ttt) cc_final: 0.0810 (ttt) REVERT: I 434 MET cc_start: 0.1378 (mpp) cc_final: 0.0943 (mpp) REVERT: I 537 PHE cc_start: 0.7047 (t80) cc_final: 0.6735 (t80) REVERT: I 581 CYS cc_start: 0.5461 (t) cc_final: 0.5222 (t) REVERT: L 28 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7682 (mmmt) REVERT: L 69 HIS cc_start: 0.4666 (t70) cc_final: 0.4437 (t70) REVERT: L 97 LEU cc_start: 0.8603 (pp) cc_final: 0.8042 (pt) REVERT: L 117 VAL cc_start: 0.8813 (m) cc_final: 0.8472 (p) REVERT: L 148 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7551 (tmm160) REVERT: L 158 ARG cc_start: 0.8058 (ppt170) cc_final: 0.7822 (ptm-80) REVERT: L 163 GLN cc_start: 0.7970 (pt0) cc_final: 0.7613 (pp30) REVERT: L 167 ASP cc_start: 0.8961 (t0) cc_final: 0.8662 (t0) REVERT: L 171 ARG cc_start: 0.8352 (mtm110) cc_final: 0.7892 (ptt180) REVERT: L 185 ASN cc_start: 0.8277 (m-40) cc_final: 0.7842 (m-40) REVERT: L 217 PHE cc_start: 0.8107 (m-80) cc_final: 0.7643 (m-10) REVERT: L 247 ARG cc_start: 0.7458 (ttm170) cc_final: 0.6831 (mtt180) REVERT: L 250 HIS cc_start: 0.6692 (t-90) cc_final: 0.6397 (t-90) REVERT: L 279 MET cc_start: 0.6379 (ttp) cc_final: 0.6099 (ttp) REVERT: L 287 MET cc_start: 0.8274 (ptt) cc_final: 0.7839 (ppp) REVERT: L 294 GLU cc_start: 0.8531 (mp0) cc_final: 0.8226 (mp0) REVERT: L 301 LYS cc_start: 0.8685 (pttt) cc_final: 0.8131 (pttt) REVERT: L 302 LEU cc_start: 0.9177 (mt) cc_final: 0.8104 (mt) REVERT: L 305 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7256 (mpp80) REVERT: L 351 ARG cc_start: 0.8419 (ttt180) cc_final: 0.8019 (mmp80) REVERT: L 352 PHE cc_start: 0.8481 (m-10) cc_final: 0.8245 (m-10) REVERT: L 358 GLU cc_start: 0.7351 (pp20) cc_final: 0.6760 (pp20) REVERT: L 366 PHE cc_start: 0.7639 (m-80) cc_final: 0.7373 (m-80) REVERT: L 389 SER cc_start: 0.9002 (p) cc_final: 0.8600 (p) REVERT: L 393 ASP cc_start: 0.7512 (t0) cc_final: 0.6857 (m-30) REVERT: L 414 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8642 (mppt) REVERT: L 433 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7729 (mmtt) REVERT: L 435 HIS cc_start: 0.7233 (m90) cc_final: 0.6900 (m90) REVERT: L 475 ARG cc_start: 0.8772 (ttt180) cc_final: 0.7624 (tpp80) REVERT: L 477 MET cc_start: 0.8100 (tmm) cc_final: 0.7581 (tmm) REVERT: L 522 CYS cc_start: 0.8011 (t) cc_final: 0.6504 (m) REVERT: L 529 ARG cc_start: 0.8428 (mtt180) cc_final: 0.8227 (mtp180) REVERT: L 554 MET cc_start: 0.8088 (tpp) cc_final: 0.7742 (tpp) REVERT: L 625 ARG cc_start: 0.7836 (mmp-170) cc_final: 0.7351 (mmp-170) REVERT: L 657 HIS cc_start: 0.7280 (p-80) cc_final: 0.6828 (p90) REVERT: L 670 HIS cc_start: 0.8320 (m-70) cc_final: 0.7871 (m-70) REVERT: M 124 LEU cc_start: 0.8187 (mp) cc_final: 0.7936 (mm) REVERT: M 149 LYS cc_start: 0.8750 (tttm) cc_final: 0.7933 (tptp) REVERT: M 177 LEU cc_start: 0.7031 (mm) cc_final: 0.6556 (tp) REVERT: M 420 GLN cc_start: 0.6052 (pp30) cc_final: 0.5613 (pp30) REVERT: M 434 MET cc_start: -0.2482 (tpt) cc_final: -0.4020 (ptp) REVERT: R 25 LYS cc_start: 0.6500 (mptt) cc_final: 0.6276 (mptt) REVERT: R 27 TRP cc_start: 0.7492 (t60) cc_final: 0.6928 (t60) REVERT: R 37 ILE cc_start: 0.7461 (mp) cc_final: 0.6757 (mp) REVERT: R 39 VAL cc_start: 0.9037 (m) cc_final: 0.8317 (t) REVERT: R 48 HIS cc_start: 0.7617 (t-90) cc_final: 0.7268 (t70) REVERT: R 50 MET cc_start: 0.6227 (ptt) cc_final: 0.5785 (ptt) REVERT: R 91 ARG cc_start: 0.6824 (mtt90) cc_final: 0.6406 (mtt90) REVERT: R 98 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.5543 (m110) outliers start: 9 outliers final: 4 residues processed: 1153 average time/residue: 0.5293 time to fit residues: 950.4807 Evaluate side-chains 971 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 966 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 345 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 415 optimal weight: 0.3980 chunk 449 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 412 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 191 ASN A 207 HIS A 250 ASN A 301 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS B 90 ASN B 208 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 80 GLN C 116 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 297 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN G 65 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 HIS I 185 ASN I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 GLN ** M 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN R 108 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 38016 Z= 0.279 Angle : 0.711 9.871 51366 Z= 0.376 Chirality : 0.044 0.201 5749 Planarity : 0.005 0.127 6583 Dihedral : 4.786 29.022 5047 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.16 % Favored : 92.43 % Rotamer: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4597 helix: 0.56 (0.10), residues: 2691 sheet: -0.76 (0.24), residues: 418 loop : -2.05 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 166 HIS 0.012 0.002 HIS A 201 PHE 0.053 0.002 PHE L 428 TYR 0.032 0.002 TYR B 318 ARG 0.018 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1124 time to evaluate : 4.009 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: 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: 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 83 ASP cc_start: 0.6638 (t0) cc_final: 0.5975 (t0) REVERT: A 95 MET cc_start: 0.5289 (pmm) cc_final: 0.4464 (ptm) REVERT: A 103 ILE cc_start: 0.7641 (pt) cc_final: 0.7325 (pt) REVERT: A 117 MET cc_start: 0.7784 (mtt) cc_final: 0.7097 (mtt) REVERT: A 137 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7614 (mmtt) REVERT: A 204 LEU cc_start: 0.7304 (mt) cc_final: 0.6822 (mt) REVERT: A 234 VAL cc_start: 0.8286 (t) cc_final: 0.7820 (t) REVERT: A 235 ILE cc_start: 0.8447 (mt) cc_final: 0.8123 (mt) REVERT: A 254 VAL cc_start: 0.6626 (t) cc_final: 0.6398 (t) REVERT: A 293 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 332 CYS cc_start: 0.8064 (m) cc_final: 0.6544 (p) REVERT: A 363 ARG cc_start: 0.6609 (ptt-90) cc_final: 0.6360 (ptt-90) REVERT: A 365 ILE cc_start: 0.7537 (mt) cc_final: 0.7233 (mt) REVERT: A 387 ASN cc_start: 0.5587 (t0) cc_final: 0.5261 (t0) REVERT: A 421 ASP cc_start: 0.6721 (t0) cc_final: 0.6077 (t70) REVERT: A 437 GLU cc_start: 0.7154 (tt0) cc_final: 0.6686 (tm-30) REVERT: A 438 ASP cc_start: 0.6434 (m-30) cc_final: 0.5818 (m-30) REVERT: A 472 PHE cc_start: 0.6814 (m-10) cc_final: 0.6465 (m-10) REVERT: A 473 GLU cc_start: 0.6708 (pp20) cc_final: 0.6384 (pp20) REVERT: A 489 MET cc_start: 0.6439 (ppp) cc_final: 0.6099 (ppp) REVERT: A 496 LEU cc_start: 0.8182 (mt) cc_final: 0.7738 (mm) REVERT: B 77 LYS cc_start: 0.8454 (mttt) cc_final: 0.7248 (mmmt) REVERT: B 88 MET cc_start: 0.7627 (tmm) cc_final: 0.6389 (tmm) REVERT: B 90 ASN cc_start: 0.7730 (m110) cc_final: 0.6624 (m110) REVERT: B 93 LYS cc_start: 0.9414 (mttt) cc_final: 0.8338 (mmtt) REVERT: B 94 GLN cc_start: 0.8541 (tt0) cc_final: 0.7563 (mp10) REVERT: B 96 LEU cc_start: 0.7913 (mt) cc_final: 0.7573 (mt) REVERT: B 109 GLU cc_start: 0.7852 (pt0) cc_final: 0.6373 (pp20) REVERT: B 110 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8318 (mtpt) REVERT: B 112 ILE cc_start: 0.8300 (pt) cc_final: 0.7689 (mm) REVERT: B 146 ARG cc_start: 0.7096 (tpp80) cc_final: 0.6733 (tpp80) REVERT: B 150 LYS cc_start: 0.8830 (mttp) cc_final: 0.8349 (mmtm) REVERT: B 194 LEU cc_start: 0.7899 (mt) cc_final: 0.7087 (mt) REVERT: B 195 LEU cc_start: 0.7869 (mt) cc_final: 0.7313 (mm) REVERT: B 196 GLU cc_start: 0.7072 (mp0) cc_final: 0.6215 (mp0) REVERT: B 213 LYS cc_start: 0.7928 (mmtm) cc_final: 0.7317 (mmmm) REVERT: B 218 TYR cc_start: 0.7945 (t80) cc_final: 0.7464 (t80) REVERT: B 237 ILE cc_start: 0.8134 (mt) cc_final: 0.7389 (mm) REVERT: B 244 MET cc_start: 0.8334 (ttp) cc_final: 0.7002 (mmp) REVERT: B 247 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8372 (ttm110) REVERT: B 248 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7005 (pt0) REVERT: B 255 HIS cc_start: 0.8117 (t-90) cc_final: 0.7734 (t-90) REVERT: B 258 PHE cc_start: 0.7982 (m-80) cc_final: 0.7542 (m-80) REVERT: B 259 PHE cc_start: 0.7435 (t80) cc_final: 0.7109 (t80) REVERT: B 260 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7719 (mm-30) REVERT: B 262 PHE cc_start: 0.7542 (t80) cc_final: 0.6108 (t80) REVERT: B 263 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7791 (ttpp) REVERT: B 265 TYR cc_start: 0.7914 (m-10) cc_final: 0.7337 (m-80) REVERT: B 266 ASP cc_start: 0.7648 (m-30) cc_final: 0.6888 (m-30) REVERT: B 273 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7733 (ptt-90) REVERT: B 278 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8578 (pttp) REVERT: B 284 ASN cc_start: 0.7200 (t0) cc_final: 0.6396 (t0) REVERT: B 304 ASN cc_start: 0.8494 (m-40) cc_final: 0.8131 (m-40) REVERT: B 311 MET cc_start: 0.8418 (mpp) cc_final: 0.8106 (mpp) REVERT: B 313 ASN cc_start: 0.8769 (m110) cc_final: 0.8204 (m-40) REVERT: B 315 VAL cc_start: 0.9305 (t) cc_final: 0.8785 (p) REVERT: B 326 PHE cc_start: 0.7649 (t80) cc_final: 0.7126 (t80) REVERT: B 330 LEU cc_start: 0.9226 (mt) cc_final: 0.8822 (mt) REVERT: B 331 LYS cc_start: 0.8520 (mttt) cc_final: 0.7157 (mmtm) REVERT: B 346 HIS cc_start: 0.8349 (m-70) cc_final: 0.7989 (m-70) REVERT: B 348 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7839 (mp0) REVERT: B 349 GLU cc_start: 0.8590 (tt0) cc_final: 0.7706 (mp0) REVERT: B 352 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: B 353 ASN cc_start: 0.8525 (m110) cc_final: 0.8299 (m110) REVERT: B 354 ILE cc_start: 0.8553 (tt) cc_final: 0.8254 (pt) REVERT: B 355 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8477 (mtt90) REVERT: B 357 GLN cc_start: 0.8649 (mt0) cc_final: 0.8232 (mm110) REVERT: B 359 LEU cc_start: 0.8965 (tp) cc_final: 0.8615 (pp) REVERT: B 361 LYS cc_start: 0.9078 (ptmt) cc_final: 0.8409 (pttp) REVERT: B 364 LYS cc_start: 0.9215 (pttm) cc_final: 0.8791 (ptpp) REVERT: B 384 ASP cc_start: 0.8975 (m-30) cc_final: 0.7957 (m-30) REVERT: B 386 GLU cc_start: 0.8307 (pt0) cc_final: 0.7770 (pp20) REVERT: B 388 LEU cc_start: 0.8895 (mp) cc_final: 0.8424 (mm) REVERT: B 395 ASP cc_start: 0.7889 (m-30) cc_final: 0.7431 (m-30) REVERT: B 407 GLN cc_start: 0.8223 (mp-120) cc_final: 0.7943 (mm-40) REVERT: C 92 HIS cc_start: 0.6658 (m90) cc_final: 0.6124 (m-70) REVERT: C 104 CYS cc_start: 0.8244 (m) cc_final: 0.7311 (m) REVERT: C 131 MET cc_start: 0.7206 (ppp) cc_final: 0.6927 (ppp) REVERT: C 162 LEU cc_start: 0.9539 (mt) cc_final: 0.9323 (mt) REVERT: C 190 MET cc_start: 0.7674 (mtp) cc_final: 0.7172 (mtp) REVERT: C 191 ILE cc_start: 0.7277 (mt) cc_final: 0.6958 (mt) REVERT: C 202 LEU cc_start: 0.7954 (tp) cc_final: 0.7250 (tp) REVERT: C 224 TYR cc_start: 0.7164 (t80) cc_final: 0.6905 (t80) REVERT: C 227 TYR cc_start: 0.7391 (t80) cc_final: 0.7047 (t80) REVERT: C 312 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7457 (mmmm) REVERT: C 333 GLU cc_start: 0.8027 (pp20) cc_final: 0.7657 (pp20) REVERT: C 336 LYS cc_start: 0.8469 (ptpt) cc_final: 0.7867 (ptpp) REVERT: C 337 TYR cc_start: 0.8149 (m-80) cc_final: 0.7273 (m-80) REVERT: C 341 MET cc_start: 0.7510 (ptp) cc_final: 0.7273 (ptp) REVERT: C 359 SER cc_start: 0.6448 (m) cc_final: 0.6227 (t) REVERT: C 368 ASN cc_start: 0.8021 (p0) cc_final: 0.7292 (p0) REVERT: C 372 MET cc_start: 0.7674 (mmm) cc_final: 0.7327 (mmm) REVERT: D 1 MET cc_start: 0.3297 (mtp) cc_final: 0.3093 (mtp) REVERT: D 66 LEU cc_start: 0.8581 (mt) cc_final: 0.8301 (mt) REVERT: D 127 LEU cc_start: 0.9316 (tp) cc_final: 0.8867 (tp) REVERT: D 139 TYR cc_start: 0.6344 (m-80) cc_final: 0.5949 (m-80) REVERT: D 140 ASN cc_start: 0.8907 (t0) cc_final: 0.8687 (t0) REVERT: D 144 LYS cc_start: 0.8433 (mttt) cc_final: 0.7528 (mmtt) REVERT: D 155 TYR cc_start: 0.8459 (m-80) cc_final: 0.8027 (m-80) REVERT: D 167 TYR cc_start: 0.7070 (m-10) cc_final: 0.6788 (m-80) REVERT: D 169 ASN cc_start: 0.7147 (m-40) cc_final: 0.5937 (m-40) REVERT: D 186 HIS cc_start: 0.8284 (m-70) cc_final: 0.7847 (m90) REVERT: D 198 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7634 (tpp80) REVERT: D 200 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7271 (mmtm) REVERT: D 227 LYS cc_start: 0.8753 (tttt) cc_final: 0.7367 (tptm) REVERT: D 231 HIS cc_start: 0.7183 (m170) cc_final: 0.6466 (m170) REVERT: D 246 LEU cc_start: 0.8731 (mt) cc_final: 0.8389 (tp) REVERT: D 266 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8512 (ptpp) REVERT: D 267 MET cc_start: 0.8165 (tpp) cc_final: 0.7774 (tpt) REVERT: D 284 MET cc_start: 0.7973 (mtt) cc_final: 0.7698 (mtt) REVERT: D 300 LEU cc_start: 0.6983 (tp) cc_final: 0.6640 (tp) REVERT: D 301 ASP cc_start: 0.7743 (t0) cc_final: 0.7377 (t0) REVERT: D 306 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7972 (mm-30) REVERT: D 307 HIS cc_start: 0.6357 (t70) cc_final: 0.5430 (t70) REVERT: D 310 LEU cc_start: 0.9005 (mt) cc_final: 0.8369 (mp) REVERT: D 317 ASN cc_start: 0.7690 (m-40) cc_final: 0.7073 (m-40) REVERT: D 318 ASN cc_start: 0.9157 (p0) cc_final: 0.7528 (p0) REVERT: D 329 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7992 (mp0) REVERT: D 338 ILE cc_start: 0.8404 (mt) cc_final: 0.7991 (mt) REVERT: D 342 MET cc_start: 0.8158 (ttm) cc_final: 0.6702 (ttm) REVERT: D 351 PHE cc_start: 0.7759 (p90) cc_final: 0.7496 (p90) REVERT: D 360 HIS cc_start: 0.7584 (m-70) cc_final: 0.7292 (m170) REVERT: D 361 PHE cc_start: 0.6359 (m-80) cc_final: 0.5898 (m-80) REVERT: D 371 ASP cc_start: 0.8176 (m-30) cc_final: 0.7899 (m-30) REVERT: D 378 CYS cc_start: 0.9110 (m) cc_final: 0.8595 (m) REVERT: D 380 GLN cc_start: 0.8000 (mt0) cc_final: 0.7620 (mt0) REVERT: E 82 LEU cc_start: 0.7470 (mt) cc_final: 0.7032 (mm) REVERT: E 93 MET cc_start: 0.0997 (tmm) cc_final: -0.1222 (ttt) REVERT: E 117 MET cc_start: 0.7975 (tmm) cc_final: 0.7209 (tmm) REVERT: E 242 TRP cc_start: 0.5718 (t-100) cc_final: 0.5302 (t-100) REVERT: E 286 MET cc_start: -0.0846 (tpt) cc_final: -0.1916 (tpt) REVERT: E 299 LYS cc_start: 0.6369 (mttt) cc_final: 0.6015 (tttt) REVERT: E 302 LYS cc_start: 0.8300 (mttm) cc_final: 0.7682 (mttt) REVERT: F 73 ILE cc_start: 0.7515 (pt) cc_final: 0.7128 (mp) REVERT: F 106 TYR cc_start: 0.7221 (m-80) cc_final: 0.6790 (m-10) REVERT: F 112 PHE cc_start: 0.8029 (p90) cc_final: 0.7172 (p90) REVERT: F 181 MET cc_start: -0.5031 (ttm) cc_final: -0.5356 (ttm) REVERT: F 254 HIS cc_start: 0.8527 (m-70) cc_final: 0.8068 (m-70) REVERT: F 258 ARG cc_start: 0.5433 (ttp80) cc_final: 0.5080 (ttp80) REVERT: F 284 ASN cc_start: 0.7692 (t0) cc_final: 0.7271 (t0) REVERT: F 289 MET cc_start: 0.8470 (ttt) cc_final: 0.7815 (mmm) REVERT: F 295 ILE cc_start: 0.7952 (mt) cc_final: 0.7736 (mt) REVERT: F 309 PHE cc_start: 0.7701 (t80) cc_final: 0.7221 (t80) REVERT: G 47 LEU cc_start: 0.9165 (tt) cc_final: 0.8943 (mm) REVERT: G 96 LEU cc_start: 0.8904 (tp) cc_final: 0.8431 (pp) REVERT: G 121 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6905 (tm-30) REVERT: G 130 ASP cc_start: 0.8766 (m-30) cc_final: 0.8486 (m-30) REVERT: G 138 THR cc_start: 0.8604 (p) cc_final: 0.8371 (p) REVERT: G 145 LEU cc_start: 0.7331 (mt) cc_final: 0.7060 (mt) REVERT: G 148 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.7877 (ptm-80) REVERT: G 149 ASN cc_start: 0.8708 (m-40) cc_final: 0.8103 (m-40) REVERT: G 160 ARG cc_start: 0.8485 (ttt180) cc_final: 0.7893 (mtt-85) REVERT: G 172 LYS cc_start: 0.9003 (tttt) cc_final: 0.8191 (tttt) REVERT: G 199 LYS cc_start: 0.7009 (tttt) cc_final: 0.6629 (tttt) REVERT: G 200 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7086 (mt-10) REVERT: H 24 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8344 (tm-30) REVERT: H 54 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.6598 (ttp-110) REVERT: H 110 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.8023 (ttp-110) REVERT: H 118 PHE cc_start: 0.7103 (t80) cc_final: 0.6820 (t80) REVERT: H 133 PHE cc_start: 0.7745 (t80) cc_final: 0.6820 (t80) REVERT: H 137 VAL cc_start: 0.8388 (m) cc_final: 0.8161 (p) REVERT: H 145 VAL cc_start: 0.8940 (t) cc_final: 0.8724 (t) REVERT: H 163 LEU cc_start: 0.8406 (mp) cc_final: 0.7965 (mp) REVERT: I 105 TYR cc_start: 0.3595 (t80) cc_final: 0.2768 (t80) REVERT: I 122 GLU cc_start: 0.8147 (pt0) cc_final: 0.7677 (pp20) REVERT: I 297 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7884 (tptp) REVERT: I 430 CYS cc_start: 0.5813 (t) cc_final: 0.5003 (t) REVERT: I 511 MET cc_start: 0.2013 (tpt) cc_final: 0.1551 (tpt) REVERT: L 28 LYS cc_start: 0.8263 (mmpt) cc_final: 0.7948 (mmmt) REVERT: L 69 HIS cc_start: 0.6112 (t70) cc_final: 0.5599 (t70) REVERT: L 82 THR cc_start: 0.7642 (t) cc_final: 0.7380 (p) REVERT: L 97 LEU cc_start: 0.8546 (pp) cc_final: 0.7967 (pt) REVERT: L 148 ARG cc_start: 0.8122 (ttp-170) cc_final: 0.7564 (tmm160) REVERT: L 157 ILE cc_start: 0.7431 (mt) cc_final: 0.7113 (mm) REVERT: L 158 ARG cc_start: 0.8003 (ppt170) cc_final: 0.7434 (ttp80) REVERT: L 160 HIS cc_start: 0.7300 (t-90) cc_final: 0.7016 (t70) REVERT: L 167 ASP cc_start: 0.8983 (t0) cc_final: 0.8583 (t0) REVERT: L 171 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7861 (ptt180) REVERT: L 189 MET cc_start: 0.8258 (ptp) cc_final: 0.7721 (ppp) REVERT: L 217 PHE cc_start: 0.8097 (m-80) cc_final: 0.7567 (m-10) REVERT: L 242 ASN cc_start: 0.8408 (t0) cc_final: 0.8188 (t0) REVERT: L 245 ILE cc_start: 0.8858 (tp) cc_final: 0.7942 (pt) REVERT: L 246 GLU cc_start: 0.8327 (pp20) cc_final: 0.8056 (pp20) REVERT: L 250 HIS cc_start: 0.6711 (t-90) cc_final: 0.6413 (t70) REVERT: L 279 MET cc_start: 0.6467 (ttp) cc_final: 0.6193 (ttp) REVERT: L 288 LEU cc_start: 0.8468 (tp) cc_final: 0.7977 (tp) REVERT: L 301 LYS cc_start: 0.8579 (pttt) cc_final: 0.7943 (ptpt) REVERT: L 302 LEU cc_start: 0.9190 (mt) cc_final: 0.7931 (mt) REVERT: L 305 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7422 (mpp80) REVERT: L 317 MET cc_start: 0.7952 (mmp) cc_final: 0.7623 (mmp) REVERT: L 351 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8230 (mmt180) REVERT: L 358 GLU cc_start: 0.7265 (pp20) cc_final: 0.6711 (pp20) REVERT: L 366 PHE cc_start: 0.7771 (m-80) cc_final: 0.7541 (m-80) REVERT: L 389 SER cc_start: 0.8905 (p) cc_final: 0.8471 (p) REVERT: L 393 ASP cc_start: 0.7704 (t0) cc_final: 0.6780 (m-30) REVERT: L 394 ASP cc_start: 0.6627 (t0) cc_final: 0.6414 (t0) REVERT: L 395 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8338 (mmmt) REVERT: L 396 LEU cc_start: 0.8650 (mt) cc_final: 0.8325 (mt) REVERT: L 397 LYS cc_start: 0.8000 (mmpt) cc_final: 0.7590 (mmmt) REVERT: L 414 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8704 (mmtm) REVERT: L 434 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: L 448 ASP cc_start: 0.7337 (t0) cc_final: 0.6850 (t70) REVERT: L 475 ARG cc_start: 0.8278 (ttt180) cc_final: 0.7602 (tpp80) REVERT: L 477 MET cc_start: 0.8057 (tmm) cc_final: 0.7507 (tmm) REVERT: L 521 LYS cc_start: 0.6971 (pttt) cc_final: 0.6578 (mttt) REVERT: L 522 CYS cc_start: 0.7878 (t) cc_final: 0.6383 (m) REVERT: L 533 GLU cc_start: 0.7012 (tt0) cc_final: 0.6729 (tp30) REVERT: L 603 MET cc_start: 0.7759 (ptm) cc_final: 0.7454 (ptm) REVERT: L 625 ARG cc_start: 0.7950 (mmp-170) cc_final: 0.7581 (mmp-170) REVERT: L 657 HIS cc_start: 0.7490 (p-80) cc_final: 0.6980 (p90) REVERT: L 670 HIS cc_start: 0.8429 (m-70) cc_final: 0.7911 (m-70) REVERT: L 673 LYS cc_start: 0.8262 (mppt) cc_final: 0.7982 (tptp) REVERT: M 149 LYS cc_start: 0.8584 (tttm) cc_final: 0.7866 (tptp) REVERT: M 155 MET cc_start: 0.2843 (ppp) cc_final: 0.2404 (ppp) REVERT: M 420 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.5056 (pm20) REVERT: R 24 VAL cc_start: 0.7772 (p) cc_final: 0.7516 (m) REVERT: R 39 VAL cc_start: 0.8617 (m) cc_final: 0.8157 (t) REVERT: R 48 HIS cc_start: 0.7533 (t-90) cc_final: 0.7242 (t-90) REVERT: R 50 MET cc_start: 0.6463 (ptt) cc_final: 0.5984 (ptt) REVERT: R 91 ARG cc_start: 0.6741 (mtt90) cc_final: 0.6368 (mtt90) outliers start: 6 outliers final: 1 residues processed: 1128 average time/residue: 0.5280 time to fit residues: 930.3962 Evaluate side-chains 964 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 961 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 417 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 395 optimal weight: 5.9990 chunk 119 optimal weight: 0.