Starting phenix.real_space_refine on Sun Apr 7 00:47:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fim_31603/04_2024/7fim_31603_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.063 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5877 2.51 5 N 1595 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N GLU 48": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 408": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9213 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2588 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1884 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Chain: "R" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3115 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 5.05, per 1000 atoms: 0.55 Number of scatterers: 9213 At special positions: 0 Unit cell: (79.254, 99.603, 174.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1687 8.00 N 1595 7.00 C 5877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 36.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 90 through 92 No H-bonds generated for 'chain 'N' and resid 90 through 92' Processing helix chain 'B' and resid 11 through 29 removed outlier: 3.765A pdb=" N GLU B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.746A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.904A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.796A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.872A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.140A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.641A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 139 through 168 removed outlier: 3.580A pdb=" N ILE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 204 removed outlier: 3.752A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 215 removed outlier: 3.632A pdb=" N HIS R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 238 removed outlier: 3.935A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 255 removed outlier: 3.581A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 removed outlier: 3.564A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 278 No H-bonds generated for 'chain 'R' and resid 276 through 278' Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 303 through 335 removed outlier: 4.694A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.637A pdb=" N ILE R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 327 " --> pdb=" O ILE R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 4.015A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 386 Processing helix chain 'R' and resid 394 through 403 removed outlier: 4.076A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 421 removed outlier: 3.571A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.577A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.810A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 28 removed outlier: 3.707A pdb=" N ILE P 17 " --> pdb=" O AIB P 13 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.881A pdb=" N THR N 80 " --> pdb=" O ASP N 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP N 75 " --> pdb=" O THR N 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 124 through 126 removed outlier: 4.142A pdb=" N MET N 36 " --> pdb=" O ILE N 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE N 53 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG N 40 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TRP N 49 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA N 42 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU N 47 " --> pdb=" O ALA N 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.709A pdb=" N TYR B 64 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 75 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.656A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 183 through 186 removed outlier: 4.152A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 225 through 228 removed outlier: 4.165A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.837A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.644A pdb=" N LEU B 313 " --> pdb=" O CYS B 299 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.856A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 342 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 218 through 223 removed outlier: 3.897A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL A 248 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 82 through 84 345 hydrogen bonds defined for protein. 