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 412 GLN A 423 HIS ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 239 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS D 231 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 114 GLN ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 175 HIS H 22 ASN ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 209 ASN ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 38016 Z= 0.236 Angle : 0.682 8.935 51366 Z= 0.355 Chirality : 0.044 0.197 5749 Planarity : 0.005 0.121 6583 Dihedral : 4.740 27.304 5047 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.92 % Favored : 92.69 % Rotamer: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4597 helix: 0.66 (0.10), residues: 2682 sheet: -0.64 (0.25), residues: 409 loop : -1.99 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 370 HIS 0.010 0.002 HIS G 98 PHE 0.038 0.002 PHE L 428 TYR 0.026 0.002 TYR A 208 ARG 0.013 0.001 ARG E 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1092 time to evaluate : 3.931 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: 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: 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 83 ASP cc_start: 0.6648 (t0) cc_final: 0.6125 (t0) REVERT: A 95 MET cc_start: 0.5475 (pmm) cc_final: 0.4902 (ptm) REVERT: A 117 MET cc_start: 0.7973 (mtt) cc_final: 0.6994 (mtt) REVERT: A 130 MET cc_start: 0.7228 (mmp) cc_final: 0.6523 (mmp) REVERT: A 133 GLU cc_start: 0.7113 (mm-30) cc_final: 0.5828 (mm-30) REVERT: A 234 VAL cc_start: 0.8020 (t) cc_final: 0.7566 (t) REVERT: A 235 ILE cc_start: 0.8490 (mt) cc_final: 0.8060 (mt) REVERT: A 250 ASN cc_start: 0.6149 (t0) cc_final: 0.5209 (t0) REVERT: A 253 HIS cc_start: 0.4451 (m90) cc_final: 0.4048 (m90) REVERT: A 293 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 332 CYS cc_start: 0.7844 (m) cc_final: 0.6545 (p) REVERT: A 342 LEU cc_start: 0.7897 (mt) cc_final: 0.7609 (mt) REVERT: A 363 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.6169 (ptt-90) REVERT: A 365 ILE cc_start: 0.7489 (mt) cc_final: 0.7229 (mm) REVERT: A 387 ASN cc_start: 0.5701 (t0) cc_final: 0.5251 (t0) REVERT: A 392 MET cc_start: 0.4612 (ptt) cc_final: 0.3774 (ptt) REVERT: A 423 HIS cc_start: 0.5640 (m170) cc_final: 0.5429 (m-70) REVERT: A 425 MET cc_start: 0.6576 (ppp) cc_final: 0.6315 (tmm) REVERT: A 436 LEU cc_start: 0.6660 (pp) cc_final: 0.6449 (pp) REVERT: A 438 ASP cc_start: 0.6189 (m-30) cc_final: 0.5418 (m-30) REVERT: A 442 GLN cc_start: 0.6931 (pp30) cc_final: 0.6109 (pp30) REVERT: A 443 LEU cc_start: 0.7430 (mt) cc_final: 0.6951 (mt) REVERT: A 463 ARG cc_start: 0.5603 (tmm160) cc_final: 0.5355 (tmm160) REVERT: A 472 PHE cc_start: 0.6769 (m-10) cc_final: 0.6249 (m-80) REVERT: A 489 MET cc_start: 0.6509 (ppp) cc_final: 0.6111 (ppp) REVERT: A 496 LEU cc_start: 0.8192 (mt) cc_final: 0.7824 (mm) REVERT: B 29 ASN cc_start: 0.7289 (t0) cc_final: 0.6984 (p0) REVERT: B 77 LYS cc_start: 0.8405 (mttt) cc_final: 0.7273 (mmmt) REVERT: B 88 MET cc_start: 0.7032 (tmm) cc_final: 0.6477 (tmm) REVERT: B 90 ASN cc_start: 0.7667 (m110) cc_final: 0.7360 (m110) REVERT: B 93 LYS cc_start: 0.9246 (mttt) cc_final: 0.8877 (mttp) REVERT: B 94 GLN cc_start: 0.7987 (tt0) cc_final: 0.6878 (mt0) REVERT: B 95 LEU cc_start: 0.8618 (mt) cc_final: 0.8233 (mt) REVERT: B 106 ASN cc_start: 0.7621 (t0) cc_final: 0.6705 (m-40) REVERT: B 109 GLU cc_start: 0.7812 (pt0) cc_final: 0.6312 (pp20) REVERT: B 110 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8420 (mttp) REVERT: B 112 ILE cc_start: 0.8119 (pt) cc_final: 0.7697 (mm) REVERT: B 150 LYS cc_start: 0.8810 (mttp) cc_final: 0.8312 (mmtm) REVERT: B 172 LEU cc_start: 0.8693 (mt) cc_final: 0.8355 (mt) REVERT: B 194 LEU cc_start: 0.7835 (mt) cc_final: 0.7056 (mt) REVERT: B 195 LEU cc_start: 0.7235 (mt) cc_final: 0.6723 (mm) REVERT: B 196 GLU cc_start: 0.6704 (mp0) cc_final: 0.5948 (mp0) REVERT: B 213 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7228 (mmmm) REVERT: B 218 TYR cc_start: 0.7736 (t80) cc_final: 0.7192 (t80) REVERT: B 219 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6800 (mm-30) REVERT: B 239 GLU cc_start: 0.8658 (pt0) cc_final: 0.8126 (pp20) REVERT: B 240 CYS cc_start: 0.7394 (p) cc_final: 0.6812 (p) REVERT: B 244 MET cc_start: 0.8214 (ttp) cc_final: 0.6891 (mmp) REVERT: B 247 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8258 (ttp-110) REVERT: B 248 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7025 (pt0) REVERT: B 255 HIS cc_start: 0.7881 (t-90) cc_final: 0.7652 (t-90) REVERT: B 258 PHE cc_start: 0.7922 (m-80) cc_final: 0.7469 (m-80) REVERT: B 259 PHE cc_start: 0.7629 (t80) cc_final: 0.7194 (t80) REVERT: B 260 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7689 (mm-30) REVERT: B 262 PHE cc_start: 0.7122 (t80) cc_final: 0.6405 (t80) REVERT: B 265 TYR cc_start: 0.7951 (m-10) cc_final: 0.7252 (m-80) REVERT: B 273 ARG cc_start: 0.8507 (ptt90) cc_final: 0.7754 (ptt-90) REVERT: B 284 ASN cc_start: 0.7341 (t0) cc_final: 0.6486 (t0) REVERT: B 304 ASN cc_start: 0.8468 (m-40) cc_final: 0.8103 (m110) REVERT: B 313 ASN cc_start: 0.8514 (m110) cc_final: 0.8259 (m-40) REVERT: B 315 VAL cc_start: 0.8979 (t) cc_final: 0.8687 (p) REVERT: B 318 TYR cc_start: 0.6969 (m-80) cc_final: 0.6273 (m-80) REVERT: B 326 PHE cc_start: 0.7563 (t80) cc_final: 0.7143 (t80) REVERT: B 329 ILE cc_start: 0.9035 (mt) cc_final: 0.8740 (mt) REVERT: B 330 LEU cc_start: 0.9220 (mt) cc_final: 0.8730 (mt) REVERT: B 331 LYS cc_start: 0.8364 (mttt) cc_final: 0.7086 (mmtm) REVERT: B 346 HIS cc_start: 0.8215 (m-70) cc_final: 0.7976 (m-70) REVERT: B 348 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 349 GLU cc_start: 0.8479 (tt0) cc_final: 0.7519 (mp0) REVERT: B 350 LEU cc_start: 0.8919 (mt) cc_final: 0.8382 (mt) REVERT: B 352 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7679 (ttm-80) REVERT: B 354 ILE cc_start: 0.8540 (tt) cc_final: 0.8230 (pt) REVERT: B 355 ARG cc_start: 0.8721 (mtt180) cc_final: 0.8320 (mtt90) REVERT: B 356 THR cc_start: 0.8928 (m) cc_final: 0.8534 (m) REVERT: B 357 GLN cc_start: 0.8754 (mt0) cc_final: 0.8192 (mm110) REVERT: B 359 LEU cc_start: 0.8816 (tp) cc_final: 0.8443 (pp) REVERT: B 361 LYS cc_start: 0.8990 (ptmt) cc_final: 0.8325 (pttp) REVERT: B 362 LEU cc_start: 0.8733 (pp) cc_final: 0.7770 (pp) REVERT: B 364 LYS cc_start: 0.9134 (pttm) cc_final: 0.8758 (ptpp) REVERT: B 371 ILE cc_start: 0.8663 (tt) cc_final: 0.8382 (pt) REVERT: B 384 ASP cc_start: 0.8620 (m-30) cc_final: 0.7820 (m-30) REVERT: B 388 LEU cc_start: 0.8849 (mp) cc_final: 0.8548 (mm) REVERT: B 390 VAL cc_start: 0.9407 (t) cc_final: 0.9060 (p) REVERT: B 395 ASP cc_start: 0.7910 (m-30) cc_final: 0.7442 (m-30) REVERT: C 82 GLN cc_start: 0.8202 (mt0) cc_final: 0.7440 (mp10) REVERT: C 92 HIS cc_start: 0.6456 (m90) cc_final: 0.6176 (m-70) REVERT: C 104 CYS cc_start: 0.8358 (m) cc_final: 0.6754 (t) REVERT: C 121 ILE cc_start: 0.4421 (mm) cc_final: 0.3807 (mt) REVERT: C 162 LEU cc_start: 0.9600 (mt) cc_final: 0.9222 (mt) REVERT: C 190 MET cc_start: 0.7694 (mtp) cc_final: 0.7491 (mtp) REVERT: C 191 ILE cc_start: 0.7163 (mt) cc_final: 0.6910 (mm) REVERT: C 202 LEU cc_start: 0.8050 (tp) cc_final: 0.7293 (tp) REVERT: C 225 LYS cc_start: 0.6891 (mttt) cc_final: 0.6536 (mttm) REVERT: C 227 TYR cc_start: 0.7271 (t80) cc_final: 0.7030 (t80) REVERT: C 243 LYS cc_start: 0.8917 (tptt) cc_final: 0.8686 (mmmt) REVERT: C 274 GLU cc_start: 0.8594 (mp0) cc_final: 0.8096 (mp0) REVERT: C 292 MET cc_start: 0.1034 (tpp) cc_final: 0.0265 (tpp) REVERT: C 336 LYS cc_start: 0.8474 (ptpt) cc_final: 0.7945 (ptpp) REVERT: C 337 TYR cc_start: 0.8556 (m-80) cc_final: 0.7611 (m-80) REVERT: C 346 GLU cc_start: 0.7628 (pp20) cc_final: 0.7269 (pp20) REVERT: C 355 ASP cc_start: 0.6616 (p0) cc_final: 0.5509 (p0) REVERT: C 357 MET cc_start: 0.5015 (mmm) cc_final: 0.4241 (mmm) REVERT: C 359 SER cc_start: 0.6392 (m) cc_final: 0.6002 (t) REVERT: C 368 ASN cc_start: 0.8007 (p0) cc_final: 0.7613 (p0) REVERT: C 376 ILE cc_start: 0.8619 (mt) cc_final: 0.8359 (mm) REVERT: C 378 GLN cc_start: 0.8897 (mt0) cc_final: 0.7723 (pp30) REVERT: D 65 LEU cc_start: 0.8408 (mt) cc_final: 0.7924 (tp) REVERT: D 66 LEU cc_start: 0.8657 (mt) cc_final: 0.8297 (mt) REVERT: D 68 ASP cc_start: 0.8956 (m-30) cc_final: 0.8176 (m-30) REVERT: D 75 ASN cc_start: 0.7487 (m110) cc_final: 0.7253 (m110) REVERT: D 127 LEU cc_start: 0.9318 (tp) cc_final: 0.8841 (tp) REVERT: D 144 LYS cc_start: 0.8408 (mttt) cc_final: 0.6592 (mttm) REVERT: D 155 TYR cc_start: 0.8482 (m-80) cc_final: 0.8016 (m-80) REVERT: D 169 ASN cc_start: 0.6829 (m-40) cc_final: 0.6387 (m-40) REVERT: D 186 HIS cc_start: 0.8159 (m90) cc_final: 0.7721 (m-70) REVERT: D 195 LEU cc_start: 0.8830 (mt) cc_final: 0.8406 (mt) REVERT: D 200 LYS cc_start: 0.7959 (mmmt) cc_final: 0.6921 (mmtm) REVERT: D 224 GLU cc_start: 0.7451 (pp20) cc_final: 0.7190 (pp20) REVERT: D 227 LYS cc_start: 0.8710 (tttt) cc_final: 0.7505 (tppt) REVERT: D 231 HIS cc_start: 0.6852 (m-70) cc_final: 0.6609 (m-70) REVERT: D 267 MET cc_start: 0.8084 (tpp) cc_final: 0.7783 (tpt) REVERT: D 300 LEU cc_start: 0.7057 (tp) cc_final: 0.6644 (tp) REVERT: D 306 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7697 (mm-30) REVERT: D 307 HIS cc_start: 0.6323 (t70) cc_final: 0.5757 (t70) REVERT: D 309 LEU cc_start: 0.8583 (tt) cc_final: 0.7963 (tt) REVERT: D 310 LEU cc_start: 0.8991 (mt) cc_final: 0.8360 (mm) REVERT: D 318 ASN cc_start: 0.9121 (p0) cc_final: 0.7447 (p0) REVERT: D 328 LEU cc_start: 0.9505 (mm) cc_final: 0.8512 (mm) REVERT: D 329 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7972 (mp0) REVERT: D 342 MET cc_start: 0.7434 (ttm) cc_final: 0.7108 (ttm) REVERT: D 360 HIS cc_start: 0.7464 (m-70) cc_final: 0.7031 (m170) REVERT: D 361 PHE cc_start: 0.6349 (m-80) cc_final: 0.5945 (m-80) REVERT: D 373 GLN cc_start: 0.7791 (pp30) cc_final: 0.7285 (pp30) REVERT: D 378 CYS cc_start: 0.9092 (m) cc_final: 0.7760 (p) REVERT: D 380 GLN cc_start: 0.8039 (mt0) cc_final: 0.7618 (mt0) REVERT: D 383 ASN cc_start: 0.9107 (m-40) cc_final: 0.8194 (m110) REVERT: D 384 LEU cc_start: 0.9025 (tt) cc_final: 0.7431 (tt) REVERT: D 387 LYS cc_start: 0.9222 (mttt) cc_final: 0.8314 (mtmt) REVERT: E 78 MET cc_start: 0.5794 (mmp) cc_final: 0.5532 (mmp) REVERT: E 82 LEU cc_start: 0.7583 (mt) cc_final: 0.7129 (mm) REVERT: E 93 MET cc_start: 0.0705 (tmm) cc_final: -0.0312 (tpp) REVERT: E 117 MET cc_start: 0.7829 (tmm) cc_final: 0.7092 (tmm) REVERT: E 242 TRP cc_start: 0.5568 (t-100) cc_final: 0.5173 (t-100) REVERT: E 286 MET cc_start: -0.0878 (tpt) cc_final: -0.1962 (tpt) REVERT: E 299 LYS cc_start: 0.6503 (mttt) cc_final: 0.6129 (tttt) REVERT: E 302 LYS cc_start: 0.8276 (mttm) cc_final: 0.7712 (mttt) REVERT: E 324 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7822 (ttmt) REVERT: F 56 ILE cc_start: 0.8816 (pt) cc_final: 0.7685 (pt) REVERT: F 73 ILE cc_start: 0.7390 (pt) cc_final: 0.6857 (mp) REVERT: F 106 TYR cc_start: 0.7316 (m-80) cc_final: 0.6956 (m-10) REVERT: F 157 MET cc_start: 0.5746 (mmp) cc_final: 0.5478 (mmp) REVERT: F 181 MET cc_start: -0.4990 (ttm) cc_final: -0.5333 (ttm) REVERT: F 254 HIS cc_start: 0.8478 (m-70) cc_final: 0.8122 (m-70) REVERT: F 275 PHE cc_start: 0.7259 (t80) cc_final: 0.6781 (t80) REVERT: F 284 ASN cc_start: 0.7701 (t0) cc_final: 0.7355 (t0) REVERT: F 289 MET cc_start: 0.8304 (ttt) cc_final: 0.7755 (mmt) REVERT: F 295 ILE cc_start: 0.7784 (mt) cc_final: 0.7570 (mt) REVERT: F 309 PHE cc_start: 0.7651 (t80) cc_final: 0.7088 (t80) REVERT: G 47 LEU cc_start: 0.9159 (tt) cc_final: 0.8793 (mm) REVERT: G 49 LEU cc_start: 0.9218 (mm) cc_final: 0.8917 (pp) REVERT: G 72 TYR cc_start: 0.6925 (m-10) cc_final: 0.6611 (m-10) REVERT: G 85 LEU cc_start: 0.8361 (pt) cc_final: 0.7846 (pt) REVERT: G 118 LYS cc_start: 0.8196 (pttt) cc_final: 0.7874 (pttt) REVERT: G 121 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6851 (tm-30) REVERT: G 130 ASP cc_start: 0.8485 (m-30) cc_final: 0.7941 (m-30) REVERT: G 148 ARG cc_start: 0.8297 (ttt-90) cc_final: 0.8053 (ptm160) REVERT: G 149 ASN cc_start: 0.8758 (m-40) cc_final: 0.8091 (m-40) REVERT: G 150 GLN cc_start: 0.7618 (mt0) cc_final: 0.6916 (mp10) REVERT: G 172 LYS cc_start: 0.9013 (tttt) cc_final: 0.8189 (tttt) REVERT: G 199 LYS cc_start: 0.7093 (tttt) cc_final: 0.6759 (tttt) REVERT: G 200 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7052 (mt-10) REVERT: H 22 ASN cc_start: 0.7800 (m110) cc_final: 0.7340 (m110) REVERT: H 24 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8307 (tm-30) REVERT: H 54 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.6103 (ttp-110) REVERT: H 97 GLN cc_start: 0.7861 (tp40) cc_final: 0.7640 (tp40) REVERT: H 110 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: H 111 ASP cc_start: 0.8732 (t70) cc_final: 0.8271 (t0) REVERT: H 118 PHE cc_start: 0.7072 (t80) cc_final: 0.6826 (t80) REVERT: H 133 PHE cc_start: 0.7700 (t80) cc_final: 0.6762 (t80) REVERT: H 137 VAL cc_start: 0.8354 (m) cc_final: 0.8148 (p) REVERT: H 145 VAL cc_start: 0.8971 (t) cc_final: 0.8710 (t) REVERT: H 163 LEU cc_start: 0.8424 (mp) cc_final: 0.8058 (mp) REVERT: I 122 GLU cc_start: 0.8276 (pt0) cc_final: 0.7858 (pp20) REVERT: I 149 LYS cc_start: 0.8003 (tttt) cc_final: 0.7418 (mmtt) REVERT: I 287 CYS cc_start: 0.7735 (t) cc_final: 0.4860 (t) REVERT: I 297 LYS cc_start: 0.8352 (tmtt) cc_final: 0.7834 (tptp) REVERT: I 317 ASP cc_start: 0.6868 (p0) cc_final: 0.6055 (p0) REVERT: I 454 MET cc_start: 0.3416 (tpt) cc_final: 0.2947 (tpt) REVERT: I 511 MET cc_start: 0.1752 (tpt) cc_final: 0.1344 (tpt) REVERT: I 526 ARG cc_start: 0.5635 (mtp85) cc_final: 0.4669 (mtp85) REVERT: I 537 PHE cc_start: 0.7413 (t80) cc_final: 0.7126 (t80) REVERT: L 28 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7935 (mmmt) REVERT: L 39 ASN cc_start: 0.8304 (m-40) cc_final: 0.8031 (m-40) REVERT: L 57 LEU cc_start: 0.7970 (mt) cc_final: 0.7613 (mt) REVERT: L 69 HIS cc_start: 0.5863 (t70) cc_final: 0.5541 (t70) REVERT: L 82 THR cc_start: 0.7645 (t) cc_final: 0.7372 (p) REVERT: L 118 MET cc_start: 0.7058 (tpt) cc_final: 0.6856 (tpt) REVERT: L 120 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7478 (ttt180) REVERT: L 122 ILE cc_start: 0.8587 (pt) cc_final: 0.8225 (pt) REVERT: L 127 ASP cc_start: 0.6726 (t0) cc_final: 0.6463 (t0) REVERT: L 139 VAL cc_start: 0.7653 (p) cc_final: 0.7050 (p) REVERT: L 148 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7506 (tmm160) REVERT: L 157 ILE cc_start: 0.7406 (mt) cc_final: 0.7109 (mm) REVERT: L 158 ARG cc_start: 0.8025 (ppt170) cc_final: 0.7297 (ttp80) REVERT: L 163 GLN cc_start: 0.7764 (pt0) cc_final: 0.7440 (pp30) REVERT: L 167 ASP cc_start: 0.8947 (t0) cc_final: 0.8569 (t0) REVERT: L 171 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7833 (ptt180) REVERT: L 185 ASN cc_start: 0.8093 (m-40) cc_final: 0.7625 (m-40) REVERT: L 189 MET cc_start: 0.8717 (ptp) cc_final: 0.7324 (ppp) REVERT: L 217 PHE cc_start: 0.7803 (m-80) cc_final: 0.7553 (m-10) REVERT: L 242 ASN cc_start: 0.8193 (t0) cc_final: 0.7260 (t0) REVERT: L 246 GLU cc_start: 0.7906 (pp20) cc_final: 0.7651 (pp20) REVERT: L 250 HIS cc_start: 0.6870 (t-90) cc_final: 0.6528 (t70) REVERT: L 279 MET cc_start: 0.6395 (ttp) cc_final: 0.6151 (ttp) REVERT: L 288 LEU cc_start: 0.8448 (tp) cc_final: 0.7968 (tp) REVERT: L 294 GLU cc_start: 0.8220 (pm20) cc_final: 0.7848 (pm20) REVERT: L 301 LYS cc_start: 0.8479 (pttt) cc_final: 0.7708 (ptpt) REVERT: L 302 LEU cc_start: 0.9123 (mt) cc_final: 0.7790 (mt) REVERT: L 305 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7452 (mpp80) REVERT: L 317 MET cc_start: 0.7794 (mmp) cc_final: 0.7495 (mmp) REVERT: L 351 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8222 (mmt180) REVERT: L 358 GLU cc_start: 0.7277 (pp20) cc_final: 0.6688 (pp20) REVERT: L 364 ARG cc_start: 0.8488 (tmt170) cc_final: 0.8210 (tpt90) REVERT: L 366 PHE cc_start: 0.7766 (m-80) cc_final: 0.7559 (m-80) REVERT: L 367 LYS cc_start: 0.8631 (mttp) cc_final: 0.8261 (mmtt) REVERT: L 389 SER cc_start: 0.8570 (p) cc_final: 0.8162 (p) REVERT: L 393 ASP cc_start: 0.7478 (t0) cc_final: 0.6858 (m-30) REVERT: L 395 LYS cc_start: 0.9181 (mmpt) cc_final: 0.8450 (mmmm) REVERT: L 396 LEU cc_start: 0.8573 (mt) cc_final: 0.8341 (mt) REVERT: L 397 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7546 (mmmt) REVERT: L 414 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8614 (mmtm) REVERT: L 439 ARG cc_start: 0.6585 (ptp90) cc_final: 0.6169 (ptp90) REVERT: L 448 ASP cc_start: 0.7433 (t0) cc_final: 0.5304 (t70) REVERT: L 473 MET cc_start: 0.7874 (mtm) cc_final: 0.7301 (mtt) REVERT: L 475 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7645 (tpp80) REVERT: L 477 MET cc_start: 0.7955 (tmm) cc_final: 0.7334 (tmm) REVERT: L 522 CYS cc_start: 0.7902 (t) cc_final: 0.6300 (m) REVERT: L 533 GLU cc_start: 0.7427 (tt0) cc_final: 0.6771 (tt0) REVERT: L 552 HIS cc_start: 0.5068 (m90) cc_final: 0.4831 (m90) REVERT: L 554 MET cc_start: 0.8366 (mmp) cc_final: 0.7391 (mmm) REVERT: L 603 MET cc_start: 0.7845 (ptm) cc_final: 0.7490 (ptm) REVERT: L 625 ARG cc_start: 0.8024 (mmp-170) cc_final: 0.7637 (mmp-170) REVERT: L 657 HIS cc_start: 0.7913 (p-80) cc_final: 0.7429 (p90) REVERT: L 670 HIS cc_start: 0.8376 (m-70) cc_final: 0.7926 (m-70) REVERT: L 673 LYS cc_start: 0.8253 (mppt) cc_final: 0.7985 (tptt) REVERT: M 149 LYS cc_start: 0.8659 (tttm) cc_final: 0.7965 (tptp) REVERT: M 420 GLN cc_start: 0.5400 (pp30) cc_final: 0.4931 (pm20) REVERT: M 434 MET cc_start: -0.2188 (tpt) cc_final: -0.4414 (mtm) REVERT: M 452 MET cc_start: 0.1606 (tmm) cc_final: 0.0472 (tmm) REVERT: R 24 VAL cc_start: 0.7902 (p) cc_final: 0.7657 (m) REVERT: R 39 VAL cc_start: 0.9050 (m) cc_final: 0.8730 (t) REVERT: R 48 HIS cc_start: 0.7581 (t-90) cc_final: 0.7231 (t-90) REVERT: R 50 MET cc_start: 0.6455 (ptt) cc_final: 0.6063 (ptt) REVERT: R 91 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6337 (mtt90) outliers start: 2 outliers final: 1 residues processed: 1092 average time/residue: 0.5591 time to fit residues: 956.8617 Evaluate side-chains 961 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 960 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 182 optimal weight: 50.0000 chunk 376 optimal weight: 0.6980 chunk 305 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 chunk 396 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 93 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN F 232 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 87 ASN L 228 ASN L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 489 GLN ** L 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 38016 Z= 0.201 Angle : 0.667 10.235 51366 Z= 0.346 Chirality : 0.044 0.239 5749 Planarity : 0.005 0.119 6583 Dihedral : 4.672 29.290 5047 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.81 % Favored : 92.80 % Rotamer: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4597 helix: 0.76 (0.10), residues: 2673 sheet: -0.67 (0.24), residues: 423 loop : -1.97 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 370 HIS 0.011 0.001 HIS D 72 PHE 0.033 0.002 PHE L 428 TYR 0.039 0.002 TYR D 85 ARG 0.019 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1078 time to evaluate : 4.076 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.6805 (t0) cc_final: 0.6354 (t0) REVERT: A 95 MET cc_start: 0.5440 (pmm) cc_final: 0.4762 (ptm) REVERT: A 117 MET cc_start: 0.7889 (mtt) cc_final: 0.6915 (mtt) REVERT: A 129 ASP cc_start: 0.5909 (p0) cc_final: 0.3900 (p0) REVERT: A 130 MET cc_start: 0.6750 (mmp) cc_final: 0.6320 (mmp) REVERT: A 173 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7345 (mmmt) REVERT: A 204 LEU cc_start: 0.7573 (mt) cc_final: 0.6889 (mt) REVERT: A 218 LEU cc_start: 0.8169 (tp) cc_final: 0.7917 (tp) REVERT: A 234 VAL cc_start: 0.7879 (t) cc_final: 0.7453 (t) REVERT: A 235 ILE cc_start: 0.8543 (mt) cc_final: 0.8005 (mt) REVERT: A 250 ASN cc_start: 0.5903 (t0) cc_final: 0.4826 (t0) REVERT: A 253 HIS cc_start: 0.4355 (m90) cc_final: 0.3985 (m90) REVERT: A 332 CYS cc_start: 0.7926 (m) cc_final: 0.6648 (p) REVERT: A 342 LEU cc_start: 0.7845 (mt) cc_final: 0.7548 (mt) REVERT: A 363 ARG cc_start: 0.6859 (ptt-90) cc_final: 0.6057 (ptt-90) REVERT: A 365 ILE cc_start: 0.7276 (mt) cc_final: 0.6903 (mm) REVERT: A 379 LYS cc_start: 0.7927 (pttp) cc_final: 0.7210 (mttm) REVERT: A 387 ASN cc_start: 0.5583 (t0) cc_final: 0.5143 (t0) REVERT: A 392 MET cc_start: 0.4045 (ptt) cc_final: 0.3355 (ptt) REVERT: A 421 ASP cc_start: 0.6724 (t0) cc_final: 0.6195 (t0) REVERT: A 423 HIS cc_start: 0.5763 (m170) cc_final: 0.5109 (m-70) REVERT: A 438 ASP cc_start: 0.6048 (m-30) cc_final: 0.5591 (m-30) REVERT: A 472 PHE cc_start: 0.6539 (m-10) cc_final: 0.6325 (m-80) REVERT: A 473 GLU cc_start: 0.6575 (pp20) cc_final: 0.6287 (pp20) REVERT: A 475 SER cc_start: 0.7243 (m) cc_final: 0.7030 (p) REVERT: A 489 MET cc_start: 0.6579 (ppp) cc_final: 0.5989 (ppp) REVERT: A 496 LEU cc_start: 0.8176 (mt) cc_final: 0.7702 (mm) REVERT: B 45 ASP cc_start: 0.8296 (m-30) cc_final: 0.7425 (m-30) REVERT: B 77 LYS cc_start: 0.8465 (mttt) cc_final: 0.7271 (mmmt) REVERT: B 88 MET cc_start: 0.7015 (tmm) cc_final: 0.6107 (tmm) REVERT: B 90 ASN cc_start: 0.7577 (m110) cc_final: 0.5795 (m110) REVERT: B 93 LYS cc_start: 0.9491 (mttt) cc_final: 0.8932 (mttt) REVERT: B 94 GLN cc_start: 0.8365 (tt0) cc_final: 0.8013 (mm-40) REVERT: B 95 LEU cc_start: 0.8558 (mt) cc_final: 0.8296 (mt) REVERT: B 109 GLU cc_start: 0.7774 (pt0) cc_final: 0.6430 (pp20) REVERT: B 110 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8552 (pttt) REVERT: B 150 LYS cc_start: 0.8798 (mttp) cc_final: 0.8388 (mmtt) REVERT: B 168 LEU cc_start: 0.7975 (tp) cc_final: 0.7556 (tp) REVERT: B 171 ILE cc_start: 0.8902 (mt) cc_final: 0.8400 (tp) REVERT: B 195 LEU cc_start: 0.7187 (mt) cc_final: 0.6475 (mm) REVERT: B 196 GLU cc_start: 0.6836 (mp0) cc_final: 0.5871 (mp0) REVERT: B 213 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7210 (mmmm) REVERT: B 218 TYR cc_start: 0.7771 (t80) cc_final: 0.7098 (t80) REVERT: B 219 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 239 GLU cc_start: 0.8318 (pt0) cc_final: 0.8022 (pp20) REVERT: B 240 CYS cc_start: 0.7364 (p) cc_final: 0.6583 (p) REVERT: B 244 MET cc_start: 0.8230 (ttp) cc_final: 0.6994 (mmp) REVERT: B 247 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8474 (ttm110) REVERT: B 248 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6910 (pt0) REVERT: B 252 GLU cc_start: 0.7653 (pm20) cc_final: 0.7445 (pm20) REVERT: B 258 PHE cc_start: 0.7931 (m-80) cc_final: 0.7321 (m-80) REVERT: B 259 PHE cc_start: 0.7620 (t80) cc_final: 0.7191 (t80) REVERT: B 260 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7575 (mm-30) REVERT: B 262 PHE cc_start: 0.7070 (t80) cc_final: 0.6352 (t80) REVERT: B 265 TYR cc_start: 0.7662 (m-10) cc_final: 0.7205 (m-80) REVERT: B 273 ARG cc_start: 0.8482 (ptt90) cc_final: 0.7675 (ptt-90) REVERT: B 284 ASN cc_start: 0.7042 (t0) cc_final: 0.6358 (t0) REVERT: B 304 ASN cc_start: 0.8451 (m-40) cc_final: 0.8085 (m-40) REVERT: B 313 ASN cc_start: 0.8512 (m110) cc_final: 0.8225 (m-40) REVERT: B 315 VAL cc_start: 0.8967 (t) cc_final: 0.8641 (t) REVERT: B 318 TYR cc_start: 0.7011 (m-80) cc_final: 0.6243 (m-80) REVERT: B 326 PHE cc_start: 0.7556 (t80) cc_final: 0.7199 (t80) REVERT: B 328 LYS cc_start: 0.8789 (pttm) cc_final: 0.8254 (ptpp) REVERT: B 329 ILE cc_start: 0.8892 (mt) cc_final: 0.8656 (mt) REVERT: B 330 LEU cc_start: 0.9201 (mt) cc_final: 0.8941 (mt) REVERT: B 331 LYS cc_start: 0.8354 (mttt) cc_final: 0.7374 (pttm) REVERT: B 346 HIS cc_start: 0.8314 (m-70) cc_final: 0.7770 (m-70) REVERT: B 348 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7809 (mp0) REVERT: B 349 GLU cc_start: 0.8291 (tt0) cc_final: 0.7595 (mp0) REVERT: B 350 LEU cc_start: 0.8862 (mt) cc_final: 0.8427 (mt) REVERT: B 352 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: B 354 ILE cc_start: 0.8485 (tt) cc_final: 0.8182 (pt) REVERT: B 355 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8264 (mtt90) REVERT: B 356 THR cc_start: 0.8914 (m) cc_final: 0.8502 (m) REVERT: B 357 GLN cc_start: 0.8766 (mt0) cc_final: 0.8047 (mm-40) REVERT: B 359 LEU cc_start: 0.8799 (tp) cc_final: 0.8463 (pp) REVERT: B 361 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8370 (pttp) REVERT: B 364 LYS cc_start: 0.9043 (pttm) cc_final: 0.8691 (ptpp) REVERT: B 371 ILE cc_start: 0.8716 (tt) cc_final: 0.8132 (pt) REVERT: B 384 ASP cc_start: 0.8644 (m-30) cc_final: 0.7811 (m-30) REVERT: B 388 LEU cc_start: 0.8880 (mp) cc_final: 0.8569 (mm) REVERT: B 390 VAL cc_start: 0.9376 (t) cc_final: 0.9075 (p) REVERT: B 395 ASP cc_start: 0.7484 (m-30) cc_final: 0.6819 (m-30) REVERT: C 25 CYS cc_start: 0.8041 (t) cc_final: 0.7741 (t) REVERT: C 82 GLN cc_start: 0.8125 (mt0) cc_final: 0.7306 (mp10) REVERT: C 92 HIS cc_start: 0.6396 (m90) cc_final: 0.6132 (m-70) REVERT: C 104 CYS cc_start: 0.7992 (m) cc_final: 0.5992 (t) REVERT: C 121 ILE cc_start: 0.4665 (mm) cc_final: 0.3619 (mt) REVERT: C 131 MET cc_start: 0.6826 (ppp) cc_final: 0.6139 (ppp) REVERT: C 162 LEU cc_start: 0.9558 (mt) cc_final: 0.9268 (mt) REVERT: C 190 MET cc_start: 0.7791 (mtp) cc_final: 0.7356 (mtp) REVERT: C 191 ILE cc_start: 0.7167 (mt) cc_final: 0.6916 (mt) REVERT: C 202 LEU cc_start: 0.8104 (tp) cc_final: 0.7307 (tp) REVERT: C 333 GLU cc_start: 0.8005 (pp20) cc_final: 0.7459 (pp20) REVERT: C 336 LYS cc_start: 0.8509 (ptpt) cc_final: 0.7913 (ptpp) REVERT: C 337 TYR cc_start: 0.8621 (m-80) cc_final: 0.7566 (m-80) REVERT: C 339 LEU cc_start: 0.8696 (mt) cc_final: 0.8473 (mt) REVERT: C 355 ASP cc_start: 0.6571 (p0) cc_final: 0.5419 (p0) REVERT: C 357 MET cc_start: 0.4990 (mmm) cc_final: 0.4243 (mmm) REVERT: C 359 SER cc_start: 0.6274 (m) cc_final: 0.5951 (t) REVERT: C 368 ASN cc_start: 0.7933 (p0) cc_final: 0.7607 (p0) REVERT: C 376 ILE cc_start: 0.8510 (mt) cc_final: 0.8180 (mm) REVERT: C 380 MET cc_start: 0.6189 (ptm) cc_final: 0.5968 (mmt) REVERT: D 65 LEU cc_start: 0.8398 (mt) cc_final: 0.8094 (mt) REVERT: D 66 LEU cc_start: 0.8719 (mt) cc_final: 0.8286 (mt) REVERT: D 68 ASP cc_start: 0.8966 (m-30) cc_final: 0.8025 (m-30) REVERT: D 75 ASN cc_start: 0.6946 (m110) cc_final: 0.6646 (m110) REVERT: D 116 LYS cc_start: 0.8994 (mmpt) cc_final: 0.8790 (mmmt) REVERT: D 127 LEU cc_start: 0.9316 (tp) cc_final: 0.8854 (tp) REVERT: D 139 TYR cc_start: 0.6624 (m-80) cc_final: 0.5458 (m-80) REVERT: D 143 TYR cc_start: 0.7509 (t80) cc_final: 0.6883 (t80) REVERT: D 144 LYS cc_start: 0.8635 (mttt) cc_final: 0.6012 (mmtt) REVERT: D 155 TYR cc_start: 0.8745 (m-80) cc_final: 0.7971 (m-80) REVERT: D 163 GLN cc_start: 0.8441 (mp10) cc_final: 0.8135 (mp10) REVERT: D 167 TYR cc_start: 0.6953 (m-80) cc_final: 0.6591 (m-80) REVERT: D 169 ASN cc_start: 0.6706 (m-40) cc_final: 0.6040 (m-40) REVERT: D 186 HIS cc_start: 0.8058 (m90) cc_final: 0.7708 (m-70) REVERT: D 200 LYS cc_start: 0.7728 (mmmt) cc_final: 0.6876 (mmtm) REVERT: D 227 LYS cc_start: 0.8645 (tttt) cc_final: 0.7177 (tppt) REVERT: D 231 HIS cc_start: 0.7166 (m170) cc_final: 0.6453 (m170) REVERT: D 267 MET cc_start: 0.7982 (tpp) cc_final: 0.7041 (tpt) REVERT: D 300 LEU cc_start: 0.7004 (tp) cc_final: 0.6439 (tp) REVERT: D 306 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7629 (mm-30) REVERT: D 307 HIS cc_start: 0.6697 (t70) cc_final: 0.5656 (t-90) REVERT: D 310 LEU cc_start: 0.9077 (mt) cc_final: 0.8818 (mm) REVERT: D 318 ASN cc_start: 0.9167 (p0) cc_final: 0.7412 (p0) REVERT: D 328 LEU cc_start: 0.9488 (mm) cc_final: 0.8455 (mm) REVERT: D 329 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7962 (mp0) REVERT: D 342 MET cc_start: 0.7602 (ttm) cc_final: 0.7323 (ttm) REVERT: D 345 GLU cc_start: 0.7979 (tp30) cc_final: 0.7671 (tp30) REVERT: D 347 ARG cc_start: 0.7170 (ptt90) cc_final: 0.6422 (ptt90) REVERT: D 361 PHE cc_start: 0.6356 (m-80) cc_final: 0.6091 (m-80) REVERT: D 373 GLN cc_start: 0.7882 (pp30) cc_final: 0.7573 (pp30) REVERT: D 376 SER cc_start: 0.8156 (t) cc_final: 0.7325 (p) REVERT: D 378 CYS cc_start: 0.9066 (m) cc_final: 0.7808 (p) REVERT: D 380 GLN cc_start: 0.7997 (mt0) cc_final: 0.7767 (mt0) REVERT: E 78 MET cc_start: 0.5568 (mmp) cc_final: 0.5183 (mmp) REVERT: E 82 LEU cc_start: 0.7632 (mt) cc_final: 0.7279 (mm) REVERT: E 117 MET cc_start: 0.7771 (tmm) cc_final: 0.7063 (tmm) REVERT: E 134 ILE cc_start: 0.8734 (pt) cc_final: 0.8471 (pt) REVERT: E 242 TRP cc_start: 0.5205 (t-100) cc_final: 0.4896 (t-100) REVERT: E 286 MET cc_start: -0.0912 (tpt) cc_final: -0.2000 (tpt) REVERT: E 299 LYS cc_start: 0.6500 (mttt) cc_final: 0.6084 (tttt) REVERT: E 302 LYS cc_start: 0.8382 (mttm) cc_final: 0.7742 (mttt) REVERT: E 324 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7925 (ttmt) REVERT: F 73 ILE cc_start: 0.7296 (pt) cc_final: 0.7071 (mp) REVERT: F 116 PHE cc_start: 0.7321 (m-10) cc_final: 0.7077 (m-10) REVERT: F 157 MET cc_start: 0.5764 (mmp) cc_final: 0.5528 (mmp) REVERT: F 181 MET cc_start: -0.5045 (ttm) cc_final: -0.5298 (ttm) REVERT: F 254 HIS cc_start: 0.8468 (m-70) cc_final: 0.8160 (m-70) REVERT: F 256 ILE cc_start: 0.7956 (mp) cc_final: 0.7520 (mp) REVERT: F 275 PHE cc_start: 0.7081 (t80) cc_final: 0.6705 (t80) REVERT: F 284 ASN cc_start: 0.7711 (t0) cc_final: 0.7352 (t0) REVERT: F 289 MET cc_start: 0.8339 (ttt) cc_final: 0.7782 (mmt) REVERT: F 309 PHE cc_start: 0.7653 (t80) cc_final: 0.7280 (t80) REVERT: G 49 LEU cc_start: 0.9288 (mm) cc_final: 0.8944 (pp) REVERT: G 52 VAL cc_start: 0.6959 (p) cc_final: 0.6556 (p) REVERT: G 72 TYR cc_start: 0.6766 (m-10) cc_final: 0.6512 (m-10) REVERT: G 85 LEU cc_start: 0.8581 (pt) cc_final: 0.8001 (pt) REVERT: G 118 LYS cc_start: 0.8091 (pttt) cc_final: 0.7789 (pttt) REVERT: G 121 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6710 (tm-30) REVERT: G 130 ASP cc_start: 0.8709 (m-30) cc_final: 0.8163 (m-30) REVERT: G 150 GLN cc_start: 0.7407 (mt0) cc_final: 0.6679 (mp10) REVERT: G 152 LEU cc_start: 0.7857 (tp) cc_final: 0.7373 (mm) REVERT: G 172 LYS cc_start: 0.9014 (tttt) cc_final: 0.8184 (tttt) REVERT: G 199 LYS cc_start: 0.7076 (tttt) cc_final: 0.6787 (tttt) REVERT: G 200 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6987 (mt-10) REVERT: H 22 ASN cc_start: 0.7708 (m110) cc_final: 0.7431 (m110) REVERT: H 24 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8353 (tm-30) REVERT: H 50 MET cc_start: 0.4165 (mmt) cc_final: 0.3888 (mmt) REVERT: H 96 HIS cc_start: 0.6196 (t-90) cc_final: 0.4880 (t-90) REVERT: H 98 TRP cc_start: 0.7605 (m100) cc_final: 0.7243 (m100) REVERT: H 110 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.8041 (ttp-110) REVERT: H 118 PHE cc_start: 0.6985 (t80) cc_final: 0.6780 (t80) REVERT: H 120 LEU cc_start: 0.8844 (tt) cc_final: 0.8569 (tt) REVERT: H 133 PHE cc_start: 0.7692 (t80) cc_final: 0.6716 (t80) REVERT: H 137 VAL cc_start: 0.8323 (m) cc_final: 0.8120 (p) REVERT: H 150 GLU cc_start: 0.8764 (pp20) cc_final: 0.8259 (pp20) REVERT: H 163 LEU cc_start: 0.8461 (mp) cc_final: 0.8012 (mp) REVERT: I 110 PHE cc_start: 0.5738 (t80) cc_final: 0.5477 (t80) REVERT: I 122 GLU cc_start: 0.8216 (pt0) cc_final: 0.7749 (pp20) REVERT: I 149 LYS cc_start: 0.7956 (tttt) cc_final: 0.7369 (tptm) REVERT: I 155 MET cc_start: 0.7218 (tpp) cc_final: 0.6723 (tpp) REVERT: I 297 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8170 (tptp) REVERT: I 317 ASP cc_start: 0.6295 (p0) cc_final: 0.5722 (p0) REVERT: I 319 TYR cc_start: 0.6095 (m-80) cc_final: 0.5858 (m-80) REVERT: I 430 CYS cc_start: 0.5703 (t) cc_final: 0.5256 (t) REVERT: I 454 MET cc_start: 0.2961 (tpt) cc_final: 0.2723 (tpt) REVERT: I 511 MET cc_start: 0.1502 (tpt) cc_final: 0.1163 (tpt) REVERT: I 537 PHE cc_start: 0.7212 (t80) cc_final: 0.6859 (t80) REVERT: L 28 LYS cc_start: 0.8210 (mmpt) cc_final: 0.7911 (mmmt) REVERT: L 39 ASN cc_start: 0.8103 (m-40) cc_final: 0.7892 (m-40) REVERT: L 57 LEU cc_start: 0.7822 (mt) cc_final: 0.7609 (mt) REVERT: L 82 THR cc_start: 0.7806 (t) cc_final: 0.7528 (p) REVERT: L 122 ILE cc_start: 0.8452 (pt) cc_final: 0.7969 (pt) REVERT: L 127 ASP cc_start: 0.6616 (t0) cc_final: 0.6359 (t0) REVERT: L 139 VAL cc_start: 0.7600 (p) cc_final: 0.7221 (p) REVERT: L 157 ILE cc_start: 0.7408 (mt) cc_final: 0.7122 (mm) REVERT: L 158 ARG cc_start: 0.8005 (ppt170) cc_final: 0.7159 (ttp80) REVERT: L 163 GLN cc_start: 0.7717 (pt0) cc_final: 0.7425 (pp30) REVERT: L 167 ASP cc_start: 0.8915 (t0) cc_final: 0.8395 (t0) REVERT: L 171 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7754 (ptt180) REVERT: L 185 ASN cc_start: 0.8096 (m-40) cc_final: 0.7693 (m-40) REVERT: L 189 MET cc_start: 0.8321 (ptp) cc_final: 0.7743 (ppp) REVERT: L 205 PHE cc_start: 0.6488 (t80) cc_final: 0.6248 (t80) REVERT: L 242 ASN cc_start: 0.8134 (t0) cc_final: 0.7146 (t0) REVERT: L 246 GLU cc_start: 0.7854 (pp20) cc_final: 0.7637 (pp20) REVERT: L 250 HIS cc_start: 0.6891 (t-90) cc_final: 0.6286 (t70) REVERT: L 279 MET cc_start: 0.6417 (ttp) cc_final: 0.6210 (ttp) REVERT: L 288 LEU cc_start: 0.8367 (tp) cc_final: 0.7974 (tp) REVERT: L 294 GLU cc_start: 0.8398 (pm20) cc_final: 0.7964 (pm20) REVERT: L 301 LYS cc_start: 0.8398 (pttt) cc_final: 0.7826 (ptpt) REVERT: L 302 LEU cc_start: 0.8997 (mt) cc_final: 0.8351 (mt) REVERT: L 305 ARG cc_start: 0.7736 (mtt90) cc_final: 0.7240 (mpt-90) REVERT: L 313 MET cc_start: 0.7601 (tpp) cc_final: 0.7022 (mtp) REVERT: L 358 GLU cc_start: 0.7277 (pp20) cc_final: 0.6662 (pp20) REVERT: L 364 ARG cc_start: 0.8439 (tmt170) cc_final: 0.8167 (tpt90) REVERT: L 366 PHE cc_start: 0.7429 (m-80) cc_final: 0.7068 (m-80) REVERT: L 367 LYS cc_start: 0.8631 (mttp) cc_final: 0.8417 (mmtm) REVERT: L 395 LYS cc_start: 0.9164 (mmpt) cc_final: 0.8407 (mmmm) REVERT: L 396 LEU cc_start: 0.8645 (mt) cc_final: 0.8361 (mp) REVERT: L 397 LYS cc_start: 0.8223 (mmpt) cc_final: 0.7521 (mmmt) REVERT: L 414 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8626 (mmtm) REVERT: L 434 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: L 435 HIS cc_start: 0.7209 (m90) cc_final: 0.6155 (m90) REVERT: L 451 GLU cc_start: 0.8640 (pt0) cc_final: 0.8323 (pp20) REVERT: L 452 LYS cc_start: 0.8467 (mppt) cc_final: 0.7960 (mttm) REVERT: L 457 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8604 (mmtt) REVERT: L 473 MET cc_start: 0.7847 (mtm) cc_final: 0.7185 (mtt) REVERT: L 475 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7258 (tpp80) REVERT: L 477 MET cc_start: 0.7985 (tmm) cc_final: 0.7485 (tmm) REVERT: L 522 CYS cc_start: 0.7882 (t) cc_final: 0.7071 (m) REVERT: L 552 HIS cc_start: 0.5122 (m90) cc_final: 0.4817 (m90) REVERT: L 554 MET cc_start: 0.8160 (mmp) cc_final: 0.7258 (mmm) REVERT: L 603 MET cc_start: 0.7832 (ptm) cc_final: 0.7435 (ptm) REVERT: L 625 ARG cc_start: 0.8040 (mmp-170) cc_final: 0.7666 (mmp-170) REVERT: L 657 HIS cc_start: 0.7930 (p-80) cc_final: 0.7400 (p90) REVERT: L 670 HIS cc_start: 0.8290 (m-70) cc_final: 0.7953 (m-70) REVERT: M 46 LYS cc_start: 0.7370 (pptt) cc_final: 0.6809 (pptt) REVERT: M 149 LYS cc_start: 0.8619 (tttm) cc_final: 0.7920 (tptp) REVERT: M 155 MET cc_start: 0.3657 (ppp) cc_final: 0.3029 (ppp) REVERT: M 420 GLN cc_start: 0.6592 (pp30) cc_final: 0.5496 (pm20) REVERT: M 434 MET cc_start: -0.3328 (tpt) cc_final: -0.4349 (mtt) REVERT: R 37 ILE cc_start: 0.7539 (mp) cc_final: 0.7061 (mp) REVERT: R 39 VAL cc_start: 0.9077 (m) cc_final: 0.8543 (t) REVERT: R 48 HIS cc_start: 0.7572 (t-90) cc_final: 0.7249 (t-90) REVERT: R 50 MET cc_start: 0.6544 (ptt) cc_final: 0.6142 (ptt) REVERT: R 91 ARG cc_start: 0.6852 (mtt90) cc_final: 0.6391 (mtt90) outliers start: 2 outliers final: 1 residues processed: 1080 average time/residue: 0.5368 time to fit residues: 904.8830 Evaluate side-chains 957 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 955 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 0.8980 chunk 397 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 259 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 442 optimal weight: 0.7980 chunk 367 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 412 GLN A 498 ASN A 501 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 HIS ** M 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 GLN M 357 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 38016 Z= 0.197 Angle : 0.669 10.058 51366 Z= 0.345 Chirality : 0.043 0.193 5749 Planarity : 0.005 0.135 6583 Dihedral : 4.675 25.877 5047 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.87 % Favored : 92.78 % Rotamer: Outliers : 0.02 % Allowed : 1.80 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4597 helix: 0.84 (0.10), residues: 2678 sheet: -0.55 (0.25), residues: 417 loop : -1.96 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 166 HIS 0.007 0.001 HIS C 374 PHE 0.043 0.002 PHE G 15 TYR 0.043 0.002 TYR B 132 ARG 0.023 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1087 time to evaluate : 4.066 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7070 (t0) cc_final: 0.6590 (t0) REVERT: A 95 MET cc_start: 0.5287 (pmm) cc_final: 0.4459 (ptm) REVERT: A 103 ILE cc_start: 0.7567 (pt) cc_final: 0.7367 (pt) REVERT: A 117 MET cc_start: 0.8039 (mtt) cc_final: 0.6953 (mtt) REVERT: A 129 ASP cc_start: 0.7016 (p0) cc_final: 0.6014 (p0) REVERT: A 133 GLU cc_start: 0.6360 (mp0) cc_final: 0.5650 (mp0) REVERT: A 136 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7070 (ptt90) REVERT: A 137 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7573 (mmpt) REVERT: A 173 LYS cc_start: 0.7824 (mmpt) cc_final: 0.7404 (mmmt) REVERT: A 204 LEU cc_start: 0.6771 (mt) cc_final: 0.6437 (mt) REVERT: A 218 LEU cc_start: 0.8032 (tp) cc_final: 0.7327 (tp) REVERT: A 234 VAL cc_start: 0.7877 (t) cc_final: 0.7469 (t) REVERT: A 237 MET cc_start: 0.7763 (ptt) cc_final: 0.7552 (ptt) REVERT: A 250 ASN cc_start: 0.5773 (t0) cc_final: 0.4696 (t0) REVERT: A 253 HIS cc_start: 0.4286 (m90) cc_final: 0.3881 (m90) REVERT: A 332 CYS cc_start: 0.7850 (m) cc_final: 0.6667 (p) REVERT: A 342 LEU cc_start: 0.7792 (mt) cc_final: 0.7478 (mt) REVERT: A 363 ARG cc_start: 0.6922 (ptt-90) cc_final: 0.6128 (ptt-90) REVERT: A 365 ILE cc_start: 0.7452 (mt) cc_final: 0.7015 (mm) REVERT: A 379 LYS cc_start: 0.8453 (pttp) cc_final: 0.7498 (mttm) REVERT: A 380 MET cc_start: 0.6897 (mmp) cc_final: 0.6679 (mmp) REVERT: A 387 ASN cc_start: 0.5498 (t0) cc_final: 0.5155 (t0) REVERT: A 389 LEU cc_start: 0.5276 (mt) cc_final: 0.4996 (mt) REVERT: A 392 MET cc_start: 0.4003 (ptt) cc_final: 0.3097 (ptt) REVERT: A 423 HIS cc_start: 0.5483 (m170) cc_final: 0.5131 (m-70) REVERT: A 425 MET cc_start: 0.6085 (tmm) cc_final: 0.5702 (tmm) REVERT: A 438 ASP cc_start: 0.6042 (m-30) cc_final: 0.5527 (m-30) REVERT: A 472 PHE cc_start: 0.6562 (m-10) cc_final: 0.6270 (m-80) REVERT: A 473 GLU cc_start: 0.6633 (pp20) cc_final: 0.6397 (pp20) REVERT: A 478 MET cc_start: 0.7306 (mmp) cc_final: 0.6797 (mmm) REVERT: A 496 LEU cc_start: 0.8224 (mt) cc_final: 0.7754 (mm) REVERT: B 29 ASN cc_start: 0.7329 (t0) cc_final: 0.7074 (p0) REVERT: B 34 ASN cc_start: 0.6129 (m-40) cc_final: 0.5537 (t0) REVERT: B 35 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7966 (mm-40) REVERT: B 77 LYS cc_start: 0.8546 (mttt) cc_final: 0.7338 (mmmt) REVERT: B 88 MET cc_start: 0.6923 (tmm) cc_final: 0.6397 (tmm) REVERT: B 93 LYS cc_start: 0.9472 (mttt) cc_final: 0.8624 (mmtt) REVERT: B 95 LEU cc_start: 0.8496 (mt) cc_final: 0.8229 (mt) REVERT: B 106 ASN cc_start: 0.7210 (t0) cc_final: 0.6381 (m-40) REVERT: B 109 GLU cc_start: 0.7936 (pt0) cc_final: 0.6096 (pp20) REVERT: B 110 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8460 (mttt) REVERT: B 150 LYS cc_start: 0.8806 (mttp) cc_final: 0.8347 (mmtt) REVERT: B 168 LEU cc_start: 0.7988 (tp) cc_final: 0.7201 (tp) REVERT: B 171 ILE cc_start: 0.8725 (mt) cc_final: 0.8119 (tp) REVERT: B 173 ARG cc_start: 0.8082 (mmp80) cc_final: 0.7542 (mmm160) REVERT: B 176 HIS cc_start: 0.7061 (m90) cc_final: 0.6293 (m90) REVERT: B 196 GLU cc_start: 0.6782 (mp0) cc_final: 0.6443 (mp0) REVERT: B 203 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 209 LYS cc_start: 0.8141 (tppt) cc_final: 0.7821 (tptt) REVERT: B 213 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7197 (mmmm) REVERT: B 218 TYR cc_start: 0.7796 (t80) cc_final: 0.7186 (t80) REVERT: B 219 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6861 (mm-30) REVERT: B 239 GLU cc_start: 0.8296 (pt0) cc_final: 0.7999 (pp20) REVERT: B 244 MET cc_start: 0.8197 (ttp) cc_final: 0.6574 (tmm) REVERT: B 247 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8458 (ttp-110) REVERT: B 248 GLU cc_start: 0.7779 (mt-10) cc_final: 0.6614 (pt0) REVERT: B 258 PHE cc_start: 0.7917 (m-80) cc_final: 0.7332 (m-80) REVERT: B 259 PHE cc_start: 0.7749 (t80) cc_final: 0.7435 (t80) REVERT: B 260 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7693 (mm-30) REVERT: B 262 PHE cc_start: 0.7065 (t80) cc_final: 0.6324 (t80) REVERT: B 265 TYR cc_start: 0.7698 (m-10) cc_final: 0.7118 (m-80) REVERT: B 273 ARG cc_start: 0.8465 (ptt90) cc_final: 0.7968 (mtm110) REVERT: B 284 ASN cc_start: 0.7279 (t0) cc_final: 0.6492 (t0) REVERT: B 304 ASN cc_start: 0.8461 (m-40) cc_final: 0.8121 (m110) REVERT: B 313 ASN cc_start: 0.8688 (m110) cc_final: 0.8307 (m-40) REVERT: B 315 VAL cc_start: 0.8972 (t) cc_final: 0.8596 (p) REVERT: B 318 TYR cc_start: 0.7135 (m-80) cc_final: 0.6513 (m-80) REVERT: B 326 PHE cc_start: 0.7495 (t80) cc_final: 0.7206 (t80) REVERT: B 327 GLU cc_start: 0.7898 (tp30) cc_final: 0.7559 (tp30) REVERT: B 328 LYS cc_start: 0.9077 (pttp) cc_final: 0.7970 (ptpp) REVERT: B 330 LEU cc_start: 0.9373 (mt) cc_final: 0.9038 (mt) REVERT: B 331 LYS cc_start: 0.8358 (mttt) cc_final: 0.7322 (pttm) REVERT: B 346 HIS cc_start: 0.8298 (m-70) cc_final: 0.7727 (m-70) REVERT: B 348 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7784 (mp0) REVERT: B 349 GLU cc_start: 0.8459 (tt0) cc_final: 0.7572 (mp0) REVERT: B 352 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: B 353 ASN cc_start: 0.8359 (m110) cc_final: 0.8108 (m110) REVERT: B 354 ILE cc_start: 0.8485 (tt) cc_final: 0.8237 (pt) REVERT: B 355 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8263 (mtt90) REVERT: B 356 THR cc_start: 0.8888 (m) cc_final: 0.8510 (m) REVERT: B 357 GLN cc_start: 0.8756 (mt0) cc_final: 0.8106 (mm-40) REVERT: B 359 LEU cc_start: 0.8792 (tp) cc_final: 0.8483 (pp) REVERT: B 361 LYS cc_start: 0.8897 (ptmt) cc_final: 0.8329 (pttp) REVERT: B 364 LYS cc_start: 0.9046 (pttm) cc_final: 0.8674 (ptpp) REVERT: B 384 ASP cc_start: 0.8897 (m-30) cc_final: 0.8011 (m-30) REVERT: B 386 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7398 (tm-30) REVERT: B 388 LEU cc_start: 0.8899 (mp) cc_final: 0.8486 (mm) REVERT: B 390 VAL cc_start: 0.9395 (t) cc_final: 0.9092 (p) REVERT: B 391 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7038 (tp-100) REVERT: B 395 ASP cc_start: 0.7471 (m-30) cc_final: 0.6714 (m-30) REVERT: C 25 CYS cc_start: 0.7664 (t) cc_final: 0.7420 (t) REVERT: C 42 LEU cc_start: 0.6224 (pt) cc_final: 0.5913 (pp) REVERT: C 82 GLN cc_start: 0.8119 (mt0) cc_final: 0.7273 (mp10) REVERT: C 92 HIS cc_start: 0.6405 (m90) cc_final: 0.6156 (m-70) REVERT: C 104 CYS cc_start: 0.8095 (m) cc_final: 0.6338 (t) REVERT: C 121 ILE cc_start: 0.4657 (mm) cc_final: 0.3667 (mt) REVERT: C 162 LEU cc_start: 0.9614 (mt) cc_final: 0.9269 (mt) REVERT: C 166 MET cc_start: 0.6518 (mtp) cc_final: 0.5707 (mtm) REVERT: C 190 MET cc_start: 0.7768 (mtp) cc_final: 0.7279 (mtp) REVERT: C 191 ILE cc_start: 0.7046 (mt) cc_final: 0.6752 (mt) REVERT: C 202 LEU cc_start: 0.8274 (tp) cc_final: 0.6973 (tp) REVERT: C 227 TYR cc_start: 0.6960 (t80) cc_final: 0.6603 (t80) REVERT: C 333 GLU cc_start: 0.8059 (pp20) cc_final: 0.7256 (pp20) REVERT: C 336 LYS cc_start: 0.8479 (ptpt) cc_final: 0.7874 (ptpp) REVERT: C 337 TYR cc_start: 0.8679 (m-80) cc_final: 0.7527 (m-80) REVERT: C 355 ASP cc_start: 0.6504 (p0) cc_final: 0.5343 (p0) REVERT: C 357 MET cc_start: 0.4973 (mmm) cc_final: 0.4261 (mmm) REVERT: C 359 SER cc_start: 0.6376 (m) cc_final: 0.5982 (t) REVERT: C 368 ASN cc_start: 0.7975 (p0) cc_final: 0.7659 (p0) REVERT: D 65 LEU cc_start: 0.8396 (mt) cc_final: 0.7850 (tp) REVERT: D 66 LEU cc_start: 0.8662 (mt) cc_final: 0.8297 (mt) REVERT: D 68 ASP cc_start: 0.8982 (m-30) cc_final: 0.8146 (m-30) REVERT: D 75 ASN cc_start: 0.7080 (m110) cc_final: 0.6665 (m110) REVERT: D 93 GLN cc_start: 0.7256 (tm-30) cc_final: 0.7054 (tm-30) REVERT: D 116 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8856 (mmmt) REVERT: D 127 LEU cc_start: 0.9315 (tp) cc_final: 0.8860 (tp) REVERT: D 139 TYR cc_start: 0.6633 (m-80) cc_final: 0.5564 (m-80) REVERT: D 142 ASP cc_start: 0.8025 (m-30) cc_final: 0.7119 (m-30) REVERT: D 143 TYR cc_start: 0.7576 (t80) cc_final: 0.6428 (t80) REVERT: D 146 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7123 (mt-10) REVERT: D 155 TYR cc_start: 0.8777 (m-80) cc_final: 0.8080 (m-80) REVERT: D 169 ASN cc_start: 0.6693 (m-40) cc_final: 0.5966 (m-40) REVERT: D 173 LEU cc_start: 0.7496 (mt) cc_final: 0.7248 (tp) REVERT: D 206 GLN cc_start: 0.8039 (mp10) cc_final: 0.7687 (mp10) REVERT: D 224 GLU cc_start: 0.7435 (pp20) cc_final: 0.7210 (pp20) REVERT: D 227 LYS cc_start: 0.8508 (tttt) cc_final: 0.7124 (tppt) REVERT: D 231 HIS cc_start: 0.7197 (m170) cc_final: 0.6467 (m170) REVERT: D 257 GLN cc_start: 0.8724 (mp10) cc_final: 0.8388 (mp10) REVERT: D 267 MET cc_start: 0.8014 (tpp) cc_final: 0.7064 (tpt) REVERT: D 300 LEU cc_start: 0.6887 (tp) cc_final: 0.6569 (tp) REVERT: D 306 GLU cc_start: 0.8627 (mt-10) cc_final: 0.7972 (mm-30) REVERT: D 307 HIS cc_start: 0.6707 (t70) cc_final: 0.5844 (t-90) REVERT: D 310 LEU cc_start: 0.8989 (mt) cc_final: 0.8732 (mm) REVERT: D 318 ASN cc_start: 0.8752 (p0) cc_final: 0.7377 (p0) REVERT: D 320 THR cc_start: 0.7942 (p) cc_final: 0.7645 (p) REVERT: D 328 LEU cc_start: 0.9462 (mm) cc_final: 0.8446 (mm) REVERT: D 329 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7917 (mp0) REVERT: D 345 GLU cc_start: 0.7994 (tp30) cc_final: 0.7615 (tp30) REVERT: D 347 ARG cc_start: 0.7196 (ptt90) cc_final: 0.6502 (ptt90) REVERT: D 361 PHE cc_start: 0.6481 (m-80) cc_final: 0.6141 (m-80) REVERT: D 372 LYS cc_start: 0.8769 (ptpt) cc_final: 0.7656 (pttm) REVERT: D 375 GLN cc_start: 0.8630 (pt0) cc_final: 0.8188 (pp30) REVERT: D 376 SER cc_start: 0.8180 (t) cc_final: 0.6951 (p) REVERT: D 378 CYS cc_start: 0.8979 (m) cc_final: 0.7784 (p) REVERT: D 380 GLN cc_start: 0.8026 (mt0) cc_final: 0.7605 (mt0) REVERT: D 383 ASN cc_start: 0.9043 (m-40) cc_final: 0.7812 (m110) REVERT: D 384 LEU cc_start: 0.8717 (tp) cc_final: 0.7515 (tt) REVERT: D 387 LYS cc_start: 0.9176 (mttt) cc_final: 0.8400 (mttt) REVERT: E 78 MET cc_start: 0.5355 (mmp) cc_final: 0.5048 (mmp) REVERT: E 82 LEU cc_start: 0.7695 (mt) cc_final: 0.7061 (mm) REVERT: E 93 MET cc_start: 0.3259 (tmm) cc_final: 0.1526 (tmm) REVERT: E 117 MET cc_start: 0.7473 (tmm) cc_final: 0.7184 (tmm) REVERT: E 134 ILE cc_start: 0.8855 (pt) cc_final: 0.8582 (pt) REVERT: E 242 TRP cc_start: 0.5057 (t-100) cc_final: 0.4724 (t-100) REVERT: E 286 MET cc_start: -0.0973 (tpt) cc_final: -0.2022 (tpt) REVERT: E 299 LYS cc_start: 0.6391 (mttt) cc_final: 0.6009 (tttt) REVERT: E 302 LYS cc_start: 0.8454 (mttm) cc_final: 0.7781 (mttt) REVERT: E 324 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7657 (ttmt) REVERT: F 73 ILE cc_start: 0.7302 (pt) cc_final: 0.7024 (mp) REVERT: F 116 PHE cc_start: 0.7373 (m-10) cc_final: 0.7154 (m-10) REVERT: F 181 MET cc_start: -0.5017 (ttm) cc_final: -0.5287 (ttm) REVERT: F 254 HIS cc_start: 0.8449 (m-70) cc_final: 0.8202 (m-70) REVERT: F 275 PHE cc_start: 0.7073 (t80) cc_final: 0.6779 (t80) REVERT: F 284 ASN cc_start: 0.7716 (t0) cc_final: 0.7329 (t0) REVERT: F 289 MET cc_start: 0.8311 (ttt) cc_final: 0.7701 (mmt) REVERT: F 309 PHE cc_start: 0.7695 (t80) cc_final: 0.7240 (t80) REVERT: G 31 ILE cc_start: 0.8777 (pt) cc_final: 0.8536 (pt) REVERT: G 49 LEU cc_start: 0.9620 (mm) cc_final: 0.9032 (pp) REVERT: G 52 VAL cc_start: 0.6797 (p) cc_final: 0.6365 (p) REVERT: G 66 LEU cc_start: 0.8101 (tp) cc_final: 0.7793 (tp) REVERT: G 68 ASN cc_start: 0.8884 (m110) cc_final: 0.8654 (m110) REVERT: G 72 TYR cc_start: 0.5893 (m-10) cc_final: 0.5164 (m-10) REVERT: G 96 LEU cc_start: 0.8511 (tp) cc_final: 0.8296 (tt) REVERT: G 112 PRO cc_start: 0.7984 (Cg_exo) cc_final: 0.7644 (Cg_endo) REVERT: G 121 GLU cc_start: 0.7465 (tm-30) cc_final: 0.6740 (tm-30) REVERT: G 130 ASP cc_start: 0.8758 (m-30) cc_final: 0.8133 (m-30) REVERT: G 148 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7920 (ttm-80) REVERT: G 150 GLN cc_start: 0.7470 (mt0) cc_final: 0.7083 (mp10) REVERT: G 172 LYS cc_start: 0.9019 (tttt) cc_final: 0.8174 (tttt) REVERT: G 199 LYS cc_start: 0.7137 (tttt) cc_final: 0.6804 (tttt) REVERT: G 200 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6964 (mt-10) REVERT: H 22 ASN cc_start: 0.7713 (m110) cc_final: 0.7345 (m110) REVERT: H 24 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 51 ASN cc_start: 0.8395 (m-40) cc_final: 0.7774 (m-40) REVERT: H 90 TYR cc_start: 0.7546 (m-80) cc_final: 0.7010 (m-80) REVERT: H 96 HIS cc_start: 0.6646 (t-90) cc_final: 0.5431 (t70) REVERT: H 98 TRP cc_start: 0.7692 (m100) cc_final: 0.7163 (m100) REVERT: H 110 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.8076 (ttp-110) REVERT: H 118 PHE cc_start: 0.7018 (t80) cc_final: 0.6774 (t80) REVERT: H 120 LEU cc_start: 0.8823 (tt) cc_final: 0.8600 (tt) REVERT: H 133 PHE cc_start: 0.7657 (t80) cc_final: 0.6717 (t80) REVERT: H 145 VAL cc_start: 0.8939 (t) cc_final: 0.8700 (t) REVERT: H 163 LEU cc_start: 0.8387 (mp) cc_final: 0.7897 (mp) REVERT: I 122 GLU cc_start: 0.8362 (pt0) cc_final: 0.7748 (pp20) REVERT: I 149 LYS cc_start: 0.7950 (tttt) cc_final: 0.7423 (tptm) REVERT: I 268 MET cc_start: 0.6726 (tpt) cc_final: 0.6004 (tpt) REVERT: I 269 MET cc_start: 0.7743 (mpp) cc_final: 0.7185 (mpp) REVERT: I 297 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7921 (tptp) REVERT: I 317 ASP cc_start: 0.6312 (p0) cc_final: 0.5688 (p0) REVERT: I 319 TYR cc_start: 0.6230 (m-80) cc_final: 0.5950 (m-80) REVERT: I 430 CYS cc_start: 0.5789 (t) cc_final: 0.5333 (t) REVERT: I 454 MET cc_start: 0.3085 (tpt) cc_final: 0.2725 (tpt) REVERT: I 511 MET cc_start: 0.1365 (tpt) cc_final: 0.1095 (tpt) REVERT: L 28 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7946 (mmmt) REVERT: L 39 ASN cc_start: 0.7966 (m-40) cc_final: 0.7694 (m-40) REVERT: L 57 LEU cc_start: 0.7823 (mt) cc_final: 0.7468 (mt) REVERT: L 82 THR cc_start: 0.7626 (t) cc_final: 0.7217 (p) REVERT: L 118 MET cc_start: 0.6858 (tpt) cc_final: 0.6580 (tpt) REVERT: L 122 ILE cc_start: 0.8358 (pt) cc_final: 0.8008 (pt) REVERT: L 127 ASP cc_start: 0.6750 (t0) cc_final: 0.6476 (t0) REVERT: L 157 ILE cc_start: 0.7386 (mt) cc_final: 0.7087 (mm) REVERT: L 158 ARG cc_start: 0.7985 (ppt170) cc_final: 0.7342 (ttp80) REVERT: L 163 GLN cc_start: 0.7722 (pt0) cc_final: 0.7446 (pp30) REVERT: L 167 ASP cc_start: 0.8877 (t0) cc_final: 0.8366 (t0) REVERT: L 171 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7813 (ptt180) REVERT: L 184 ARG cc_start: 0.8266 (tmt170) cc_final: 0.7998 (tpt90) REVERT: L 185 ASN cc_start: 0.8119 (m-40) cc_final: 0.7613 (m-40) REVERT: L 205 PHE cc_start: 0.6524 (t80) cc_final: 0.6081 (t80) REVERT: L 219 MET cc_start: 0.8424 (mmt) cc_final: 0.8011 (mmp) REVERT: L 234 ILE cc_start: 0.7972 (pt) cc_final: 0.7728 (pt) REVERT: L 242 ASN cc_start: 0.8369 (t0) cc_final: 0.7993 (t0) REVERT: L 247 ARG cc_start: 0.7507 (ttm170) cc_final: 0.7294 (ttm170) REVERT: L 249 MET cc_start: 0.7182 (tpp) cc_final: 0.6594 (tpp) REVERT: L 250 HIS cc_start: 0.6725 (t-90) cc_final: 0.6352 (t70) REVERT: L 279 MET cc_start: 0.6624 (ttp) cc_final: 0.6248 (ttp) REVERT: L 288 LEU cc_start: 0.8179 (tp) cc_final: 0.7917 (tp) REVERT: L 301 LYS cc_start: 0.8393 (pttt) cc_final: 0.7863 (ptpt) REVERT: L 302 LEU cc_start: 0.8969 (mt) cc_final: 0.8082 (mt) REVERT: L 305 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7365 (mpp80) REVERT: L 317 MET cc_start: 0.8170 (mtm) cc_final: 0.7755 (mmm) REVERT: L 358 GLU cc_start: 0.7316 (pp20) cc_final: 0.6661 (pp20) REVERT: L 364 ARG cc_start: 0.8321 (tmt170) cc_final: 0.7942 (tpt90) REVERT: L 390 LEU cc_start: 0.8180 (mt) cc_final: 0.7873 (mt) REVERT: L 393 ASP cc_start: 0.7130 (t0) cc_final: 0.6303 (t0) REVERT: L 395 LYS cc_start: 0.9173 (mmpt) cc_final: 0.8284 (mmmm) REVERT: L 396 LEU cc_start: 0.8517 (mt) cc_final: 0.8107 (mm) REVERT: L 397 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7420 (mmmt) REVERT: L 414 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8533 (mmtm) REVERT: L 433 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7031 (mmtt) REVERT: L 435 HIS cc_start: 0.7100 (m90) cc_final: 0.6879 (m-70) REVERT: L 448 ASP cc_start: 0.6847 (t70) cc_final: 0.6229 (t70) REVERT: L 451 GLU cc_start: 0.8710 (pt0) cc_final: 0.7988 (pp20) REVERT: L 457 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8529 (mmtt) REVERT: L 473 MET cc_start: 0.7845 (mtm) cc_final: 0.7006 (mtt) REVERT: L 475 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7524 (tpp80) REVERT: L 477 MET cc_start: 0.8024 (tmm) cc_final: 0.7495 (tmm) REVERT: L 522 CYS cc_start: 0.7655 (t) cc_final: 0.6935 (m) REVERT: L 533 GLU cc_start: 0.7643 (tp30) cc_final: 0.6971 (tp30) REVERT: L 535 PHE cc_start: 0.7902 (t80) cc_final: 0.7349 (t80) REVERT: L 554 MET cc_start: 0.7966 (mmp) cc_final: 0.7305 (tpt) REVERT: L 599 MET cc_start: 0.8999 (mmp) cc_final: 0.8743 (mmm) REVERT: L 603 MET cc_start: 0.7886 (ptm) cc_final: 0.7459 (ptm) REVERT: L 625 ARG cc_start: 0.8197 (mmp-170) cc_final: 0.7793 (mmp-170) REVERT: L 657 HIS cc_start: 0.8089 (p-80) cc_final: 0.7699 (p90) REVERT: L 670 HIS cc_start: 0.8483 (m-70) cc_final: 0.7590 (m-70) REVERT: L 673 LYS cc_start: 0.8192 (tptt) cc_final: 0.7683 (tptt) REVERT: M 46 LYS cc_start: 0.7523 (pptt) cc_final: 0.7002 (pptt) REVERT: M 110 PHE cc_start: 0.7261 (t80) cc_final: 0.6904 (t80) REVERT: M 149 LYS cc_start: 0.8606 (tttm) cc_final: 0.7899 (tptm) REVERT: M 155 MET cc_start: 0.3643 (ppp) cc_final: 0.2928 (ppp) REVERT: M 454 MET cc_start: 0.6905 (tpt) cc_final: 0.6127 (mmm) REVERT: R 25 LYS cc_start: 0.6185 (mptt) cc_final: 0.5982 (mptt) REVERT: R 48 HIS cc_start: 0.7500 (t-90) cc_final: 0.7218 (t-90) REVERT: R 50 MET cc_start: 0.6477 (ptt) cc_final: 0.6111 (ptt) REVERT: R 91 ARG cc_start: 0.6861 (mtt90) cc_final: 0.6385 (mtt90) outliers start: 1 outliers final: 0 residues processed: 1088 average time/residue: 0.5356 time to fit residues: 913.7911 Evaluate side-chains 954 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 251 optimal weight: 0.1980 chunk 322 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 372 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 203 optimal weight: 50.