1005 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: 2.52 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1492 1.31 - 1.44: 2686 1.44 - 1.57: 5168 1.57 - 1.69: 1 1.69 - 1.82: 73 Bond restraints: 9420 Sorted by residual: bond pdb=" C GLU P 3 " pdb=" N GLY P 4 " ideal model delta sigma weight residual 1.333 1.392 -0.059 1.43e-02 4.89e+03 1.68e+01 bond pdb=" C AIB P 2 " pdb=" N GLU P 3 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " ideal model delta sigma weight residual 1.527 1.586 -0.059 1.75e-02 3.27e+03 1.13e+01 bond pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.30e+00 bond pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.31e-02 5.83e+03 5.18e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 129 105.53 - 112.65: 4753 112.65 - 119.77: 3342 119.77 - 126.90: 4408 126.90 - 134.02: 138 Bond angle restraints: 12770 Sorted by residual: angle pdb=" N ARG A 265 " pdb=" CA ARG A 265 " pdb=" C ARG A 265 " ideal model delta sigma weight residual 114.31 104.68 9.63 1.29e+00 6.01e-01 5.58e+01 angle pdb=" N LEU R 411 " pdb=" CA LEU R 411 " pdb=" C LEU R 411 " ideal model delta sigma weight residual 111.28 106.76 4.52 1.09e+00 8.42e-01 1.72e+01 angle pdb=" CB LYS P 16 " pdb=" CG LYS P 16 " pdb=" CD LYS P 16 " ideal model delta sigma weight residual 111.30 120.47 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.58 114.32 7.26 1.95e+00 2.63e-01 1.39e+01 angle pdb=" CA AIB P 2 " pdb=" C AIB P 2 " pdb=" N GLU P 3 " ideal model delta sigma weight residual 116.20 123.36 -7.16 2.00e+00 2.50e-01 1.28e+01 ... (remaining 12765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5015 17.46 - 34.91: 456 34.91 - 52.37: 74 52.37 - 69.83: 10 69.83 - 87.28: 11 Dihedral angle restraints: 5566 sinusoidal: 2199 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 164.38 -71.38 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA PRO R 55 " pdb=" C PRO R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR B 70 " pdb=" C THR B 70 " pdb=" N ASP B 71 " pdb=" CA ASP B 71 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1064 0.052 - 0.104: 290 0.104 - 0.155: 49 0.155 - 0.207: 4 0.207 - 0.259: 3 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA LEU R 411 " pdb=" N LEU R 411 " pdb=" C LEU R 411 " pdb=" CB LEU R 411 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE R 357 " pdb=" CA ILE R 357 " pdb=" CG1 ILE R 357 " pdb=" CG2 ILE R 357 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL R 319 " pdb=" CA VAL R 319 " pdb=" CG1 VAL R 319 " pdb=" CG2 VAL R 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1407 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 311 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 312 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO R 56 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO G 55 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.025 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1410 2.76 - 3.30: 9011 3.30 - 3.83: 15442 3.83 - 4.37: 17902 4.37 - 4.90: 30002 Nonbonded interactions: 73767 Sorted by model distance: nonbonded pdb=" OD1 ASP N 52 " pdb=" OG SER N 61 " model vdw 2.226 2.440 nonbonded pdb=" O PHE R 367 " pdb=" NZ LYS R 383 " model vdw 2.244 2.520 nonbonded pdb=" O SER N 54 " pdb=" NH1 ARG N 74 " model vdw 2.249 2.520 nonbonded pdb=" OG SER B 152 " pdb=" O VAL B 192 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.256 2.440 ... (remaining 73762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.010 