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 501 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS D 228 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 552 HIS L 553 HIS ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 38016 Z= 0.230 Angle : 0.685 10.490 51366 Z= 0.359 Chirality : 0.045 0.767 5749 Planarity : 0.005 0.129 6583 Dihedral : 4.706 31.719 5047 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.11 % Favored : 92.50 % Rotamer: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.34 (0.12), residues: 4597 helix: 0.77 (0.10), residues: 2672 sheet: -0.53 (0.25), residues: 412 loop : -1.91 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 82 HIS 0.009 0.001 HIS I 306 PHE 0.037 0.002 PHE G 15 TYR 0.033 0.002 TYR D 85 ARG 0.007 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1065 time to evaluate : 4.047 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7050 (t0) cc_final: 0.6643 (t0) REVERT: A 95 MET cc_start: 0.4999 (pmm) cc_final: 0.4567 (ptm) REVERT: A 117 MET cc_start: 0.7994 (mtt) cc_final: 0.6999 (mtt) REVERT: A 130 MET cc_start: 0.6891 (mmp) cc_final: 0.6344 (mmp) REVERT: A 173 LYS cc_start: 0.7831 (mmpt) cc_final: 0.7586 (mmmm) REVERT: A 204 LEU cc_start: 0.7519 (mt) cc_final: 0.6684 (mt) REVERT: A 218 LEU cc_start: 0.8035 (tp) cc_final: 0.7154 (tp) REVERT: A 234 VAL cc_start: 0.7911 (t) cc_final: 0.7441 (t) REVERT: A 235 ILE cc_start: 0.8556 (mt) cc_final: 0.8018 (mt) REVERT: A 240 ASN cc_start: 0.6495 (m-40) cc_final: 0.6153 (m-40) REVERT: A 250 ASN cc_start: 0.5986 (t0) cc_final: 0.4792 (t0) REVERT: A 253 HIS cc_start: 0.4205 (m90) cc_final: 0.3681 (m90) REVERT: A 332 CYS cc_start: 0.8080 (m) cc_final: 0.6952 (p) REVERT: A 342 LEU cc_start: 0.8225 (mt) cc_final: 0.7966 (mt) REVERT: A 345 ASN cc_start: 0.7292 (p0) cc_final: 0.6535 (p0) REVERT: A 363 ARG cc_start: 0.6976 (ptt-90) cc_final: 0.5940 (ptt-90) REVERT: A 365 ILE cc_start: 0.7484 (mt) cc_final: 0.7086 (mm) REVERT: A 379 LYS cc_start: 0.8021 (pttp) cc_final: 0.7406 (mttm) REVERT: A 387 ASN cc_start: 0.5667 (t0) cc_final: 0.5270 (t0) REVERT: A 389 LEU cc_start: 0.5647 (mt) cc_final: 0.5404 (mt) REVERT: A 392 MET cc_start: 0.4378 (ptt) cc_final: 0.3868 (ptt) REVERT: A 417 TYR cc_start: 0.6953 (m-10) cc_final: 0.6584 (m-10) REVERT: A 423 HIS cc_start: 0.6679 (m170) cc_final: 0.6279 (m-70) REVERT: A 438 ASP cc_start: 0.6246 (m-30) cc_final: 0.5459 (m-30) REVERT: A 472 PHE cc_start: 0.6691 (m-10) cc_final: 0.6452 (m-80) REVERT: A 478 MET cc_start: 0.7393 (mmp) cc_final: 0.6832 (mmm) REVERT: A 489 MET cc_start: 0.6489 (ppp) cc_final: 0.6145 (ppp) REVERT: A 496 LEU cc_start: 0.8185 (mt) cc_final: 0.7936 (mm) REVERT: B 77 LYS cc_start: 0.8447 (mttt) cc_final: 0.7473 (mmmt) REVERT: B 93 LYS cc_start: 0.9424 (mttt) cc_final: 0.8481 (mmtt) REVERT: B 94 GLN cc_start: 0.8282 (tt0) cc_final: 0.7907 (mp10) REVERT: B 96 LEU cc_start: 0.7773 (mt) cc_final: 0.7536 (mt) REVERT: B 109 GLU cc_start: 0.7953 (pt0) cc_final: 0.6323 (pp20) REVERT: B 110 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8324 (mtmt) REVERT: B 125 MET cc_start: 0.6075 (mmp) cc_final: 0.5076 (mmp) REVERT: B 150 LYS cc_start: 0.8835 (mttp) cc_final: 0.8392 (mmtt) REVERT: B 168 LEU cc_start: 0.8068 (tp) cc_final: 0.7663 (tp) REVERT: B 170 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8631 (ptpt) REVERT: B 171 ILE cc_start: 0.8799 (mt) cc_final: 0.8217 (tp) REVERT: B 173 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7876 (mmm160) REVERT: B 177 GLN cc_start: 0.8769 (pt0) cc_final: 0.7793 (pp30) REVERT: B 213 LYS cc_start: 0.7804 (mmtm) cc_final: 0.7116 (mmmm) REVERT: B 218 TYR cc_start: 0.7889 (t80) cc_final: 0.7320 (t80) REVERT: B 219 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6859 (mm-30) REVERT: B 247 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8490 (ttm110) REVERT: B 258 PHE cc_start: 0.7961 (m-80) cc_final: 0.7349 (m-80) REVERT: B 259 PHE cc_start: 0.7779 (t80) cc_final: 0.7553 (t80) REVERT: B 260 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7683 (mm-30) REVERT: B 262 PHE cc_start: 0.7073 (t80) cc_final: 0.6318 (t80) REVERT: B 265 TYR cc_start: 0.7684 (m-10) cc_final: 0.7149 (m-80) REVERT: B 273 ARG cc_start: 0.8486 (ptt90) cc_final: 0.7709 (ptt-90) REVERT: B 284 ASN cc_start: 0.7261 (t0) cc_final: 0.6666 (t0) REVERT: B 297 GLN cc_start: 0.7119 (tp40) cc_final: 0.6743 (tp40) REVERT: B 304 ASN cc_start: 0.8486 (m-40) cc_final: 0.8142 (m-40) REVERT: B 313 ASN cc_start: 0.8770 (m110) cc_final: 0.8416 (m-40) REVERT: B 315 VAL cc_start: 0.8993 (t) cc_final: 0.8603 (t) REVERT: B 318 TYR cc_start: 0.7218 (m-80) cc_final: 0.6513 (m-80) REVERT: B 328 LYS cc_start: 0.9140 (pttp) cc_final: 0.8387 (ptpp) REVERT: B 330 LEU cc_start: 0.9388 (mt) cc_final: 0.8832 (mt) REVERT: B 331 LYS cc_start: 0.8336 (mttt) cc_final: 0.7133 (mmtt) REVERT: B 346 HIS cc_start: 0.8309 (m-70) cc_final: 0.7794 (m-70) REVERT: B 348 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7736 (mp0) REVERT: B 349 GLU cc_start: 0.8477 (tt0) cc_final: 0.7551 (mp0) REVERT: B 352 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: B 353 ASN cc_start: 0.8462 (m110) cc_final: 0.8109 (m110) REVERT: B 355 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8372 (mtt90) REVERT: B 356 THR cc_start: 0.8946 (m) cc_final: 0.8584 (m) REVERT: B 357 GLN cc_start: 0.8816 (mt0) cc_final: 0.8189 (mm110) REVERT: B 359 LEU cc_start: 0.8841 (tp) cc_final: 0.8481 (pp) REVERT: B 361 LYS cc_start: 0.8933 (ptmt) cc_final: 0.8362 (pttp) REVERT: B 364 LYS cc_start: 0.9051 (pttm) cc_final: 0.8697 (ptpp) REVERT: B 370 HIS cc_start: 0.7454 (m90) cc_final: 0.7205 (m90) REVERT: B 384 ASP cc_start: 0.8947 (m-30) cc_final: 0.8393 (m-30) REVERT: B 388 LEU cc_start: 0.8832 (mp) cc_final: 0.8516 (mm) REVERT: B 390 VAL cc_start: 0.9220 (t) cc_final: 0.9001 (p) REVERT: B 395 ASP cc_start: 0.7411 (m-30) cc_final: 0.6886 (m-30) REVERT: C 25 CYS cc_start: 0.8197 (t) cc_final: 0.7727 (t) REVERT: C 42 LEU cc_start: 0.6475 (pt) cc_final: 0.6029 (pp) REVERT: C 92 HIS cc_start: 0.6354 (m90) cc_final: 0.6138 (m-70) REVERT: C 104 CYS cc_start: 0.8347 (m) cc_final: 0.6374 (t) REVERT: C 162 LEU cc_start: 0.9623 (mt) cc_final: 0.9290 (mt) REVERT: C 166 MET cc_start: 0.6901 (mtp) cc_final: 0.6402 (mtm) REVERT: C 190 MET cc_start: 0.7695 (mtp) cc_final: 0.7171 (mtp) REVERT: C 191 ILE cc_start: 0.7258 (mt) cc_final: 0.6867 (mt) REVERT: C 202 LEU cc_start: 0.8288 (tp) cc_final: 0.6946 (tp) REVERT: C 224 TYR cc_start: 0.6950 (t80) cc_final: 0.6735 (t80) REVERT: C 336 LYS cc_start: 0.8494 (ptpt) cc_final: 0.7899 (ptpp) REVERT: C 337 TYR cc_start: 0.8716 (m-80) cc_final: 0.7509 (m-80) REVERT: C 339 LEU cc_start: 0.8759 (mt) cc_final: 0.8458 (mt) REVERT: C 344 ASP cc_start: 0.7763 (m-30) cc_final: 0.7453 (m-30) REVERT: C 355 ASP cc_start: 0.6952 (p0) cc_final: 0.6511 (p0) REVERT: C 359 SER cc_start: 0.6212 (m) cc_final: 0.5980 (t) REVERT: C 368 ASN cc_start: 0.7923 (p0) cc_final: 0.7707 (p0) REVERT: D 66 LEU cc_start: 0.8656 (mt) cc_final: 0.8311 (mt) REVERT: D 68 ASP cc_start: 0.9033 (m-30) cc_final: 0.8183 (m-30) REVERT: D 116 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8918 (mmmt) REVERT: D 127 LEU cc_start: 0.9366 (tp) cc_final: 0.8985 (tp) REVERT: D 139 TYR cc_start: 0.6558 (m-80) cc_final: 0.5719 (m-80) REVERT: D 143 TYR cc_start: 0.7695 (t80) cc_final: 0.6983 (t80) REVERT: D 148 TYR cc_start: 0.6611 (m-10) cc_final: 0.5956 (m-10) REVERT: D 155 TYR cc_start: 0.8819 (m-80) cc_final: 0.8116 (m-80) REVERT: D 169 ASN cc_start: 0.6694 (m-40) cc_final: 0.6212 (m-40) REVERT: D 173 LEU cc_start: 0.7493 (mt) cc_final: 0.7231 (tp) REVERT: D 227 LYS cc_start: 0.8509 (tttt) cc_final: 0.7056 (tppt) REVERT: D 231 HIS cc_start: 0.7213 (m170) cc_final: 0.6551 (m170) REVERT: D 267 MET cc_start: 0.8083 (tpp) cc_final: 0.7562 (tpt) REVERT: D 300 LEU cc_start: 0.7129 (tp) cc_final: 0.6670 (tp) REVERT: D 306 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8058 (mm-30) REVERT: D 307 HIS cc_start: 0.6674 (t70) cc_final: 0.6359 (t70) REVERT: D 310 LEU cc_start: 0.9038 (mt) cc_final: 0.8791 (mm) REVERT: D 318 ASN cc_start: 0.8834 (p0) cc_final: 0.7389 (p0) REVERT: D 328 LEU cc_start: 0.9496 (mm) cc_final: 0.8508 (mm) REVERT: D 329 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7949 (mp0) REVERT: D 345 GLU cc_start: 0.8014 (tp30) cc_final: 0.7548 (tp30) REVERT: D 347 ARG cc_start: 0.7198 (ptt90) cc_final: 0.6444 (ptt90) REVERT: D 351 PHE cc_start: 0.8012 (p90) cc_final: 0.7749 (p90) REVERT: D 361 PHE cc_start: 0.6455 (m-80) cc_final: 0.6169 (m-80) REVERT: D 372 LYS cc_start: 0.8790 (ptpt) cc_final: 0.8263 (pttm) REVERT: D 376 SER cc_start: 0.8261 (t) cc_final: 0.7365 (p) REVERT: D 378 CYS cc_start: 0.9028 (m) cc_final: 0.7912 (p) REVERT: D 380 GLN cc_start: 0.8081 (mt0) cc_final: 0.7803 (mt0) REVERT: D 384 LEU cc_start: 0.8810 (tp) cc_final: 0.7688 (tt) REVERT: D 387 LYS cc_start: 0.9224 (mttt) cc_final: 0.8324 (mtmm) REVERT: E 78 MET cc_start: 0.4619 (mmp) cc_final: 0.4214 (mmp) REVERT: E 93 MET cc_start: 0.3354 (tmm) cc_final: 0.2365 (tmm) REVERT: E 117 MET cc_start: 0.7537 (tmm) cc_final: 0.7237 (tmm) REVERT: E 134 ILE cc_start: 0.8838 (pt) cc_final: 0.8605 (pt) REVERT: E 242 TRP cc_start: 0.5216 (t-100) cc_final: 0.4736 (t-100) REVERT: E 286 MET cc_start: -0.0991 (tpt) cc_final: -0.2046 (tpt) REVERT: E 299 LYS cc_start: 0.6405 (mttt) cc_final: 0.6062 (tttt) REVERT: E 302 LYS cc_start: 0.8339 (mttm) cc_final: 0.7770 (mttt) REVERT: E 324 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7777 (ttmt) REVERT: F 73 ILE cc_start: 0.7277 (pt) cc_final: 0.6909 (mp) REVERT: F 181 MET cc_start: -0.4960 (ttm) cc_final: -0.5242 (ttm) REVERT: F 252 PHE cc_start: 0.7891 (t80) cc_final: 0.7660 (t80) REVERT: F 254 HIS cc_start: 0.8445 (m-70) cc_final: 0.8156 (m-70) REVERT: F 275 PHE cc_start: 0.7166 (t80) cc_final: 0.6844 (t80) REVERT: F 284 ASN cc_start: 0.7718 (t0) cc_final: 0.7403 (t0) REVERT: F 289 MET cc_start: 0.8276 (ttt) cc_final: 0.7730 (mmm) REVERT: F 309 PHE cc_start: 0.7733 (t80) cc_final: 0.7275 (t80) REVERT: G 31 ILE cc_start: 0.8678 (pt) cc_final: 0.8454 (pt) REVERT: G 68 ASN cc_start: 0.8962 (m110) cc_final: 0.8606 (m110) REVERT: G 72 TYR cc_start: 0.6130 (m-10) cc_final: 0.5134 (m-10) REVERT: G 85 LEU cc_start: 0.8688 (pt) cc_final: 0.8339 (pt) REVERT: G 96 LEU cc_start: 0.8633 (tp) cc_final: 0.8218 (tt) REVERT: G 112 PRO cc_start: 0.8027 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: G 130 ASP cc_start: 0.8716 (m-30) cc_final: 0.8087 (m-30) REVERT: G 148 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.7927 (ttm-80) REVERT: G 150 GLN cc_start: 0.7524 (mt0) cc_final: 0.7194 (mp10) REVERT: G 160 ARG cc_start: 0.8422 (ttt180) cc_final: 0.7925 (mtt-85) REVERT: G 172 LYS cc_start: 0.9057 (tttt) cc_final: 0.8222 (tttt) REVERT: G 199 LYS cc_start: 0.7278 (tttt) cc_final: 0.6924 (tttt) REVERT: G 200 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6982 (mt-10) REVERT: H 22 ASN cc_start: 0.7790 (m110) cc_final: 0.7342 (m110) REVERT: H 24 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8352 (tm-30) REVERT: H 90 TYR cc_start: 0.7630 (m-80) cc_final: 0.7025 (m-80) REVERT: H 96 HIS cc_start: 0.6786 (t-90) cc_final: 0.5596 (t70) REVERT: H 98 TRP cc_start: 0.7738 (m100) cc_final: 0.7081 (m100) REVERT: H 110 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.8084 (ttp-110) REVERT: H 111 ASP cc_start: 0.8446 (t70) cc_final: 0.8155 (t0) REVERT: H 115 ARG cc_start: 0.6670 (ptp-110) cc_final: 0.6374 (ptp-170) REVERT: H 118 PHE cc_start: 0.6956 (t80) cc_final: 0.6746 (t80) REVERT: H 133 PHE cc_start: 0.7629 (t80) cc_final: 0.6708 (t80) REVERT: H 137 VAL cc_start: 0.8322 (p) cc_final: 0.8111 (p) REVERT: H 163 LEU cc_start: 0.8384 (mp) cc_final: 0.7924 (mp) REVERT: I 122 GLU cc_start: 0.8381 (pt0) cc_final: 0.7705 (pp20) REVERT: I 149 LYS cc_start: 0.7981 (tttt) cc_final: 0.7448 (tptm) REVERT: I 268 MET cc_start: 0.6893 (tpt) cc_final: 0.5842 (tpt) REVERT: I 269 MET cc_start: 0.8003 (mpp) cc_final: 0.7312 (mpp) REVERT: I 297 LYS cc_start: 0.8340 (tmtt) cc_final: 0.8027 (tptp) REVERT: I 430 CYS cc_start: 0.5882 (t) cc_final: 0.5272 (t) REVERT: I 454 MET cc_start: 0.3246 (tpt) cc_final: 0.2744 (tpt) REVERT: I 511 MET cc_start: 0.1508 (tpt) cc_final: 0.1148 (tpt) REVERT: L 28 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7701 (mmmt) REVERT: L 39 ASN cc_start: 0.7921 (m-40) cc_final: 0.7688 (m-40) REVERT: L 57 LEU cc_start: 0.7845 (mt) cc_final: 0.7616 (mt) REVERT: L 82 THR cc_start: 0.7897 (t) cc_final: 0.7649 (p) REVERT: L 122 ILE cc_start: 0.8249 (pt) cc_final: 0.7941 (pt) REVERT: L 127 ASP cc_start: 0.6735 (t0) cc_final: 0.6384 (t0) REVERT: L 157 ILE cc_start: 0.7442 (mt) cc_final: 0.7149 (mm) REVERT: L 158 ARG cc_start: 0.8020 (ppt170) cc_final: 0.7327 (ttp80) REVERT: L 167 ASP cc_start: 0.8872 (t0) cc_final: 0.8354 (t0) REVERT: L 171 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7837 (ptt180) REVERT: L 185 ASN cc_start: 0.8169 (m-40) cc_final: 0.7588 (m-40) REVERT: L 189 MET cc_start: 0.8268 (ptp) cc_final: 0.7417 (ptp) REVERT: L 211 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8116 (mm-30) REVERT: L 234 ILE cc_start: 0.8039 (pt) cc_final: 0.7792 (pt) REVERT: L 242 ASN cc_start: 0.8388 (t0) cc_final: 0.8015 (t0) REVERT: L 249 MET cc_start: 0.7061 (tpp) cc_final: 0.6445 (tpp) REVERT: L 250 HIS cc_start: 0.6846 (t-90) cc_final: 0.6537 (t70) REVERT: L 279 MET cc_start: 0.6736 (ttp) cc_final: 0.6316 (ttp) REVERT: L 301 LYS cc_start: 0.8448 (pttt) cc_final: 0.7907 (ptpt) REVERT: L 302 LEU cc_start: 0.9157 (mt) cc_final: 0.8148 (mt) REVERT: L 305 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7500 (mpp80) REVERT: L 358 GLU cc_start: 0.7360 (pp20) cc_final: 0.6753 (pp20) REVERT: L 364 ARG cc_start: 0.8387 (tmt170) cc_final: 0.7454 (ttp80) REVERT: L 366 PHE cc_start: 0.7966 (m-10) cc_final: 0.7536 (m-10) REVERT: L 390 LEU cc_start: 0.8656 (mt) cc_final: 0.8367 (mt) REVERT: L 393 ASP cc_start: 0.7554 (t0) cc_final: 0.6408 (t0) REVERT: L 395 LYS cc_start: 0.8990 (mmpt) cc_final: 0.8549 (mmmm) REVERT: L 397 LYS cc_start: 0.8294 (mmpt) cc_final: 0.7623 (mmmt) REVERT: L 414 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8793 (mmtm) REVERT: L 433 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7083 (mmtt) REVERT: L 450 SER cc_start: 0.8611 (p) cc_final: 0.8405 (p) REVERT: L 451 GLU cc_start: 0.8832 (pt0) cc_final: 0.7904 (pp20) REVERT: L 457 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8571 (mmtt) REVERT: L 473 MET cc_start: 0.7886 (mtm) cc_final: 0.7140 (mtm) REVERT: L 474 PHE cc_start: 0.7602 (m-80) cc_final: 0.7380 (m-80) REVERT: L 475 ARG cc_start: 0.8218 (ttt180) cc_final: 0.7429 (tpp80) REVERT: L 477 MET cc_start: 0.8150 (tmm) cc_final: 0.7646 (tmm) REVERT: L 479 ILE cc_start: 0.8772 (mm) cc_final: 0.8429 (mt) REVERT: L 488 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7586 (mtm110) REVERT: L 522 CYS cc_start: 0.7854 (t) cc_final: 0.6880 (m) REVERT: L 533 GLU cc_start: 0.7777 (tp30) cc_final: 0.7122 (tp30) REVERT: L 534 ILE cc_start: 0.7820 (tp) cc_final: 0.7510 (pt) REVERT: L 535 PHE cc_start: 0.6838 (t80) cc_final: 0.6539 (t80) REVERT: L 552 HIS cc_start: 0.5263 (m-70) cc_final: 0.5051 (m90) REVERT: L 554 MET cc_start: 0.7260 (mmp) cc_final: 0.6885 (tpp) REVERT: L 603 MET cc_start: 0.7814 (ptm) cc_final: 0.7414 (ptm) REVERT: L 625 ARG cc_start: 0.8614 (mmp-170) cc_final: 0.8122 (mmp-170) REVERT: L 657 HIS cc_start: 0.8220 (p-80) cc_final: 0.7826 (p90) REVERT: L 670 HIS cc_start: 0.8399 (m-70) cc_final: 0.7775 (m-70) REVERT: L 673 LYS cc_start: 0.8389 (tptt) cc_final: 0.7848 (tptt) REVERT: M 46 LYS cc_start: 0.6504 (pptt) cc_final: 0.6219 (pptt) REVERT: M 47 MET cc_start: 0.4841 (mtp) cc_final: 0.3816 (mtp) REVERT: M 149 LYS cc_start: 0.8688 (tttm) cc_final: 0.7965 (tptm) REVERT: M 155 MET cc_start: 0.3571 (ppp) cc_final: 0.3024 (ppp) REVERT: M 428 HIS cc_start: 0.8630 (t70) cc_final: 0.8389 (t70) REVERT: R 24 VAL cc_start: 0.7808 (p) cc_final: 0.7536 (m) REVERT: R 25 LYS cc_start: 0.6100 (mptt) cc_final: 0.5710 (mptt) REVERT: R 48 HIS cc_start: 0.7664 (t-90) cc_final: 0.7441 (t70) REVERT: R 50 MET cc_start: 0.6728 (ptt) cc_final: 0.6206 (ptt) REVERT: R 91 ARG cc_start: 0.6940 (mtt90) cc_final: 0.6417 (mtt90) outliers start: 1 outliers final: 0 residues processed: 1066 average time/residue: 0.5560 time to fit residues: 931.6079 Evaluate side-chains 962 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 962 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 132 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 300 optimal weight: 0.5980 chunk 217 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 412 GLN A 501 HIS B 220 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS C 374 HIS D 186 