Extract box with map and model: 5.370 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.980 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 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 0.059 9420 Z= 0.226 Angle : 0.835 9.816 12770 Z= 0.458 Chirality : 0.047 0.259 1410 Planarity : 0.005 0.080 1620 Dihedral : 13.919 87.284 3372 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.41 % Allowed : 0.31 % Favored : 99.29 % 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: -2.72 (0.23), residues: 1130 helix: -1.95 (0.21), residues: 438 sheet: -1.54 (0.35), residues: 222 loop : -1.56 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 72 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE N 110 TYR 0.015 0.001 TYR P 10 ARG 0.016 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.6826 (m-10) cc_final: 0.6184 (m-80) REVERT: N 48 GLU cc_start: 0.8312 (pp20) cc_final: 0.7945 (pp20) REVERT: N 111 ASP cc_start: 0.7222 (m-30) cc_final: 0.6950 (t0) REVERT: N 114 SER cc_start: 0.8260 (t) cc_final: 0.7461 (m) REVERT: N 115 THR cc_start: 0.8470 (p) cc_final: 0.8207 (p) REVERT: B 17 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 49 GLN cc_start: 0.6725 (pp30) cc_final: 0.6380 (pp30) REVERT: B 63 ILE cc_start: 0.6849 (mt) cc_final: 0.6571 (mm) REVERT: B 194 SER cc_start: 0.8287 (t) cc_final: 0.8079 (p) REVERT: B 248 THR cc_start: 0.7754 (p) cc_final: 0.7542 (p) REVERT: B 251 ASP cc_start: 0.7170 (t0) cc_final: 0.6789 (m-30) REVERT: B 264 GLN cc_start: 0.7312 (pt0) cc_final: 0.6703 (tm-30) REVERT: B 285 LYS cc_start: 0.6623 (pptt) cc_final: 0.5466 (mmpt) REVERT: A 265 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6787 (tpt170) REVERT: A 343 ASP cc_start: 0.8150 (m-30) cc_final: 0.7592 (m-30) REVERT: A 356 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6531 (mtm180) REVERT: A 377 ASN cc_start: 0.6999 (m-40) cc_final: 0.6494 (m110) REVERT: R 44 ARG cc_start: 0.9093 (ttp-110) cc_final: 0.8760 (ttp80) REVERT: R 74 ASP cc_start: 0.7590 (t0) cc_final: 0.7258 (t0) REVERT: R 170 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7141 (mmm-85) REVERT: R 336 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7188 (mtmt) REVERT: R 397 MET cc_start: 0.6642 (mmp) cc_final: 0.5786 (mtt) REVERT: G 9 ILE cc_start: 0.8573 (mt) cc_final: 0.8284 (mm) REVERT: G 14 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8627 (pttt) REVERT: G 17 GLU cc_start: 0.9169 (pp20) cc_final: 0.8939 (pp20) REVERT: P 25 TRP cc_start: 0.6556 (t60) cc_final: 0.6266 (t60) outliers start: 4 outliers final: 2 residues processed: 319 average time/residue: 0.2649 time to fit residues: 109.2361 Evaluate side-chains 195 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain R residue 320 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 76 ASN A 267 GLN R 177 ASN R 210 GLN R 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9420 Z= 0.283 Angle : 0.634 11.319 12770 Z= 0.328 Chirality : 0.044 0.183 1410 Planarity : 0.005 0.078 1620 Dihedral : 5.235 57.326 1273 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.36 % Allowed : 11.30 % Favored : 85.34 % 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: -1.78 (0.24), residues: 1130 helix: -0.75 (0.24), residues: 443 sheet: -1.34 (0.35), residues: 230 loop : -1.34 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 49 HIS 0.009 0.001 HIS R 212 PHE 0.019 0.002 PHE N 110 TYR 0.019 0.002 TYR R 145 ARG 0.006 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7290 (m-10) cc_final: 0.6596 (m-10) REVERT: N 111 ASP cc_start: 0.7564 (m-30) cc_final: 0.7101 (t0) REVERT: N 114 SER cc_start: 0.8522 (t) cc_final: 0.7932 (t) REVERT: N 122 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7803 (pt0) REVERT: B 174 TRP cc_start: 0.8304 (m100) cc_final: 0.7966 (m100) REVERT: B 231 GLU cc_start: 0.7780 (pt0) cc_final: 0.6797 (pt0) REVERT: B 248 THR cc_start: 0.7632 (p) cc_final: 0.7399 (p) REVERT: B 264 GLN cc_start: 0.7437 (pt0) cc_final: 0.6724 (pt0) REVERT: B 285 LYS cc_start: 0.7041 (pptt) cc_final: 0.6011 (mmpt) REVERT: A 229 ASP cc_start: 0.8112 (t0) cc_final: 0.7892 (p0) REVERT: A 356 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6555 (mtm-85) REVERT: A 392 GLU cc_start: 0.7840 (pm20) cc_final: 0.7392 (mp0) REVERT: R 74 ASP cc_start: 0.7629 (t0) cc_final: 0.7363 (t0) REVERT: R 170 ARG cc_start: 0.7697 (tpp80) cc_final: 0.7298 (mmm-85) REVERT: R 215 ASP cc_start: 0.8209 (m-30) cc_final: 0.7440 (p0) REVERT: R 303 MET cc_start: 0.8641 (ptp) cc_final: 0.8407 (ptp) REVERT: R 304 ASN cc_start: 0.7284 (m-40) cc_final: 0.6244 (t0) REVERT: R 329 CYS cc_start: 0.8039 (t) cc_final: 0.7722 (m) REVERT: R 336 LYS cc_start: 0.7739 (mmtt) cc_final: 0.6863 (mtmm) REVERT: R 397 MET cc_start: 0.6875 (mmp) cc_final: 0.5901 (mtm) REVERT: R 412 GLU cc_start: 0.7575 (tp30) cc_final: 0.7280 (tm-30) REVERT: G 9 ILE cc_start: 0.8553 (mt) cc_final: 0.7971 (mm) REVERT: G 13 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8185 (ptp-110) REVERT: G 14 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8691 (pttt) REVERT: G 42 GLU cc_start: 0.8791 (pp20) cc_final: 0.8589 (pp20) outliers start: 33 outliers final: 23 residues processed: 224 average time/residue: 0.2519 time to fit residues: 74.4590 Evaluate side-chains 201 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 76 ASN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9420 Z= 0.238 Angle : 0.580 7.567 12770 Z= 0.302 Chirality : 0.043 0.149 1410 Planarity : 0.004 0.079 1620 Dihedral : 4.730 50.335 1267 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.67 % Allowed : 14.66 % Favored : 81.67 % 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: -1.43 (0.25), residues: 1130 helix: -0.31 (0.24), residues: 452 sheet: -1.27 (0.35), residues: 231 loop : -1.25 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 49 HIS 0.003 0.001 HIS G 44 PHE 0.020 0.001 PHE A 376 TYR 0.017 0.001 TYR N 34 ARG 0.010 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.042 Fit side-chains TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.7961 (pp20) cc_final: 0.7571 (pt0) REVERT: N 122 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7789 (pt0) REVERT: B 132 LYS cc_start: 0.8931 (pttt) cc_final: 0.8595 (pttm) REVERT: B 139 ARG cc_start: 0.6999 (ptp-170) cc_final: 0.6748 (ptm160) REVERT: B 177 GLU cc_start: 0.7151 (mp0) cc_final: 0.6886 (mp0) REVERT: B 231 GLU cc_start: 0.7727 (pt0) cc_final: 0.6613 (pt0) REVERT: B 264 GLN cc_start: 0.7548 (pt0) cc_final: 0.6815 (pt0) REVERT: B 265 GLU cc_start: 0.8497 (tt0) cc_final: 0.8276 (tt0) REVERT: B 285 LYS cc_start: 0.7169 (pptt) cc_final: 0.6183 (mmpt) REVERT: A 15 GLU cc_start: 0.8242 (mp0) cc_final: 0.7930 (mp0) REVERT: A 229 ASP cc_start: 0.8262 (t0) cc_final: 0.8054 (p0) REVERT: A 333 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7502 (mtp180) REVERT: A 392 GLU cc_start: 0.7874 (pm20) cc_final: 0.7181 (mm-30) REVERT: R 74 ASP cc_start: 0.7623 (t0) cc_final: 0.7388 (t0) REVERT: R 170 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7095 (mmm-85) REVERT: R 215 ASP cc_start: 0.8159 (m-30) cc_final: 0.7354 (p0) REVERT: R 329 CYS cc_start: 0.7948 (t) cc_final: 0.7695 (m) REVERT: R 336 LYS cc_start: 0.7636 (mmtt) cc_final: 0.6852 (mtmm) REVERT: R 397 MET cc_start: 0.6878 (mmp) cc_final: 0.5990 (mtm) REVERT: G 9 ILE cc_start: 0.8682 (mt) cc_final: 0.8438 (mm) REVERT: G 14 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8704 (pttt) REVERT: P 19 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6774 (tt0) outliers start: 36 outliers final: 29 residues processed: 214 average time/residue: 0.2421 time to fit residues: 68.8277 Evaluate side-chains 201 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.218 Angle : 0.565 10.360 12770 Z= 0.291 Chirality : 0.042 0.204 1410 Planarity : 0.004 0.079 1620 Dihedral : 4.615 51.975 1267 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.67 % Allowed : 17.92 % Favored : 78.41 % 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: -1.23 (0.25), residues: 1130 helix: 0.05 (0.25), residues: 446 sheet: -1.33 (0.33), residues: 245 loop : -1.25 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.004 0.001 HIS R 363 PHE 0.021 0.001 PHE A 376 TYR 0.014 0.001 TYR R 145 ARG 0.005 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8023 (pp20) cc_final: 0.7647 (pt0) REVERT: N 122 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7811 (pt0) REVERT: B 132 LYS cc_start: 0.8884 (pttt) cc_final: 0.8576 (pttm) REVERT: B 139 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.6729 (ptm160) REVERT: B 177 GLU cc_start: 0.7168 (mp0) cc_final: 0.6888 (mp0) REVERT: B 231 GLU cc_start: 0.7842 (pt0) cc_final: 0.6576 (pt0) REVERT: B 239 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: B 264 GLN cc_start: 0.7513 (pt0) cc_final: 0.6782 (pt0) REVERT: B 265 GLU cc_start: 0.8572 (tt0) cc_final: 0.8347 (tt0) REVERT: B 285 LYS cc_start: 0.7004 (pptt) cc_final: 0.6075 (mmpt) REVERT: A 15 GLU cc_start: 0.8284 (mp0) cc_final: 0.7970 (mp0) REVERT: A 20 ARG cc_start: 0.8231 (ptp-170) cc_final: 0.7973 (mtm110) REVERT: A 229 ASP cc_start: 0.8315 (t0) cc_final: 0.8000 (p0) REVERT: A 392 GLU cc_start: 0.7848 (pm20) cc_final: 0.7185 (mm-30) REVERT: R 74 ASP cc_start: 0.7663 (t0) cc_final: 0.7414 (t0) REVERT: R 303 MET cc_start: 0.8678 (ptp) cc_final: 0.8230 (ptp) REVERT: R 329 CYS cc_start: 0.7858 (t) cc_final: 0.7640 (m) REVERT: R 336 LYS cc_start: 0.7677 (mmtt) cc_final: 0.6886 (mtmm) REVERT: R 397 MET cc_start: 0.6878 (mmp) cc_final: 0.5969 (mtm) REVERT: R 408 GLU cc_start: 0.8189 (mp0) cc_final: 0.7856 (mp0) REVERT: G 14 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8781 (ptmt) REVERT: G 28 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (mm) REVERT: P 19 GLN cc_start: 0.7116 (mm-40) cc_final: 0.6883 (tt0) outliers start: 36 outliers final: 27 residues processed: 206 average time/residue: 0.2460 time to fit residues: 68.2411 Evaluate side-chains 201 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.209 Angle : 0.553 9.140 12770 Z= 0.284 Chirality : 0.042 0.215 1410 Planarity : 0.004 0.079 1620 Dihedral : 4.538 55.096 1267 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.18 % Allowed : 18.94 % Favored : 76.88 % 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: -1.06 (0.25), residues: 1130 helix: 0.33 (0.26), residues: 439 sheet: -1.41 (0.32), residues: 251 loop : -1.17 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 49 HIS 0.003 0.001 HIS R 363 PHE 0.022 0.001 PHE A 376 TYR 0.013 0.001 TYR R 145 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.137 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7686 (m-80) cc_final: 0.7062 (m-80) REVERT: N 48 GLU cc_start: 0.8012 (pp20) cc_final: 0.7688 (pt0) REVERT: N 89 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7317 (mtpt) REVERT: N 122 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7671 (pt0) REVERT: B 132 LYS cc_start: 0.8848 (pttt) cc_final: 0.8561 (pttm) REVERT: B 139 ARG cc_start: 0.6860 (ptp-170) cc_final: 0.6645 (ptm160) REVERT: B 177 GLU cc_start: 0.7154 (mp0) cc_final: 0.6889 (mp0) REVERT: B 196 SER cc_start: 0.8079 (t) cc_final: 0.7312 (t) REVERT: B 222 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.5583 (ppp) REVERT: B 231 GLU cc_start: 0.7855 (pt0) cc_final: 0.7537 (pt0) REVERT: B 239 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: B 264 GLN cc_start: 0.7522 (pt0) cc_final: 0.6783 (pt0) REVERT: B 265 GLU cc_start: 0.8626 (tt0) cc_final: 0.8369 (tt0) REVERT: B 285 LYS cc_start: 0.7140 (pptt) cc_final: 0.6202 (mmpt) REVERT: A 15 GLU cc_start: 0.8340 (mp0) cc_final: 0.7897 (mp0) REVERT: A 20 ARG cc_start: 0.8263 (ptp-170) cc_final: 0.8000 (mtm110) REVERT: A 221 MET cc_start: 0.8400 (mmm) cc_final: 0.8075 (tpp) REVERT: A 229 ASP cc_start: 0.8336 (t0) cc_final: 0.7846 (p0) REVERT: A 333 ARG cc_start: 0.7855 (mmp80) cc_final: 0.7395 (mtp-110) REVERT: A 343 ASP cc_start: 0.8101 (m-30) cc_final: 0.7578 (t70) REVERT: A 392 