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS F 253 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS I 316 ASN I 358 ASN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 HIS ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5476 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 38016 Z= 0.197 Angle : 0.693 10.635 51366 Z= 0.358 Chirality : 0.044 0.255 5749 Planarity : 0.005 0.122 6583 Dihedral : 4.665 24.907 5047 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4597 helix: 0.83 (0.10), residues: 2679 sheet: -0.43 (0.24), residues: 417 loop : -1.95 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 27 HIS 0.011 0.001 HIS A 201 PHE 0.039 0.002 PHE G 15 TYR 0.025 0.002 TYR B 98 ARG 0.013 0.000 ARG M 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1065 time to evaluate : 4.356 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: 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 83 ASP cc_start: 0.6920 (t0) cc_final: 0.6522 (t0) REVERT: A 95 MET cc_start: 0.5920 (pmm) cc_final: 0.4523 (ptm) REVERT: A 102 PHE cc_start: 0.5611 (t80) cc_final: 0.5349 (t80) REVERT: A 117 MET cc_start: 0.7957 (mtt) cc_final: 0.6943 (mtt) REVERT: A 173 LYS cc_start: 0.7713 (mmpt) cc_final: 0.7438 (mmmt) REVERT: A 218 LEU cc_start: 0.7950 (tp) cc_final: 0.7140 (tp) REVERT: A 234 VAL cc_start: 0.7822 (t) cc_final: 0.7396 (t) REVERT: A 235 ILE cc_start: 0.8539 (mt) cc_final: 0.7978 (mt) REVERT: A 237 MET cc_start: 0.7089 (ptt) cc_final: 0.6871 (ptt) REVERT: A 240 ASN cc_start: 0.6343 (m-40) cc_final: 0.6029 (m-40) REVERT: A 250 ASN cc_start: 0.5654 (t0) cc_final: 0.4539 (t0) REVERT: A 253 HIS cc_start: 0.4137 (m90) cc_final: 0.3738 (m90) REVERT: A 301 GLN cc_start: 0.6387 (pm20) cc_final: 0.6087 (pm20) REVERT: A 332 CYS cc_start: 0.7622 (m) cc_final: 0.6582 (p) REVERT: A 342 LEU cc_start: 0.8196 (mt) cc_final: 0.7940 (mt) REVERT: A 344 ARG cc_start: 0.6539 (pmt-80) cc_final: 0.5824 (pmt-80) REVERT: A 363 ARG cc_start: 0.7026 (ptt-90) cc_final: 0.6522 (ptt-90) REVERT: A 380 MET cc_start: 0.6943 (mmp) cc_final: 0.5824 (mmm) REVERT: A 387 ASN cc_start: 0.5195 (t0) cc_final: 0.4722 (t0) REVERT: A 392 MET cc_start: 0.4023 (ptt) cc_final: 0.3009 (ptt) REVERT: A 414 PHE cc_start: 0.7028 (t80) cc_final: 0.6809 (t80) REVERT: A 421 ASP cc_start: 0.6520 (t0) cc_final: 0.6138 (t0) REVERT: A 423 HIS cc_start: 0.5217 (m170) cc_final: 0.4960 (m-70) REVERT: A 424 ARG cc_start: 0.7599 (ptt90) cc_final: 0.6941 (ptt-90) REVERT: A 425 MET cc_start: 0.6993 (tmm) cc_final: 0.6676 (tmm) REVERT: A 436 LEU cc_start: 0.7040 (pp) cc_final: 0.6809 (pp) REVERT: A 472 PHE cc_start: 0.6610 (m-10) cc_final: 0.6164 (m-80) REVERT: A 478 MET cc_start: 0.7351 (mmp) cc_final: 0.6838 (mmm) REVERT: A 489 MET cc_start: 0.6365 (ppp) cc_final: 0.6119 (ppp) REVERT: A 496 LEU cc_start: 0.8174 (mt) cc_final: 0.7877 (mm) REVERT: B 77 LYS cc_start: 0.8460 (mttt) cc_final: 0.7699 (mttp) REVERT: B 90 ASN cc_start: 0.7978 (m110) cc_final: 0.7545 (m110) REVERT: B 93 LYS cc_start: 0.9370 (mttt) cc_final: 0.8821 (pttm) REVERT: B 96 LEU cc_start: 0.7656 (mt) cc_final: 0.7298 (mt) REVERT: B 109 GLU cc_start: 0.7609 (pt0) cc_final: 0.6189 (pp20) REVERT: B 125 MET cc_start: 0.5884 (mmp) cc_final: 0.5200 (mmp) REVERT: B 168 LEU cc_start: 0.7991 (tp) cc_final: 0.7472 (tp) REVERT: B 171 ILE cc_start: 0.8840 (mt) cc_final: 0.8249 (tp) REVERT: B 177 GLN cc_start: 0.8712 (pt0) cc_final: 0.7741 (pp30) REVERT: B 194 LEU cc_start: 0.7809 (mt) cc_final: 0.6982 (mt) REVERT: B 213 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7105 (mmmm) REVERT: B 218 TYR cc_start: 0.7669 (t80) cc_final: 0.7399 (t80) REVERT: B 219 GLU cc_start: 0.7524 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 247 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8434 (ttm110) REVERT: B 258 PHE cc_start: 0.7548 (m-80) cc_final: 0.7179 (m-80) REVERT: B 259 PHE cc_start: 0.7673 (t80) cc_final: 0.7454 (t80) REVERT: B 260 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7683 (mm-30) REVERT: B 262 PHE cc_start: 0.7026 (t80) cc_final: 0.6252 (t80) REVERT: B 265 TYR cc_start: 0.7513 (m-10) cc_final: 0.7043 (m-80) REVERT: B 273 ARG cc_start: 0.8416 (ptt90) cc_final: 0.7664 (ptt-90) REVERT: B 284 ASN cc_start: 0.7331 (t0) cc_final: 0.6632 (t0) REVERT: B 304 ASN cc_start: 0.8452 (m-40) cc_final: 0.8127 (m-40) REVERT: B 313 ASN cc_start: 0.8736 (m110) cc_final: 0.8395 (m-40) REVERT: B 315 VAL cc_start: 0.8919 (t) cc_final: 0.8435 (t) REVERT: B 318 TYR cc_start: 0.7105 (m-80) cc_final: 0.6304 (m-80) REVERT: B 328 LYS cc_start: 0.8908 (pttp) cc_final: 0.8086 (ptpp) REVERT: B 330 LEU cc_start: 0.9035 (mt) cc_final: 0.8695 (pp) REVERT: B 331 LYS cc_start: 0.8498 (mttt) cc_final: 0.8103 (ptmm) REVERT: B 346 HIS cc_start: 0.8254 (m-70) cc_final: 0.7811 (m-70) REVERT: B 348 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7636 (mp0) REVERT: B 349 GLU cc_start: 0.8287 (tt0) cc_final: 0.7553 (mp0) REVERT: B 352 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: B 355 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8277 (mtt90) REVERT: B 356 THR cc_start: 0.8812 (m) cc_final: 0.8493 (m) REVERT: B 357 GLN cc_start: 0.8806 (mt0) cc_final: 0.7990 (mm-40) REVERT: B 359 LEU cc_start: 0.8880 (tp) cc_final: 0.8437 (pp) REVERT: B 361 LYS cc_start: 0.8850 (ptmt) cc_final: 0.8229 (pttp) REVERT: B 364 LYS cc_start: 0.8976 (pttm) cc_final: 0.8594 (ptpp) REVERT: B 370 HIS cc_start: 0.7349 (m90) cc_final: 0.7131 (m90) REVERT: B 384 ASP cc_start: 0.8762 (m-30) cc_final: 0.8217 (m-30) REVERT: B 386 GLU cc_start: 0.8260 (mp0) cc_final: 0.7560 (mp0) REVERT: B 388 LEU cc_start: 0.8845 (mp) cc_final: 0.8446 (mm) REVERT: B 390 VAL cc_start: 0.9224 (t) cc_final: 0.9021 (p) REVERT: B 395 ASP cc_start: 0.7275 (m-30) cc_final: 0.6663 (m-30) REVERT: C 25 CYS cc_start: 0.8077 (t) cc_final: 0.7513 (t) REVERT: C 42 LEU cc_start: 0.6202 (pt) cc_final: 0.5879 (pt) REVERT: C 104 CYS cc_start: 0.8335 (m) cc_final: 0.6294 (t) REVERT: C 105 HIS cc_start: 0.8505 (m-70) cc_final: 0.8132 (m90) REVERT: C 121 ILE cc_start: 0.4599 (mm) cc_final: 0.3529 (mt) REVERT: C 162 LEU cc_start: 0.9291 (mt) cc_final: 0.8849 (mt) REVERT: C 166 MET cc_start: 0.6708 (mtp) cc_final: 0.6171 (mtp) REVERT: C 190 MET cc_start: 0.7617 (mtp) cc_final: 0.7087 (mtp) REVERT: C 191 ILE cc_start: 0.7186 (mt) cc_final: 0.6819 (mt) REVERT: C 199 GLU cc_start: 0.6417 (pm20) cc_final: 0.6018 (pp20) REVERT: C 202 LEU cc_start: 0.8301 (tp) cc_final: 0.7416 (tp) REVERT: C 336 LYS cc_start: 0.8470 (ptpt) cc_final: 0.7862 (ptpp) REVERT: C 337 TYR cc_start: 0.8635 (m-80) cc_final: 0.8022 (m-10) REVERT: C 339 LEU cc_start: 0.8771 (mt) cc_final: 0.8394 (mt) REVERT: C 344 ASP cc_start: 0.7681 (m-30) cc_final: 0.7348 (m-30) REVERT: C 359 SER cc_start: 0.6323 (m) cc_final: 0.5963 (t) REVERT: C 368 ASN cc_start: 0.7839 (p0) cc_final: 0.7583 (p0) REVERT: D 68 ASP cc_start: 0.8974 (m-30) cc_final: 0.8107 (m-30) REVERT: D 93 GLN cc_start: 0.6666 (tm-30) cc_final: 0.6303 (tm-30) REVERT: D 127 LEU cc_start: 0.9309 (tp) cc_final: 0.8913 (tp) REVERT: D 139 TYR cc_start: 0.6554 (m-80) cc_final: 0.5782 (m-80) REVERT: D 143 TYR cc_start: 0.7746 (t80) cc_final: 0.7497 (t80) REVERT: D 144 LYS cc_start: 0.7447 (mttt) cc_final: 0.5594 (mmmt) REVERT: D 148 TYR cc_start: 0.6353 (m-10) cc_final: 0.5898 (m-10) REVERT: D 155 TYR cc_start: 0.8815 (m-80) cc_final: 0.8082 (m-80) REVERT: D 169 ASN cc_start: 0.6555 (m-40) cc_final: 0.5014 (m-40) REVERT: D 173 LEU cc_start: 0.7455 (mt) cc_final: 0.7169 (tp) REVERT: D 195 LEU cc_start: 0.8710 (mt) cc_final: 0.8469 (mt) REVERT: D 200 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7303 (mppt) REVERT: D 227 LYS cc_start: 0.8466 (tttt) cc_final: 0.7090 (tppt) REVERT: D 231 HIS cc_start: 0.7211 (m170) cc_final: 0.6513 (m170) REVERT: D 235 LEU cc_start: 0.7061 (tp) cc_final: 0.6774 (tp) REVERT: D 245 MET cc_start: 0.7900 (tpt) cc_final: 0.6722 (tpt) REVERT: D 267 MET cc_start: 0.8039 (tpp) cc_final: 0.7553 (tpt) REVERT: D 300 LEU cc_start: 0.6936 (tp) cc_final: 0.6591 (tp) REVERT: D 306 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8013 (mm-30) REVERT: D 307 HIS cc_start: 0.6651 (t70) cc_final: 0.6434 (t70) REVERT: D 310 LEU cc_start: 0.9071 (mt) cc_final: 0.8833 (mm) REVERT: D 318 ASN cc_start: 0.8736 (p0) cc_final: 0.7440 (p0) REVERT: D 328 LEU cc_start: 0.9443 (mm) cc_final: 0.8466 (mm) REVERT: D 329 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7913 (mp0) REVERT: D 345 GLU cc_start: 0.8023 (tp30) cc_final: 0.7556 (tp30) REVERT: D 347 ARG cc_start: 0.7191 (ptt90) cc_final: 0.6209 (ptt90) REVERT: D 361 PHE cc_start: 0.6440 (m-80) cc_final: 0.6153 (m-80) REVERT: D 372 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8135 (pttp) REVERT: D 376 SER cc_start: 0.8193 (t) cc_final: 0.7324 (p) REVERT: D 378 CYS cc_start: 0.8880 (m) cc_final: 0.7831 (p) REVERT: D 380 GLN cc_start: 0.8000 (mt0) cc_final: 0.7581 (mt0) REVERT: D 383 ASN cc_start: 0.9038 (m-40) cc_final: 0.7727 (m110) REVERT: D 384 LEU cc_start: 0.8689 (tp) cc_final: 0.7502 (tt) REVERT: D 387 LYS cc_start: 0.9233 (mttt) cc_final: 0.8251 (mtmm) REVERT: E 93 MET cc_start: 0.3194 (tmm) cc_final: 0.2302 (tmm) REVERT: E 117 MET cc_start: 0.7437 (tmm) cc_final: 0.7202 (tmm) REVERT: E 242 TRP cc_start: 0.5017 (t-100) cc_final: 0.4616 (t-100) REVERT: E 286 MET cc_start: -0.1026 (tpt) cc_final: -0.2076 (tpt) REVERT: E 299 LYS cc_start: 0.6318 (mttt) cc_final: 0.6041 (tttt) REVERT: E 302 LYS cc_start: 0.8336 (mttm) cc_final: 0.7728 (mttt) REVERT: E 324 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7713 (ttmt) REVERT: F 73 ILE cc_start: 0.6903 (pt) cc_final: 0.6590 (mp) REVERT: F 181 MET cc_start: -0.4974 (ttm) cc_final: -0.5245 (ttm) REVERT: F 252 PHE cc_start: 0.7826 (t80) cc_final: 0.7539 (t80) REVERT: F 254 HIS cc_start: 0.8478 (m-70) cc_final: 0.8197 (m-70) REVERT: F 275 PHE cc_start: 0.7101 (t80) cc_final: 0.6829 (t80) REVERT: F 284 ASN cc_start: 0.7744 (t0) cc_final: 0.7413 (t0) REVERT: F 289 MET cc_start: 0.8142 (ttt) cc_final: 0.7704 (mmm) REVERT: F 305 PHE cc_start: 0.5683 (t80) cc_final: 0.3498 (t80) REVERT: F 309 PHE cc_start: 0.7700 (t80) cc_final: 0.7268 (t80) REVERT: G 49 LEU cc_start: 0.8724 (mm) cc_final: 0.8287 (pp) REVERT: G 68 ASN cc_start: 0.9019 (m110) cc_final: 0.8749 (m110) REVERT: G 72 TYR cc_start: 0.5958 (m-10) cc_final: 0.5009 (m-10) REVERT: G 85 LEU cc_start: 0.8719 (pt) cc_final: 0.8396 (pt) REVERT: G 96 LEU cc_start: 0.8530 (tp) cc_final: 0.8190 (tt) REVERT: G 112 PRO cc_start: 0.7780 (Cg_exo) cc_final: 0.7508 (Cg_endo) REVERT: G 118 LYS cc_start: 0.7539 (pttt) cc_final: 0.6918 (pttt) REVERT: G 130 ASP cc_start: 0.8692 (m-30) cc_final: 0.8131 (m-30) REVERT: G 150 GLN cc_start: 0.7459 (mt0) cc_final: 0.7161 (mp10) REVERT: G 152 LEU cc_start: 0.7714 (tp) cc_final: 0.7421 (tt) REVERT: G 160 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7984 (mtt-85) REVERT: G 165 LYS cc_start: 0.6972 (mtmm) cc_final: 0.6620 (mtmm) REVERT: G 172 LYS cc_start: 0.8826 (tttt) cc_final: 0.8079 (tttt) REVERT: G 194 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.6604 (ttt180) REVERT: G 199 LYS cc_start: 0.7159 (tttt) cc_final: 0.6792 (tttt) REVERT: H 22 ASN cc_start: 0.7824 (m110) cc_final: 0.7374 (m110) REVERT: H 24 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8334 (tm-30) REVERT: H 90 TYR cc_start: 0.7537 (m-80) cc_final: 0.6954 (m-80) REVERT: H 96 HIS cc_start: 0.6749 (t-90) cc_final: 0.5558 (t70) REVERT: H 98 TRP cc_start: 0.7680 (m100) cc_final: 0.6930 (m100) REVERT: H 110 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8047 (ttp-110) REVERT: H 115 ARG cc_start: 0.6589 (ptp-110) cc_final: 0.6379 (ptp-170) REVERT: H 118 PHE cc_start: 0.6925 (t80) cc_final: 0.6656 (t80) REVERT: H 133 PHE cc_start: 0.7547 (t80) cc_final: 0.6677 (t80) REVERT: H 137 VAL cc_start: 0.8282 (p) cc_final: 0.8070 (p) REVERT: H 163 LEU cc_start: 0.8362 (mp) cc_final: 0.8047 (mp) REVERT: I 87 THR cc_start: 0.6397 (m) cc_final: 0.6029 (p) REVERT: I 122 GLU cc_start: 0.8318 (pt0) cc_final: 0.7638 (pp20) REVERT: I 149 LYS cc_start: 0.7839 (tttt) cc_final: 0.7315 (tptm) REVERT: I 268 MET cc_start: 0.6087 (tpt) cc_final: 0.5347 (tpt) REVERT: I 269 MET cc_start: 0.7884 (mpp) cc_final: 0.7248 (mpp) REVERT: I 297 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7961 (tptp) REVERT: I 317 ASP cc_start: 0.6673 (p0) cc_final: 0.6297 (p0) REVERT: I 430 CYS cc_start: 0.5836 (t) cc_final: 0.5122 (t) REVERT: I 511 MET cc_start: 0.1254 (tpt) cc_final: 0.0982 (tpt) REVERT: I 537 PHE cc_start: 0.7423 (t80) cc_final: 0.7029 (t80) REVERT: L 28 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7767 (mmmt) REVERT: L 39 ASN cc_start: 0.7818 (m-40) cc_final: 0.7522 (m-40) REVERT: L 57 LEU cc_start: 0.7777 (mt) cc_final: 0.7560 (mt) REVERT: L 122 ILE cc_start: 0.8043 (pt) cc_final: 0.7728 (pt) REVERT: L 127 ASP cc_start: 0.6481 (t0) cc_final: 0.6086 (t0) REVERT: L 157 ILE cc_start: 0.7360 (mt) cc_final: 0.7084 (mm) REVERT: L 158 ARG cc_start: 0.7903 (ppt170) cc_final: 0.7334 (ttp80) REVERT: L 167 ASP cc_start: 0.8799 (t0) cc_final: 0.8329 (t0) REVERT: L 171 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7828 (ptt180) REVERT: L 184 ARG cc_start: 0.8451 (tmt170) cc_final: 0.7835 (tpt90) REVERT: L 189 MET cc_start: 0.8054 (ptp) cc_final: 0.6912 (ptp) REVERT: L 219 MET cc_start: 0.8395 (mmt) cc_final: 0.7891 (mmp) REVERT: L 242 ASN cc_start: 0.8346 (t0) cc_final: 0.7933 (t0) REVERT: L 249 MET cc_start: 0.7052 (tpp) cc_final: 0.6437 (tpp) REVERT: L 250 HIS cc_start: 0.6971 (t-90) cc_final: 0.6672 (t70) REVERT: L 279 MET cc_start: 0.6616 (ttp) cc_final: 0.5820 (ttp) REVERT: L 288 LEU cc_start: 0.8201 (tp) cc_final: 0.7856 (tp) REVERT: L 301 LYS cc_start: 0.8388 (pttt) cc_final: 0.7674 (ptpp) REVERT: L 302 LEU cc_start: 0.8921 (mt) cc_final: 0.7616 (mt) REVERT: L 305 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7440 (mpp80) REVERT: L 317 MET cc_start: 0.8136 (mmp) cc_final: 0.7858 (mmm) REVERT: L 357 LEU cc_start: 0.8174 (pp) cc_final: 0.7940 (pp) REVERT: L 358 GLU cc_start: 0.7335 (pp20) cc_final: 0.6686 (pp20) REVERT: L 364 ARG cc_start: 0.8335 (tmt170) cc_final: 0.7321 (ttp80) REVERT: L 366 PHE cc_start: 0.7977 (m-10) cc_final: 0.7663 (m-10) REVERT: L 367 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8249 (mmtt) REVERT: L 389 SER cc_start: 0.8245 (p) cc_final: 0.7969 (p) REVERT: L 390 LEU cc_start: 0.8602 (mt) cc_final: 0.8321 (mt) REVERT: L 395 LYS cc_start: 0.8933 (mmpt) cc_final: 0.8411 (mmmm) REVERT: L 397 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7698 (mmmt) REVERT: L 414 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8553 (mmtm) REVERT: L 435 HIS cc_start: 0.7007 (m90) cc_final: 0.6803 (m90) REVERT: L 439 ARG cc_start: 0.6854 (ptp-170) cc_final: 0.6389 (ptp90) REVERT: L 448 ASP cc_start: 0.7432 (t0) cc_final: 0.7052 (t0) REVERT: L 450 SER cc_start: 0.8219 (p) cc_final: 0.7926 (p) REVERT: L 451 GLU cc_start: 0.8892 (pt0) cc_final: 0.8362 (pp20) REVERT: L 457 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8346 (mmtt) REVERT: L 473 MET cc_start: 0.7829 (mtm) cc_final: 0.7222 (mtt) REVERT: L 475 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7816 (tpp80) REVERT: L 477 MET cc_start: 0.8099 (tmm) cc_final: 0.7626 (tmm) REVERT: L 488 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7529 (mtm110) REVERT: L 489 GLN cc_start: 0.6796 (mp10) cc_final: 0.6426 (mm-40) REVERT: L 522 CYS cc_start: 0.7914 (t) cc_final: 0.7079 (m) REVERT: L 530 HIS cc_start: 0.8347 (t-170) cc_final: 0.7775 (t-90) REVERT: L 533 GLU cc_start: 0.7770 (tp30) cc_final: 0.6900 (tp30) REVERT: L 534 ILE cc_start: 0.7804 (tp) cc_final: 0.7441 (pt) REVERT: L 535 PHE cc_start: 0.6788 (t80) cc_final: 0.6487 (t80) REVERT: L 552 HIS cc_start: 0.4285 (m-70) cc_final: 0.4064 (m90) REVERT: L 554 MET cc_start: 0.7120 (mmp) cc_final: 0.6753 (tpp) REVERT: L 598 GLN cc_start: 0.7757 (mp10) cc_final: 0.7491 (mm110) REVERT: L 599 MET cc_start: 0.8974 (mmp) cc_final: 0.8663 (mmm) REVERT: L 603 MET cc_start: 0.7486 (ptm) cc_final: 0.7097 (ptm) REVERT: L 625 ARG cc_start: 0.8183 (mmp-170) cc_final: 0.7755 (mmp-170) REVERT: L 657 HIS cc_start: 0.8165 (p-80) cc_final: 0.7808 (p90) REVERT: L 670 HIS cc_start: 0.8179 (m-70) cc_final: 0.7785 (m-70) REVERT: L 673 LYS cc_start: 0.8249 (tptt) cc_final: 0.7740 (tptt) REVERT: M 110 PHE cc_start: 0.7358 (t80) cc_final: 0.6949 (t80) REVERT: M 123 TYR cc_start: 0.6910 (t80) cc_final: 0.5542 (t80) REVERT: M 149 LYS cc_start: 0.8682 (tttm) cc_final: 0.7946 (tptp) REVERT: M 420 GLN cc_start: 0.7143 (pp30) cc_final: 0.6343 (pm20) REVERT: M 454 MET cc_start: 0.6914 (mmm) cc_final: 0.6181 (mmm) REVERT: R 50 MET cc_start: 0.6636 (ptt) cc_final: 0.6201 (ptt) REVERT: R 91 ARG cc_start: 0.6924 (mtt90) cc_final: 0.6389 (mtt90) outliers start: 0 outliers final: 0 residues processed: 1065 average time/residue: 0.5474 time to fit residues: 913.8359 Evaluate side-chains 972 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 972 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 0.9980 chunk 421 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 410 optimal weight: 20.0000 chunk 247 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 322 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 409 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 412 GLN A 430 ASN A 501 HIS B 220 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS D 175 GLN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 171 GLN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN N 41 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 38016 Z= 0.233 Angle : 0.722 11.382 51366 Z= 0.379 Chirality : 0.045 0.207 5749 Planarity : 0.005 0.122 6583 Dihedral : 4.750 31.417 5047 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.33 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.34 (0.12), residues: 4597 helix: 0.77 (0.10), residues: 2675 sheet: -0.56 (0.24), residues: 435 loop : -1.92 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 82 HIS 0.009 0.001 HIS I 306 PHE 0.038 0.002 PHE G 15 TYR 0.041 0.002 TYR B 132 ARG 0.014 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1058 time to evaluate : 4.259 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: 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 83 ASP cc_start: 0.6750 (t0) cc_final: 0.6470 (t0) REVERT: A 95 