GLU cc_start: 0.7784 (pm20) cc_final: 0.7170 (mt-10) REVERT: R 74 ASP cc_start: 0.7676 (t0) cc_final: 0.7427 (t0) REVERT: R 215 ASP cc_start: 0.8177 (m-30) cc_final: 0.7410 (p0) REVERT: R 329 CYS cc_start: 0.7948 (t) cc_final: 0.7724 (m) REVERT: R 336 LYS cc_start: 0.7677 (mmtt) cc_final: 0.6863 (mtmm) REVERT: R 397 MET cc_start: 0.6822 (mmp) cc_final: 0.5904 (mtm) REVERT: G 14 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8777 (ptmt) REVERT: P 19 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6532 (mt0) outliers start: 41 outliers final: 31 residues processed: 197 average time/residue: 0.2399 time to fit residues: 63.4708 Evaluate side-chains 205 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 220 HIS ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9420 Z= 0.232 Angle : 0.565 9.653 12770 Z= 0.289 Chirality : 0.042 0.199 1410 Planarity : 0.004 0.080 1620 Dihedral : 4.550 58.832 1267 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.58 % Allowed : 18.53 % Favored : 76.88 % 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: -0.95 (0.25), residues: 1130 helix: 0.42 (0.26), residues: 439 sheet: -1.37 (0.32), residues: 246 loop : -1.11 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.002 0.001 HIS G 44 PHE 0.022 0.001 PHE A 376 TYR 0.022 0.001 TYR P 10 ARG 0.010 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 0.950 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7824 (m-80) cc_final: 0.7367 (m-80) REVERT: N 48 GLU cc_start: 0.7968 (pp20) cc_final: 0.7667 (pt0) REVERT: N 122 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7648 (pt0) REVERT: B 132 LYS cc_start: 0.8824 (pttt) cc_final: 0.8552 (pttm) REVERT: B 139 ARG cc_start: 0.6787 (ptp-170) cc_final: 0.6480 (ptm160) REVERT: B 177 GLU cc_start: 0.7116 (mp0) cc_final: 0.6866 (mp0) REVERT: B 196 SER cc_start: 0.8123 (t) cc_final: 0.7316 (t) REVERT: B 222 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6529 (pmm) REVERT: B 231 GLU cc_start: 0.7891 (pt0) cc_final: 0.6927 (pt0) REVERT: B 239 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: B 264 GLN cc_start: 0.7671 (pt0) cc_final: 0.6902 (pt0) REVERT: B 265 GLU cc_start: 0.8646 (tt0) cc_final: 0.8391 (tt0) REVERT: B 285 LYS cc_start: 0.7169 (pptt) cc_final: 0.6223 (mmpt) REVERT: A 15 GLU cc_start: 0.8365 (mp0) cc_final: 0.7910 (mp0) REVERT: A 20 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.8017 (mtm110) REVERT: A 221 MET cc_start: 0.8388 (mmm) cc_final: 0.8087 (tpp) REVERT: A 229 ASP cc_start: 0.8363 (t0) cc_final: 0.7854 (p0) REVERT: A 343 ASP cc_start: 0.8090 (m-30) cc_final: 0.7587 (t70) REVERT: A 392 GLU cc_start: 0.7771 (pm20) cc_final: 0.7284 (mm-30) REVERT: R 74 ASP cc_start: 0.7703 (t0) cc_final: 0.7462 (t0) REVERT: R 198 ASP cc_start: 0.6918 (p0) cc_final: 0.6712 (p0) REVERT: R 215 ASP cc_start: 0.8152 (m-30) cc_final: 0.7347 (p0) REVERT: R 303 MET cc_start: 0.8661 (ptp) cc_final: 0.8211 (ptp) REVERT: R 336 LYS cc_start: 0.7470 (mmtt) cc_final: 0.6632 (mtmm) REVERT: R 397 MET cc_start: 0.6843 (mmp) cc_final: 0.5910 (mtm) REVERT: G 14 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8803 (ptmt) REVERT: G 48 ASP cc_start: 0.5522 (t70) cc_final: 0.5172 (t0) REVERT: P 19 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6734 (mt0) outliers start: 45 outliers final: 34 residues processed: 199 average time/residue: 0.2380 time to fit residues: 64.0652 Evaluate side-chains 199 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 383 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.200 Angle : 0.569 10.661 12770 Z= 0.287 Chirality : 0.042 0.212 1410 Planarity : 0.004 0.080 1620 Dihedral : 4.488 58.621 1267 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 19.35 % Favored : 76.68 % 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: -0.83 (0.25), residues: 1130 helix: 0.53 (0.26), residues: 440 sheet: -1.31 (0.32), residues: 246 loop : -1.06 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.002 0.001 HIS A 220 PHE 0.022 