MET cc_start: 0.6029 (pmm) cc_final: 0.4113 (ptm) REVERT: A 103 ILE cc_start: 0.7681 (pt) cc_final: 0.7464 (pt) REVERT: A 117 MET cc_start: 0.8023 (mtt) cc_final: 0.6971 (mtt) REVERT: A 132 GLU cc_start: 0.7474 (mp0) cc_final: 0.6999 (pm20) REVERT: A 136 ARG cc_start: 0.7976 (ptt-90) cc_final: 0.7382 (ptp-170) REVERT: A 173 LYS cc_start: 0.7870 (mmpt) cc_final: 0.7529 (mmmt) REVERT: A 204 LEU cc_start: 0.7581 (mt) cc_final: 0.6583 (mt) REVERT: A 218 LEU cc_start: 0.8006 (tp) cc_final: 0.7207 (tp) REVERT: A 234 VAL cc_start: 0.7787 (t) cc_final: 0.7295 (t) REVERT: A 235 ILE cc_start: 0.8579 (mt) cc_final: 0.8047 (mt) REVERT: A 240 ASN cc_start: 0.6584 (m-40) cc_final: 0.6247 (m-40) REVERT: A 248 LEU cc_start: 0.7677 (mt) cc_final: 0.7477 (mt) REVERT: A 250 ASN cc_start: 0.5923 (t0) cc_final: 0.4860 (t0) REVERT: A 253 HIS cc_start: 0.4545 (m90) cc_final: 0.4128 (m90) REVERT: A 301 GLN cc_start: 0.6461 (pm20) cc_final: 0.5098 (pm20) REVERT: A 332 CYS cc_start: 0.7877 (m) cc_final: 0.7028 (p) REVERT: A 342 LEU cc_start: 0.8468 (mt) cc_final: 0.8013 (mt) REVERT: A 343 GLN cc_start: 0.5736 (tm-30) cc_final: 0.5526 (tm-30) REVERT: A 345 ASN cc_start: 0.7605 (p0) cc_final: 0.7329 (p0) REVERT: A 351 SER cc_start: 0.5505 (p) cc_final: 0.4677 (p) REVERT: A 363 ARG cc_start: 0.7136 (ptt-90) cc_final: 0.6402 (ptt-90) REVERT: A 365 ILE cc_start: 0.7755 (mt) cc_final: 0.7463 (mt) REVERT: A 380 MET cc_start: 0.6738 (mmp) cc_final: 0.6182 (mmm) REVERT: A 387 ASN cc_start: 0.4978 (t0) cc_final: 0.4599 (t0) REVERT: A 392 MET cc_start: 0.4352 (ptt) cc_final: 0.3760 (ptt) REVERT: A 423 HIS cc_start: 0.5777 (m170) cc_final: 0.5387 (m-70) REVERT: A 424 ARG cc_start: 0.7521 (ptt90) cc_final: 0.6685 (ptt180) REVERT: A 436 LEU cc_start: 0.7256 (pp) cc_final: 0.6874 (pp) REVERT: A 437 GLU cc_start: 0.5999 (tm-30) cc_final: 0.5526 (tm-30) REVERT: A 438 ASP cc_start: 0.6557 (m-30) cc_final: 0.6124 (m-30) REVERT: A 440 LEU cc_start: 0.7665 (mt) cc_final: 0.7170 (mm) REVERT: A 478 MET cc_start: 0.7403 (mmp) cc_final: 0.6852 (mmm) REVERT: A 496 LEU cc_start: 0.8191 (mt) cc_final: 0.7932 (mm) REVERT: B 66 GLU cc_start: 0.7874 (pp20) cc_final: 0.7249 (pp20) REVERT: B 77 LYS cc_start: 0.8658 (mttt) cc_final: 0.7794 (mttp) REVERT: B 88 MET cc_start: 0.7009 (tmm) cc_final: 0.6727 (tmm) REVERT: B 93 LYS cc_start: 0.9400 (mttt) cc_final: 0.8530 (mmtt) REVERT: B 94 GLN cc_start: 0.8432 (tt0) cc_final: 0.7942 (mp10) REVERT: B 96 LEU cc_start: 0.7793 (mt) cc_final: 0.7591 (mt) REVERT: B 109 GLU cc_start: 0.7258 (pt0) cc_final: 0.6304 (pp20) REVERT: B 125 MET cc_start: 0.5581 (mmp) cc_final: 0.4992 (mmp) REVERT: B 168 LEU cc_start: 0.8146 (tp) cc_final: 0.7930 (tp) REVERT: B 172 LEU cc_start: 0.9218 (mt) cc_final: 0.8532 (mt) REVERT: B 177 GLN cc_start: 0.8779 (pt0) cc_final: 0.7866 (pp30) REVERT: B 196 GLU cc_start: 0.6953 (mp0) cc_final: 0.6513 (mp0) REVERT: B 213 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7577 (mmmm) REVERT: B 218 TYR cc_start: 0.7772 (t80) cc_final: 0.7524 (t80) REVERT: B 219 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 239 GLU cc_start: 0.8626 (pp20) cc_final: 0.8411 (pp20) REVERT: B 247 ARG cc_start: 0.8566 (ttm110) cc_final: 0.8353 (ttm110) REVERT: B 258 PHE cc_start: 0.7669 (m-80) cc_final: 0.7160 (m-80) REVERT: B 259 PHE cc_start: 0.7786 (t80) cc_final: 0.7482 (t80) REVERT: B 260 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7673 (mm-30) REVERT: B 262 PHE cc_start: 0.7096 (t80) cc_final: 0.6300 (t80) REVERT: B 265 TYR cc_start: 0.7537 (m-10) cc_final: 0.7044 (m-80) REVERT: B 273 ARG cc_start: 0.8448 (ptt90) cc_final: 0.8009 (mtm110) REVERT: B 281 VAL cc_start: 0.8387 (m) cc_final: 0.8130 (m) REVERT: B 284 ASN cc_start: 0.7420 (t0) cc_final: 0.7076 (t0) REVERT: B 297 GLN cc_start: 0.7085 (tp40) cc_final: 0.6727 (tp40) REVERT: B 304 ASN cc_start: 0.8493 (m-40) cc_final: 0.8179 (m-40) REVERT: B 313 ASN cc_start: 0.8793 (m110) cc_final: 0.8423 (m-40) REVERT: B 315 VAL cc_start: 0.9014 (t) cc_final: 0.8580 (t) REVERT: B 318 TYR cc_start: 0.7312 (m-80) cc_final: 0.6508 (m-80) REVERT: B 324 THR cc_start: 0.7862 (t) cc_final: 0.7162 (t) REVERT: B 328 LYS cc_start: 0.9036 (pttp) cc_final: 0.8739 (ptpp) REVERT: B 330 LEU cc_start: 0.9074 (mt) cc_final: 0.8844 (mt) REVERT: B 331 LYS cc_start: 0.8492 (mttt) cc_final: 0.8118 (mmtm) REVERT: B 346 HIS cc_start: 0.8276 (m-70) cc_final: 0.7657 (m-70) REVERT: B 348 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7819 (mp0) REVERT: B 349 GLU cc_start: 0.8386 (tt0) cc_final: 0.7794 (mp0) REVERT: B 352 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: B 355 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8439 (mtt90) REVERT: B 356 THR cc_start: 0.8874 (m) cc_final: 0.8548 (m) REVERT: B 357 GLN cc_start: 0.8865 (mt0) cc_final: 0.7973 (mm-40) REVERT: B 359 LEU cc_start: 0.8936 (tp) cc_final: 0.8526 (pp) REVERT: B 361 LYS cc_start: 0.8892 (ptmt) cc_final: 0.8320 (pttp) REVERT: B 364 LYS cc_start: 0.8999 (pttm) cc_final: 0.8649 (ptpp) REVERT: B 384 ASP cc_start: 0.8804 (m-30) cc_final: 0.8275 (m-30) REVERT: B 386 GLU cc_start: 0.8269 (mp0) cc_final: 0.7490 (mp0) REVERT: B 388 LEU cc_start: 0.8852 (mp) cc_final: 0.8435 (mm) REVERT: B 390 VAL cc_start: 0.9216 (t) cc_final: 0.9014 (p) REVERT: B 395 ASP cc_start: 0.7232 (m-30) cc_final: 0.6613 (m-30) REVERT: C 13 ARG cc_start: 0.6563 (tmm-80) cc_final: 0.6140 (tmm-80) REVERT: C 42 LEU cc_start: 0.6332 (pt) cc_final: 0.5866 (pp) REVERT: C 92 HIS cc_start: 0.6510 (m-70) cc_final: 0.6260 (m90) REVERT: C 104 CYS cc_start: 0.8492 (m) cc_final: 0.6395 (t) REVERT: C 105 HIS cc_start: 0.8740 (m-70) cc_final: 0.8276 (m90) REVERT: C 162 LEU cc_start: 0.9262 (mt) cc_final: 0.8847 (mt) REVERT: C 166 MET cc_start: 0.6812 (mtp) cc_final: 0.6387 (mtp) REVERT: C 190 MET cc_start: 0.7748 (mtp) cc_final: 0.7331 (mtp) REVERT: C 191 ILE cc_start: 0.7606 (mt) cc_final: 0.7297 (mt) REVERT: C 199 GLU cc_start: 0.7413 (pm20) cc_final: 0.6729 (pp20) REVERT: C 202 LEU cc_start: 0.8270 (tp) cc_final: 0.7747 (tp) REVERT: C 225 LYS cc_start: 0.6725 (mttt) cc_final: 0.6475 (mttm) REVERT: C 292 MET cc_start: -0.0406 (mmp) cc_final: -0.0729 (mmp) REVERT: C 332 GLN cc_start: 0.7821 (mp10) cc_final: 0.7412 (mp10) REVERT: C 333 GLU cc_start: 0.8045 (pp20) cc_final: 0.7294 (pp20) REVERT: C 336 LYS cc_start: 0.8512 (ptpt) cc_final: 0.7880 (ptpp) REVERT: C 337 TYR cc_start: 0.8701 (m-80) cc_final: 0.8105 (m-10) REVERT: C 339 LEU cc_start: 0.8739 (mt) cc_final: 0.8490 (mt) REVERT: C 344 ASP cc_start: 0.7675 (m-30) cc_final: 0.7385 (m-30) REVERT: C 359 SER cc_start: 0.5932 (m) cc_final: 0.5537 (t) REVERT: C 363 ASN cc_start: 0.9061 (t0) cc_final: 0.8691 (t0) REVERT: C 368 ASN cc_start: 0.8188 (p0) cc_final: 0.7675 (p0) REVERT: C 373 LEU cc_start: 0.8014 (tp) cc_final: 0.7614 (tp) REVERT: C 374 HIS cc_start: 0.7655 (m-70) cc_final: 0.7361 (m-70) REVERT: C 393 MET cc_start: 0.7028 (ptm) cc_final: 0.6568 (ptm) REVERT: D 65 LEU cc_start: 0.8521 (mt) cc_final: 0.8193 (tp) REVERT: D 66 LEU cc_start: 0.8881 (mt) cc_final: 0.8455 (mt) REVERT: D 68 ASP cc_start: 0.9024 (m-30) cc_final: 0.8250 (m-30) REVERT: D 93 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6635 (tm-30) REVERT: D 127 LEU cc_start: 0.9361 (tp) cc_final: 0.8965 (tp) REVERT: D 139 TYR cc_start: 0.6758 (m-80) cc_final: 0.6131 (m-80) REVERT: D 142 ASP cc_start: 0.8404 (m-30) cc_final: 0.7374 (m-30) REVERT: D 143 TYR cc_start: 0.8001 (t80) cc_final: 0.6877 (t80) REVERT: D 144 LYS cc_start: 0.7588 (mttt) cc_final: 0.5710 (mmmt) REVERT: D 146 GLU cc_start: 0.7861 (mt-10) cc_final: 0.6992 (mt-10) REVERT: D 148 TYR cc_start: 0.6492 (m-10) cc_final: 0.5943 (m-10) REVERT: D 155 TYR cc_start: 0.8872 (m-80) cc_final: 0.8038 (m-80) REVERT: D 165 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 169 ASN cc_start: 0.6787 (m-40) cc_final: 0.5935 (m-40) REVERT: D 195 LEU cc_start: 0.8821 (mt) cc_final: 0.8511 (mt) REVERT: D 200 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7517 (mppt) REVERT: D 223 LEU cc_start: 0.8556 (mt) cc_final: 0.8153 (mt) REVERT: D 224 GLU cc_start: 0.7642 (pp20) cc_final: 0.7363 (pp20) REVERT: D 227 LYS cc_start: 0.8483 (tttt) cc_final: 0.7071 (tppt) REVERT: D 231 HIS cc_start: 0.7217 (m170) cc_final: 0.6607 (m170) REVERT: D 235 LEU cc_start: 0.8547 (tp) cc_final: 0.8099 (tp) REVERT: D 261 TYR cc_start: 0.7378 (t80) cc_final: 0.6887 (t80) REVERT: D 265 GLU cc_start: 0.8208 (pp20) cc_final: 0.7891 (pp20) REVERT: D 267 MET cc_start: 0.8090 (tpp) cc_final: 0.7778 (tpt) REVERT: D 306 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8083 (mm-30) REVERT: D 307 HIS cc_start: 0.6676 (t70) cc_final: 0.6283 (t70) REVERT: D 310 LEU cc_start: 0.9077 (mt) cc_final: 0.8859 (mm) REVERT: D 328 LEU cc_start: 0.9450 (mm) cc_final: 0.8908 (mm) REVERT: D 329 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7950 (mp0) REVERT: D 345 GLU cc_start: 0.8074 (tp30) cc_final: 0.7622 (tp30) REVERT: D 347 ARG cc_start: 0.7340 (ptt90) cc_final: 0.6386 (ptt90) REVERT: D 351 PHE cc_start: 0.7827 (p90) cc_final: 0.7296 (p90) REVERT: D 372 LYS cc_start: 0.8804 (ptpt) cc_final: 0.8146 (pttp) REVERT: D 376 SER cc_start: 0.8317 (t) cc_final: 0.7476 (p) REVERT: D 378 CYS cc_start: 0.8970 (m) cc_final: 0.8688 (m) REVERT: D 384 LEU cc_start: 0.8832 (tp) cc_final: 0.7602 (tt) REVERT: D 386 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6795 (mt-10) REVERT: D 387 LYS cc_start: 0.9316 (mttt) cc_final: 0.8461 (mttt) REVERT: E 93 MET cc_start: 0.3535 (tmm) cc_final: 0.2793 (tmm) REVERT: E 117 MET cc_start: 0.7546 (tmm) cc_final: 0.7281 (tmm) REVERT: E 242 TRP cc_start: 0.5091 (t-100) cc_final: 0.4699 (t-100) REVERT: E 286 MET cc_start: -0.1054 (tpt) cc_final: -0.2092 (tpt) REVERT: E 299 LYS cc_start: 0.6482 (mttt) cc_final: 0.6246 (tttt) REVERT: E 302 LYS cc_start: 0.8342 (mttm) cc_final: 0.7747 (mttt) REVERT: E 324 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7694 (ttmt) REVERT: F 73 ILE cc_start: 0.7186 (pt) cc_final: 0.6872 (mp) REVERT: F 181 MET cc_start: -0.4927 (ttm) cc_final: -0.5216 (ttm) REVERT: F 252 PHE cc_start: 0.7839 (t80) cc_final: 0.7589 (t80) REVERT: F 254 HIS cc_start: 0.8450 (m-70) cc_final: 0.8231 (m-70) REVERT: F 275 PHE cc_start: 0.7150 (t80) cc_final: 0.6884 (t80) REVERT: F 284 ASN cc_start: 0.7843 (t0) cc_final: 0.7495 (t0) REVERT: F 289 MET cc_start: 0.8289 (ttt) cc_final: 0.7769 (mmm) REVERT: F 309 PHE cc_start: 0.7736 (t80) cc_final: 0.7299 (t80) REVERT: G 45 GLU cc_start: 0.8276 (pm20) cc_final: 0.8056 (pm20) REVERT: G 49 LEU cc_start: 0.8837 (mm) cc_final: 0.8251 (pp) REVERT: G 68 ASN cc_start: 0.8978 (m110) cc_final: 0.8773 (m110) REVERT: G 72 TYR cc_start: 0.6072 (m-10) cc_final: 0.5105 (m-10) REVERT: G 85 LEU cc_start: 0.8792 (pt) cc_final: 0.8459 (pt) REVERT: G 96 LEU cc_start: 0.8568 (tp) cc_final: 0.8349 (tt) REVERT: G 112 PRO cc_start: 0.7941 (Cg_exo) cc_final: 0.7565 (Cg_endo) REVERT: G 118 LYS cc_start: 0.7578 (pttt) cc_final: 0.6973 (pttt) REVERT: G 121 GLU cc_start: 0.8216 (pp20) cc_final: 0.8001 (pp20) REVERT: G 130 ASP cc_start: 0.8744 (m-30) cc_final: 0.8168 (m-30) REVERT: G 150 GLN cc_start: 0.7554 (mt0) cc_final: 0.7267 (mp10) REVERT: G 160 ARG cc_start: 0.8389 (ttt180) cc_final: 0.7879 (mtt-85) REVERT: G 172 LYS cc_start: 0.9071 (tttt) cc_final: 0.8249 (tttt) REVERT: G 199 LYS cc_start: 0.7394 (tttt) cc_final: 0.7056 (tttt) REVERT: H 22 ASN cc_start: 0.7861 (m110) cc_final: 0.7305 (m110) REVERT: H 24 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8377 (tm-30) REVERT: H 26 GLU cc_start: 0.7622 (pp20) cc_final: 0.7359 (tm-30) REVERT: H 54 ARG cc_start: 0.6577 (ttp-110) cc_final: 0.5922 (ptp-110) REVERT: H 90 TYR cc_start: 0.7560 (m-80) cc_final: 0.7007 (m-80) REVERT: H 97 GLN cc_start: 0.7825 (tp40) cc_final: 0.7504 (tm-30) REVERT: H 110 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8225 (ttp-110) REVERT: H 118 PHE cc_start: 0.6998 (t80) cc_final: 0.6769 (t80) REVERT: H 133 PHE cc_start: 0.7604 (t80) cc_final: 0.6868 (t80) REVERT: H 137 VAL cc_start: 0.8260 (p) cc_final: 0.8059 (p) REVERT: H 163 LEU cc_start: 0.8400 (mp) cc_final: 0.7803 (mp) REVERT: I 87 THR cc_start: 0.6660 (m) cc_final: 0.6211 (p) REVERT: I 122 GLU cc_start: 0.8349 (pt0) cc_final: 0.7640 (pp20) REVERT: I 149 LYS cc_start: 0.7921 (tttt) cc_final: 0.7416 (tptm) REVERT: I 263 MET cc_start: 0.0556 (mmp) cc_final: 0.0316 (mmp) REVERT: I 268 MET cc_start: 0.6722 (tpt) cc_final: 0.6171 (tpt) REVERT: I 269 MET cc_start: 0.8026 (mpp) cc_final: 0.7330 (mpp) REVERT: I 297 LYS cc_start: 0.8360 (tmtt) cc_final: 0.8035 (tptp) REVERT: I 317 ASP cc_start: 0.6652 (p0) cc_final: 0.6446 (p0) REVERT: I 430 CYS cc_start: 0.5816 (t) cc_final: 0.5162 (t) REVERT: I 511 MET cc_start: 0.1430 (tpt) cc_final: 0.1085 (tpt) REVERT: I 537 PHE cc_start: 0.7379 (t80) cc_final: 0.7118 (t80) REVERT: L 28 LYS cc_start: 0.8109 (mmpt) cc_final: 0.7813 (mmmt) REVERT: L 39 ASN cc_start: 0.7893 (m-40) cc_final: 0.7606 (m-40) REVERT: L 122 ILE cc_start: 0.8032 (pt) cc_final: 0.7741 (pt) REVERT: L 127 ASP cc_start: 0.6514 (t0) cc_final: 0.6146 (t0) REVERT: L 148 ARG cc_start: 0.7015 (ttp-170) cc_final: 0.6746 (tmm160) REVERT: L 157 ILE cc_start: 0.7449 (mt) cc_final: 0.7188 (mm) REVERT: L 158 ARG cc_start: 0.7963 (ppt170) cc_final: 0.7564 (ttp80) REVERT: L 167 ASP cc_start: 0.8803 (t0) cc_final: 0.8363 (t0) REVERT: L 171 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7885 (ptt180) REVERT: L 185 ASN cc_start: 0.8305 (m-40) cc_final: 0.7962 (m-40) REVERT: L 189 MET cc_start: 0.7982 (ptp) cc_final: 0.7464 (ptp) REVERT: L 211 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8102 (mm-30) REVERT: L 219 MET cc_start: 0.8519 (mmt) cc_final: 0.8104 (mmp) REVERT: L 242 ASN cc_start: 0.8410 (t0) cc_final: 0.8051 (t0) REVERT: L 246 GLU cc_start: 0.8352 (pp20) cc_final: 0.8067 (pp20) REVERT: L 249 MET cc_start: 0.7196 (tpp) cc_final: 0.6595 (tpp) REVERT: L 250 HIS cc_start: 0.7019 (t-90) cc_final: 0.6722 (t-90) REVERT: L 279 MET cc_start: 0.6628 (ttp) cc_final: 0.6238 (ttp) REVERT: L 288 LEU cc_start: 0.8321 (tp) cc_final: 0.7857 (mt) REVERT: L 289 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8187 (ptpp) REVERT: L 301 LYS cc_start: 0.8478 (pttt) cc_final: 0.7837 (ptpt) REVERT: L 302 LEU cc_start: 0.9012 (mt) cc_final: 0.7768 (mt) REVERT: L 305 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7611 (mpp80) REVERT: L 317 MET cc_start: 0.8240 (mmp) cc_final: 0.7905 (mmm) REVERT: L 357 LEU cc_start: 0.8153 (pp) cc_final: 0.7913 (pp) REVERT: L 358 GLU cc_start: 0.7340 (pp20) cc_final: 0.6702 (pp20) REVERT: L 366 PHE cc_start: 0.8242 (m-10) cc_final: 0.7982 (m-10) REVERT: L 390 LEU cc_start: 0.8692 (mt) cc_final: 0.8326 (mt) REVERT: L 393 ASP cc_start: 0.7663 (t0) cc_final: 0.6916 (t70) REVERT: L 395 LYS cc_start: 0.9048 (mmpt) cc_final: 0.8636 (mmtm) REVERT: L 397 LYS cc_start: 0.8338 (mmpt) cc_final: 0.7749 (mmmt) REVERT: L 439 ARG cc_start: 0.6866 (ptp-170) cc_final: 0.6648 (ptp-170) REVERT: L 448 ASP cc_start: 0.7281 (t0) cc_final: 0.6741 (t0) REVERT: L 450 SER cc_start: 0.8293 (p) cc_final: 0.7939 (p) REVERT: L 451 GLU cc_start: 0.8984 (pt0) cc_final: 0.8392 (pp20) REVERT: L 457 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8315 (mmtt) REVERT: L 473 MET cc_start: 0.7942 (mtm) cc_final: 0.7237 (mtt) REVERT: L 477 MET cc_start: 0.8036 (tmm) cc_final: 0.7666 (tmm) REVERT: L 488 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7563 (mtm110) REVERT: L 489 GLN cc_start: 0.7326 (mp10) cc_final: 0.6397 (mm-40) REVERT: L 522 CYS cc_start: 0.8086 (t) cc_final: 0.7140 (m) REVERT: L 533 GLU cc_start: 0.7964 (tp30) cc_final: 0.6605 (tp30) REVERT: L 534 ILE cc_start: 0.7942 (tp) cc_final: 0.7571 (pt) REVERT: L 535 PHE cc_start: 0.6967 (t80) cc_final: 0.6623 (t80) REVERT: L 554 MET cc_start: 0.7332 (mmp) cc_final: 0.7097 (tpp) REVERT: L 598 GLN cc_start: 0.8087 (mp10) cc_final: 0.7630 (mm110) REVERT: L 599 MET cc_start: 0.9038 (mmp) cc_final: 0.8785 (mmm) REVERT: L 603 MET cc_start: 0.7716 (ptm) cc_final: 0.7249 (ptm) REVERT: L 625 ARG cc_start: 0.8474 (mmp-170) cc_final: 0.8169 (mmp-170) REVERT: L 657 HIS cc_start: 0.8151 (p-80) cc_final: 0.7555 (p-80) REVERT: L 670 HIS cc_start: 0.8141 (m-70) cc_final: 0.7793 (m-70) REVERT: L 673 LYS cc_start: 0.8392 (tptt) cc_final: 0.7854 (tptt) REVERT: L 717 MET cc_start: -0.1998 (ttt) cc_final: -0.2232 (ttt) REVERT: M 110 PHE cc_start: 0.7394 (t80) cc_final: 0.6980 (t80) REVERT: M 123 TYR cc_start: 0.6578 (t80) cc_final: 0.6262 (t80) REVERT: M 149 LYS cc_start: 0.8655 (tttm) cc_final: 0.7964 (tptp) REVERT: M 155 MET cc_start: 0.3516 (ppp) cc_final: 0.3155 (ppp) REVERT: M 428 HIS cc_start: 0.8727 (t70) cc_final: 0.8429 (t70) REVERT: R 24 VAL cc_start: 0.7800 (p) cc_final: 0.7504 (m) REVERT: R 25 LYS cc_start: 0.6098 (mptt) cc_final: 0.5750 (mmtp) REVERT: R 50 MET cc_start: 0.6816 (ptt) cc_final: 0.6425 (ptt) REVERT: R 91 ARG cc_start: 0.6939 (mtt90) cc_final: 0.6472 (mtt90) outliers start: 0 outliers final: 0 residues processed: 1058 average time/residue: 0.5562 time to fit residues: 924.9400 Evaluate side-chains 957 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 957 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 5.9990 chunk 434 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 412 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS B 220 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 175 HIS ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** I 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 552 HIS L 553 HIS ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 38016 Z= 0.244 Angle : 0.733 11.038 51366 Z= 0.385 Chirality : 0.045 0.240 5749 Planarity : 0.005 0.121 6583 Dihedral : 4.802 28.188 5047 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.50 % Favored : 92.19 % Rotamer: Outliers : 0.02 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 4597 helix: 0.69 (0.10), residues: 2677 sheet: -0.53 (0.24), residues: 429 loop : -1.94 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 82 HIS 0.010 0.001 HIS I 306 PHE 0.064 0.002 PHE A 472 TYR 0.044 0.002 TYR A 208 ARG 0.012 0.001 ARG D 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1070 time to evaluate : 3.985 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: 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 83 ASP cc_start: 0.6770 (t0) cc_final: 0.6501 (t0) REVERT: A 95 MET cc_start: 0.5989 (pmm) cc_final: 0.4479 (ptm) REVERT: A 102 PHE cc_start: 0.5684 (t80) cc_final: 0.5331 (t80) REVERT: A 103 ILE cc_start: 0.7703 (pt) cc_final: 0.7486 (pt) REVERT: A 117 MET cc_start: 0.7993 (mtt) cc_final: 0.6989 (mtt) REVERT: A 137 LYS cc_start: 0.8106 (mppt) cc_final: 0.7604 (mmmt) REVERT: A 173 LYS cc_start: 0.7894 (mmpt) cc_final: 0.7415 (mmmt) REVERT: A 218 LEU cc_start: 0.8054 (tp) cc_final: 0.7381 (tp) REVERT: A 234 VAL cc_start: 0.7761 (t) cc_final: 0.7434 (t) REVERT: A 240 ASN cc_start: 0.6763 (m-40) cc_final: 0.6344 (m-40) REVERT: A 250 ASN cc_start: 0.5964 (t0) cc_final: 0.5089 (t0) REVERT: A 253 HIS cc_start: 0.4491 (m90) cc_final: 0.4122 (m90) REVERT: A 324 ASN cc_start: 0.6844 (m110) cc_final: 0.5884 (m110) REVERT: A 332 CYS cc_start: 0.8029 (m) cc_final: 0.6994 (p) REVERT: A 343 GLN cc_start: 0.5758 (tm-30) cc_final: 0.5282 (tm-30) REVERT: A 351 SER cc_start: 0.6138 (p) cc_final: 0.5346 (p) REVERT: A 363 ARG cc_start: 0.7142 (ptt-90) cc_final: 0.6867 (ptt-90) REVERT: A 380 MET cc_start: 0.7009 (mmp) cc_final: 0.6442 (mmm) REVERT: A 387 ASN cc_start: 0.4658 (t0) cc_final: 0.4408 (t0) REVERT: A 392 MET cc_start: 0.4559 (ptt) cc_final: 0.4059 (ptt) REVERT: A 394 LEU cc_start: 0.7553 (tp) cc_final: 0.7112 (tp) REVERT: A 414 PHE cc_start: 0.6936 (t80) cc_final: 0.6726 (t80) REVERT: A 421 ASP cc_start: 0.6766 (t0) cc_final: 0.5393 (t0) REVERT: A 423 HIS cc_start: 0.5771 (m170) cc_final: 0.5510 (m-70) REVERT: A 436 LEU cc_start: 0.7247 (pp) cc_final: 0.7032 (pp) REVERT: A 438 ASP cc_start: 0.6600 (m-30) cc_final: 0.6298 (m-30) REVERT: A 440 LEU cc_start: 0.7576 (mt) cc_final: 0.7200 (mm) REVERT: A 463 ARG cc_start: 0.5951 (tmm160) cc_final: 0.5563 (tmm160) REVERT: A 478 MET cc_start: 0.7397 (mmp) cc_final: 0.6841 (mmm) REVERT: A 489 MET cc_start: 0.6298 (ppp) cc_final: 0.5990 (ppp) REVERT: A 496 LEU cc_start: 0.8296 (mt) cc_final: 0.7999 (mm) REVERT: B 66 GLU cc_start: 0.7815 (pp20) cc_final: 0.7597 (pp20) REVERT: B 77 LYS cc_start: 0.8575 (mttt) cc_final: 0.7790 (mttp) REVERT: B 88 MET cc_start: 0.7004 (tmm) cc_final: 0.6799 (tmm) REVERT: B 93 LYS cc_start: 0.9393 (mttt) cc_final: 0.8860 (pttm) REVERT: B 94 GLN cc_start: 0.8473 (tt0) cc_final: 0.7510 (mt0) REVERT: B 96 LEU cc_start: 0.7827 (mt) cc_final: 0.7476 (mt) REVERT: B 109 GLU cc_start: 0.7267 (pt0) cc_final: 0.6345 (pp20) REVERT: B 110 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8286 (mtmt) REVERT: B 125 MET cc_start: 0.5822 (mmp) cc_final: 0.5540 (mmp) REVERT: B 170 LYS cc_start: 0.8928 (pttm) cc_final: 0.8512 (pttt) REVERT: B 172 LEU cc_start: 0.9287 (mt) cc_final: 0.8585 (mt) REVERT: B 177 GLN cc_start: 0.8764 (pt0) cc_final: 0.7813 (pp30) REVERT: B 196 GLU cc_start: 0.6999 (mp0) cc_final: 0.6539 (mp0) REVERT: B 218 TYR cc_start: 0.7761 (t80) cc_final: 0.7501 (t80) REVERT: B 219 GLU cc_start: 0.7848 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 233 ILE cc_start: 0.8135 (mt) cc_final: 0.7898 (mt) REVERT: B 244 MET cc_start: 0.7303 (tmm) cc_final: 0.6549 (tmm) REVERT: B 245 HIS cc_start: 0.8406 (m170) cc_final: 0.8014 (m-70) REVERT: B 247 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8410 (ttm110) REVERT: B 248 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 258 PHE cc_start: 0.7622 (m-80) cc_final: 0.7184 (m-80) REVERT: B 260 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7701 (mm-30) REVERT: B 262 PHE cc_start: 0.7150 (t80) cc_final: 0.6323 (t80) REVERT: B 265 TYR cc_start: 0.7545 (m-10) cc_final: 0.7074 (m-80) REVERT: B 273 ARG cc_start: 0.8454 (ptt90) cc_final: 0.7987 (mtm110) REVERT: B 297 GLN cc_start: 0.6990 (tp40) cc_final: 0.6685 (tp40) REVERT: B 304 ASN cc_start: 0.8516 (m-40) cc_final: 0.8177 (m-40) REVERT: B 313 ASN cc_start: 0.8789 (m110) cc_final: 0.8470 (m110) REVERT: B 315 VAL cc_start: 0.9073 (t) cc_final: 0.8600 (t) REVERT: B 318 TYR cc_start: 0.7365 (m-80) cc_final: 0.6563 (m-80) REVERT: B 324 THR cc_start: 0.7997 (t) cc_final: 0.7046 (t) REVERT: B 328 LYS cc_start: 0.9083 (pttp) cc_final: 0.8645 (ptpp) REVERT: B 329 ILE cc_start: 0.8905 (mt) cc_final: 0.8598 (mt) REVERT: B 330 LEU cc_start: 0.9087 (mt) cc_final: 0.8856 (mt) REVERT: B 331 LYS cc_start: 0.8441 (mttt) cc_final: 0.8091 (mmtm) REVERT: B 346 HIS cc_start: 0.8333 (m-70) cc_final: 0.7863 (m-70) REVERT: B 348 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7726 (mp0) REVERT: B 349 GLU cc_start: 0.8361 (tt0) cc_final: 0.7681 (mp0) REVERT: B 352 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: B 355 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8434 (mtt90) REVERT: B 356 THR cc_start: 0.8837 (m) cc_final: 0.8564 (m) REVERT: B 357 GLN cc_start: 0.8945 (mt0) cc_final: 0.8064 (mm-40) REVERT: B 359 LEU cc_start: 0.8955 (tp) cc_final: 0.8644 (pp) REVERT: B 361 LYS cc_start: 0.8863 (ptmt) cc_final: 0.8304 (pttp) REVERT: B 364 LYS cc_start: 0.8942 (pttm) cc_final: 0.8652 (ptpp) REVERT: B 384 ASP cc_start: 0.8761 (m-30) cc_final: 0.8344 (m-30) REVERT: B 386 GLU cc_start: 0.8290 (mp0) cc_final: 0.7403 (mp0) REVERT: B 388 LEU cc_start: 0.8889 (mp) cc_final: 0.8440 (mm) REVERT: B 390 VAL cc_start: 0.9257 (t) cc_final: 0.9000 (p) REVERT: B 395 ASP cc_start: 0.7393 (m-30) cc_final: 0.6819 (m-30) REVERT: C 13 ARG cc_start: 0.6355 (tmm-80) cc_final: 0.5931 (tmm-80) REVERT: C 25 CYS cc_start: 0.8310 (t) cc_final: 0.7809 (t) REVERT: C 42 LEU cc_start: 0.6301 (pt) cc_final: 0.5860 (pp) REVERT: C 92 HIS cc_start: 0.6546 (m-70) cc_final: 0.6205 (m90) REVERT: C 104 CYS cc_start: 0.8682 (m) cc_final: 0.6549 (t) REVERT: C 105 HIS cc_start: 0.8722 (m-70) cc_final: 0.8224 (m90) REVERT: C 162 LEU cc_start: 0.9262 (mt) cc_final: 0.8851 (mt) REVERT: C 190 MET cc_start: 0.7675 (mtp) cc_final: 0.7310 (mtp) REVERT: C 191 ILE cc_start: 0.7719 (mt) cc_final: 0.7372 (mt) REVERT: C 225 LYS cc_start: 0.6705 (mttt) cc_final: 0.6477 (mttm) REVERT: C 292 MET cc_start: -0.0563 (mmp) cc_final: -0.1028 (mmp) REVERT: C 317 LEU cc_start: 0.5122 (tp) cc_final: 0.4856 (tp) REVERT: C 337 TYR cc_start: 0.8710 (m-80) cc_final: 0.8053 (m-10) REVERT: C 339 LEU cc_start: 0.8759 (mt) cc_final: 0.8535 (mt) REVERT: C 346 GLU cc_start: 0.7786 (pp20) cc_final: 0.7031 (pp20) REVERT: C 357 MET cc_start: 0.3498 (mmp) cc_final: 0.2453 (mmm) REVERT: C 359 SER cc_start: 0.5950 (m) cc_final: 0.5478 (t) REVERT: C 363 ASN cc_start: 0.9100 (t0) cc_final: 0.8670 (t0) REVERT: C 367 TYR cc_start: 0.7337 (m-80) cc_final: 0.6909 (m-80) REVERT: C 373 LEU cc_start: 0.8412 (tp) cc_final: 0.7856 (tp) REVERT: C 393 MET cc_start: 0.7041 (ptm) cc_final: 0.6584 (ptm) REVERT: D 52 MET cc_start: 0.4140 (mtp) cc_final: 0.3608 (mtp) REVERT: D 65 LEU cc_start: 0.8512 (mt) cc_final: 0.8179 (tp) REVERT: D 66 LEU cc_start: 0.8865 (mt) cc_final: 0.8583 (mm) REVERT: D 68 ASP cc_start: 0.9010 (m-30) cc_final: 0.8158 (m-30) REVERT: D 93 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 127 LEU cc_start: 0.9335 (tp) cc_final: 0.8928 (tp) REVERT: D 144 LYS cc_start: 0.7694 (mttt) cc_final: 0.5272 (ptpt) REVERT: D 148 TYR cc_start: 0.6969 (m-10) cc_final: 0.6217 (m-10) REVERT: D 155 TYR cc_start: 0.8893 (m-80) cc_final: 0.8003 (m-80) REVERT: D 165 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8027 (mm-30) REVERT: D 169 ASN cc_start: 0.6700 (m-40) cc_final: 0.5775 (m-40) REVERT: D 195 LEU cc_start: 0.8871 (mt) cc_final: 0.8526 (mt) REVERT: D 200 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7504 (mppt) REVERT: D 223 LEU cc_start: 0.8566 (mt) cc_final: 0.8122 (mt) REVERT: D 224 GLU cc_start: 0.7454 (pp20) cc_final: 0.7238 (pp20) REVERT: D 227 LYS cc_start: 0.8479 (tttt) cc_final: 0.7004 (tppt) REVERT: D 231 HIS cc_start: 0.7195 (m170) cc_final: 0.6659 (m170) REVERT: D 235 LEU cc_start: 0.8664 (tp) cc_final: 0.8274 (tp) REVERT: D 261 TYR cc_start: 0.7616 (t80) cc_final: 0.7146 (t80) REVERT: D 267 MET cc_start: 0.8075 (tpp) cc_final: 0.7809 (tpt) REVERT: D 300 LEU cc_start: 0.7299 (tp) cc_final: 0.7076 (tp) REVERT: D 301 ASP cc_start: 0.8023 (m-30) cc_final: 0.7750 (m-30) REVERT: D 306 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8056 (mm-30) REVERT: D 307 HIS cc_start: 0.6780 (t70) cc_final: 0.6351 (t70) REVERT: D 310 LEU cc_start: 0.9100 (mt) cc_final: 0.8681 (mp) REVERT: D 318 ASN cc_start: 0.8966 (p0) cc_final: 0.7554 (p0) REVERT: D 320 THR cc_start: 0.8524 (p) cc_final: 0.7868 (p) REVERT: D 328 LEU cc_start: 0.9449 (mm) cc_final: 0.8909 (mm) REVERT: D 329 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7969 (mp0) REVERT: D 345 GLU cc_start: 0.8034 (tp30) cc_final: 0.7688 (tp30) REVERT: D 347 ARG cc_start: 0.7364 (ptt90) cc_final: 0.6443 (ptt90) REVERT: D 351 PHE cc_start: 0.7604 (p90) cc_final: 0.7287 (p90) REVERT: D 360 HIS cc_start: 0.8136 (t70) cc_final: 0.7225 (t70) REVERT: D 372 LYS cc_start: 0.8754 (ptpt) cc_final: 0.7594 (pttp) REVERT: D 375 GLN cc_start: 0.8721 (pt0) cc_final: 0.8408 (pp30) REVERT: D 376 SER cc_start: 0.8369 (t) cc_final: 0.7660 (p) REVERT: D 380 GLN cc_start: 0.8038 (mt0) cc_final: 0.7590 (mt0) REVERT: D 383 ASN cc_start: 0.9274 (m-40) cc_final: 0.7755 (m110) REVERT: D 384 LEU cc_start: 0.8772 (tp) cc_final: 0.7490 (tp) REVERT: D 387 LYS cc_start: 0.9365 (mttt) cc_final: 0.8481 (mttt) REVERT: E 66 VAL cc_start: 0.9252 (t) cc_final: 0.8896 (t) REVERT: E 93 MET cc_start: 0.3287 (tmm) cc_final: 0.2567 (tmm) REVERT: E 117 MET cc_start: 0.7830 (tmm) cc_final: 0.7200 (tmm) REVERT: E 242 TRP cc_start: 0.5103 (t-100) cc_final: 0.4610 (t-100) REVERT: E 286 MET cc_start: -0.1052 (tpt) cc_final: -0.1973 (tpt) REVERT: E 299 LYS cc_start: 0.6542 (mttt) cc_final: 0.6289 (tttt) REVERT: E 302 LYS cc_start: 0.8366 (mttm) cc_final: 0.7750 (mttt) REVERT: E 307 SER cc_start: 0.4876 (m) cc_final: 0.4448 (p) REVERT: F 73 ILE cc_start: 0.7139 (pt) cc_final: 0.6724 (mp) REVERT: F 243 LYS cc_start: 0.8873 (ptpp) cc_final: 0.8635 (ptpp) REVERT: F 252 PHE cc_start: 0.7898 (t80) cc_final: 0.7685 (t80) REVERT: F 254 HIS cc_start: 0.8473 (m-70) cc_final: 0.8220 (m-70) REVERT: F 258 ARG cc_start: 0.5289 (ttp80) cc_final: 0.4957 (ttp80) REVERT: F 275 PHE cc_start: 0.7256 (t80) cc_final: 0.6914 (t80) REVERT: F 284 ASN cc_start: 0.7845 (t0) cc_final: 0.7577 (t0) REVERT: F 288 LEU cc_start: 0.7446 (tt) cc_final: 0.7205 (tt) REVERT: F 289 MET cc_start: 0.8146 (ttt) cc_final: 0.7756 (mmm) REVERT: F 309 PHE cc_start: 0.7716 (t80) cc_final: 0.7246 (t80) REVERT: G 49 LEU cc_start: 0.8772 (mm) cc_final: 0.8336 (pp) REVERT: G 68 ASN cc_start: 0.8923 (m110) cc_final: 0.8703 (m110) REVERT: G 72 TYR cc_start: 0.6162 (m-10) cc_final: 0.5160 (m-10) REVERT: G 85 LEU cc_start: 0.8766 (pt) cc_final: 0.8382 (pt) REVERT: G 96 LEU cc_start: 0.8628 (tp) cc_final: 0.8298 (tt) REVERT: G 112 PRO cc_start: 0.7924 (Cg_exo) cc_final: 0.7688 (Cg_endo) REVERT: G 118 LYS cc_start: 0.7793 (pttt) cc_final: 0.7514 (pttt) REVERT: G 121 GLU cc_start: 0.8532 (pp20) cc_final: 0.7368 (tm-30) REVERT: G 130 ASP cc_start: 0.8715 (m-30) cc_final: 0.8176 (m-30) REVERT: G 150 GLN cc_start: 0.7744 (mt0) cc_final: 0.7338 (mp10) REVERT: G 160 ARG cc_start: 0.8379 (ttt180) cc_final: 0.8060 (mtt-85) REVERT: G 169 ASN cc_start: 0.8457 (m110) cc_final: 0.8212 (m110) REVERT: G 179 ASP cc_start: 0.4996 (m-30) cc_final: 0.4243 (m-30) REVERT: H 22 ASN cc_start: 0.7888 (m110) cc_final: 0.7264 (m110) REVERT: H 24 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 90 TYR cc_start: 0.7616 (m-80) cc_final: 0.7038 (m-80) REVERT: H 96 HIS cc_start: 0.6295 (t70) cc_final: 0.5603 (t70) REVERT: H 98 TRP cc_start: 0.8074 (m100) cc_final: 0.6334 (m100) REVERT: H 110 ARG cc_start: 0.8487 (ttp-110) cc_final: 0.8197 (ttp-110) REVERT: H 132 ASP cc_start: 0.7718 (t0) cc_final: 0.7214 (t70) REVERT: H 133 PHE cc_start: 0.7710 (t80) cc_final: 0.6866 (t80) REVERT: H 137 VAL cc_start: 0.8251 (p) cc_final: 0.8046 (p) REVERT: H 163 LEU cc_start: 0.8378 (mp) cc_final: 0.7698 (mp) REVERT: I 87 THR cc_start: 0.6741 (m) cc_final: 0.6286 (p) REVERT: I 122 GLU cc_start: 0.8461 (pt0) cc_final: 0.7834 (pp20) REVERT: I 149 LYS cc_start: 0.8016 (tttt) cc_final: 0.7569 (tptm) REVERT: I 263 MET cc_start: 0.0744 (mmp) cc_final: 0.0481 (mmp) REVERT: I 268 MET cc_start: 0.6717 (tpt) cc_final: 0.6480 (tpt) REVERT: I 269 MET cc_start: 0.8027 (mpp) cc_final: 0.7068 (mpp) REVERT: I 297 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8006 (tptp) REVERT: I 317 ASP cc_start: 0.6811 (p0) cc_final: 0.6592 (p0) REVERT: I 430 CYS cc_start: 0.5955 (t) cc_final: 0.5241 (t) REVERT: I 511 MET cc_start: 0.1465 (tpt) cc_final: 0.1169 (tpt) REVERT: I 537 PHE cc_start: 0.7450 (t80) cc_final: 0.7240 (t80) REVERT: L 28 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7841 (mmmt) REVERT: L 39 ASN cc_start: 0.7806 (m-40) cc_final: 0.7550 (m-40) REVERT: L 57 LEU cc_start: 0.7978 (mt) cc_final: 0.7762 (mt) REVERT: L 99 ASN cc_start: 0.8193 (p0) cc_final: 0.7991 (p0) REVERT: L 122 ILE cc_start: 0.8026 (pt) cc_final: 0.7710 (pt) REVERT: L 127 ASP cc_start: 0.6474 (t0) cc_final: 0.6118 (t0) REVERT: L 157 ILE cc_start: 0.7416 (mt) cc_final: 0.7169 (mm) REVERT: L 158 ARG cc_start: 0.7947 (ppt170) cc_final: 0.7507 (ttp80) REVERT: L 167 ASP cc_start: 0.8788 (t0) cc_final: 0.8381 (t0) REVERT: L 171 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7884 (ptt180) REVERT: L 189 MET cc_start: 0.8160 (ptp) cc_final: 0.6752 (ptp) REVERT: L 211 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8109 (mm-30) REVERT: L 219 MET cc_start: 0.8532 (mmt) cc_final: 0.8047 (mmp) REVERT: L 242 ASN cc_start: 0.8437 (t0) cc_final: 0.8081 (t0) REVERT: L 246 GLU cc_start: 0.8386 (pp20) cc_final: 0.8173 (pp20) REVERT: L 249 MET cc_start: 0.7256 (tpp) cc_final: 0.6779 (tpp) REVERT: L 250 HIS cc_start: 0.7057 (t-90) cc_final: 0.6797 (t70) REVERT: L 279 MET cc_start: 0.6793 (ttp) cc_final: 0.6331 (ttp) REVERT: L 288 LEU cc_start: 0.8422 (tp) cc_final: 0.7995 (tp) REVERT: L 289 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8218 (pttm) REVERT: L 317 MET cc_start: 0.8230 (mmp) cc_final: 0.7710 (mmm) REVERT: L 357 LEU cc_start: 0.8124 (pp) cc_final: 0.7850 (pp) REVERT: L 358 GLU cc_start: 0.7253 (pp20) cc_final: 0.6668 (pp20) REVERT: L 367 LYS cc_start: 0.8287 (mmtt) cc_final: 0.8077 (mmtm) REVERT: L 390 LEU cc_start: 0.8708 (mt) cc_final: 0.8350 (mt) REVERT: L 393 ASP cc_start: 0.7550 (t0) cc_final: 0.6908 (t70) REVERT: L 395 LYS cc_start: 0.9120 (mmpt) cc_final: 0.8747 (mmmm) REVERT: L 397 LYS cc_start: 0.8324 (mmpt) cc_final: 0.7754 (mmmt) REVERT: L 433 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7213 (mmtt) REVERT: L 435 HIS cc_start: 0.7387 (m90) cc_final: 0.6904 (m-70) REVERT: L 439 ARG cc_start: 0.6927 (ptp-170) cc_final: 0.6722 (ptp-170) REVERT: L 448 ASP cc_start: 0.7200 (t0) cc_final: 0.6785 (t0) REVERT: L 452 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8331 (pttp) REVERT: L 457 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8325 (mmtt) REVERT: L 477 MET cc_start: 0.8028 (tmm) cc_final: 0.7727 (tmm) REVERT: L 504 THR cc_start: 0.1443 (t) cc_final: 0.0150 (t) REVERT: L 522 CYS cc_start: 0.8147 (t) cc_final: 0.6974 (m) REVERT: L 533 GLU cc_start: 0.8018 (tp30) cc_final: 0.6679 (tp30) REVERT: L 534 ILE cc_start: 0.8103 (tp) cc_final: 0.7803 (pt) REVERT: L 535 PHE cc_start: 0.7037 (t80) cc_final: 0.6622 (t80) REVERT: L 554 MET cc_start: 0.7288 (mmp) cc_final: 0.6967 (tpp) REVERT: L 598 GLN cc_start: 0.8185 (mp10) cc_final: 0.7582 (mm-40) REVERT: L 603 MET cc_start: 0.7816 (ptm) cc_final: 0.7341 (ptm) REVERT: L 625 ARG cc_start: 0.8597 (mmp-170) cc_final: 0.7588 (mmp80) REVERT: L 657 HIS cc_start: 0.8168 (p-80) cc_final: 0.7711 (p90) REVERT: L 670 HIS cc_start: 0.8192 (m-70) cc_final: 0.7785 (m-70) REVERT: L 673 LYS cc_start: 0.8429 (tptt) cc_final: 0.7948 (tptt) REVERT: M 110 PHE cc_start: 0.7274 (t80) cc_final: 0.6986 (t80) REVERT: M 123 TYR cc_start: 0.6656 (t80) cc_final: 0.6389 (t80) REVERT: M 149 LYS cc_start: 0.8694 (tttm) cc_final: 0.8003 (tptp) REVERT: M 155 MET cc_start: 0.3559 (ppp) cc_final: 0.3208 (ppp) REVERT: R 24 VAL cc_start: 0.7786 (p) cc_final: 0.7465 (m) REVERT: R 25 LYS cc_start: 0.6095 (mptt) cc_final: 0.5674 (mmtp) REVERT: R 50 MET cc_start: 0.6932 (ptt) cc_final: 0.6485 (ptt) REVERT: R 91 ARG cc_start: 0.7065 (mtt90) cc_final: 0.6555 (mtt90) outliers start: 1 outliers final: 1 residues processed: 1071 average time/residue: 0.5624 time to fit residues: 949.2130 Evaluate side-chains 966 residues out of total 4113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 965 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 4.9990 chunk 386 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 334 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 363 optimal weight: 0.0040 chunk 151 optimal weight: 0.0980 chunk 372 optimal weight: 0.0770 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 412 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS B 220 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 435 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN ** G 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 GLN ** I 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 HIS ** L 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 GLN ** L 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 HIS ** L 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 ASN ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.191516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.150708 restraints weight = 89516.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.156244 restraints weight = 57429.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.160392 restraints weight = 40718.891| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38016 Z= 0.197 Angle : 0.723 13.293 51366 Z= 0.374 Chirality : 0.045 0.256 5749 Planarity : 0.005 0.120 6583 Dihedral : 4.771 27.395 5047 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.14 % Favored : 92.58 % Rotamer: Outliers : 0.02 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4597 helix: 0.81 (0.10), residues: 2668 sheet: -0.59 (0.24), residues: 442 loop : -1.92 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 82 HIS 0.010 0.001 HIS A 106 PHE 0.038 0.002 PHE G 15 TYR 0.042 0.002 TYR A 374 ARG 0.020 0.001 ARG I 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13442.06 seconds wall clock time: 241 minutes 40.88 seconds (14500.88 seconds total)