0.001 PHE A 376 TYR 0.014 0.001 TYR P 10 ARG 0.015 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.128 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7675 (m-80) cc_final: 0.7200 (m-80) REVERT: N 89 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7244 (mtpt) REVERT: N 122 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7645 (pt0) REVERT: B 132 LYS cc_start: 0.8923 (pttt) cc_final: 0.8629 (pttm) REVERT: B 139 ARG cc_start: 0.6763 (ptp-170) cc_final: 0.6458 (ptm160) REVERT: B 174 TRP cc_start: 0.8248 (m100) cc_final: 0.7948 (m100) REVERT: B 177 GLU cc_start: 0.7207 (mp0) cc_final: 0.6952 (mp0) REVERT: B 196 SER cc_start: 0.8077 (t) cc_final: 0.7270 (t) REVERT: B 222 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6586 (pmm) REVERT: B 231 GLU cc_start: 0.7848 (pt0) cc_final: 0.6876 (pt0) REVERT: B 239 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: B 264 GLN cc_start: 0.7648 (pt0) cc_final: 0.6862 (pt0) REVERT: B 265 GLU cc_start: 0.8671 (tt0) cc_final: 0.8415 (tt0) REVERT: B 285 LYS cc_start: 0.7158 (pptt) cc_final: 0.6203 (mmmt) REVERT: A 15 GLU cc_start: 0.8403 (mp0) cc_final: 0.7949 (mp0) REVERT: A 20 ARG cc_start: 0.8291 (ptp-170) cc_final: 0.8022 (mtm110) REVERT: A 229 ASP cc_start: 0.8254 (t0) cc_final: 0.7768 (p0) REVERT: A 343 ASP cc_start: 0.8079 (m-30) cc_final: 0.7601 (t70) REVERT: A 392 GLU cc_start: 0.7738 (pm20) cc_final: 0.7236 (mm-30) REVERT: R 46 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6883 (p) REVERT: R 74 ASP cc_start: 0.7692 (t0) cc_final: 0.7437 (t0) REVERT: R 198 ASP cc_start: 0.6929 (p0) cc_final: 0.6722 (p0) REVERT: R 215 ASP cc_start: 0.8131 (m-30) cc_final: 0.7300 (p0) REVERT: R 303 MET cc_start: 0.8646 (ptp) cc_final: 0.8122 (ptp) REVERT: R 336 LYS cc_start: 0.7480 (mmtt) cc_final: 0.6643 (mtmm) REVERT: R 397 MET cc_start: 0.6843 (mmp) cc_final: 0.5919 (mtm) REVERT: G 48 ASP cc_start: 0.5581 (t70) cc_final: 0.5291 (t0) REVERT: P 19 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6822 (mt0) outliers start: 39 outliers final: 28 residues processed: 196 average time/residue: 0.2513 time to fit residues: 66.8253 Evaluate side-chains 195 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN A 59 GLN A 220 HIS ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9420 Z= 0.195 Angle : 0.566 10.844 12770 Z= 0.287 Chirality : 0.042 0.199 1410 Planarity : 0.004 0.081 1620 Dihedral : 4.441 56.273 1267 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.28 % Allowed : 19.35 % Favored : 76.37 % 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: -0.78 (0.25), residues: 1130 helix: 0.61 (0.26), residues: 440 sheet: -1.30 (0.32), residues: 241 loop : -1.07 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 49 HIS 0.001 0.001 HIS A 357 PHE 0.022 0.001 PHE A 376 TYR 0.013 0.001 TYR P 10 ARG 0.011 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 0.959 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7702 (m-80) cc_final: 0.7241 (m-80) REVERT: N 89 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7211 (mtpt) REVERT: N 122 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7662 (pt0) REVERT: B 64 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7873 (t80) REVERT: B 132 LYS cc_start: 0.8905 (pttt) cc_final: 0.8622 (pttm) REVERT: B 139 ARG cc_start: 0.6689 (ptp-170) cc_final: 0.6409 (ptm160) REVERT: B 174 TRP cc_start: 0.8249 (m100) cc_final: 0.7951 (m100) REVERT: B 177 GLU cc_start: 0.7195 (mp0) cc_final: 0.6951 (mp0) REVERT: B 196 SER cc_start: 0.8067 (t) cc_final: 0.7263 (t) REVERT: B 222 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6631 (pmm) REVERT: B 231 GLU cc_start: 0.7838 (pt0) cc_final: 0.6866 (pt0) REVERT: B 239 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: B 264 GLN cc_start: 0.7686 (pt0) cc_final: 0.7009 (pt0) REVERT: B 265 GLU cc_start: 0.8522 (tt0) cc_final: 0.8267 (tt0) REVERT: B 285 LYS cc_start: 0.7148 (pptt) cc_final: 0.6217 (mmmt) REVERT: A 15 GLU cc_start: 0.8393 (mp0) cc_final: 0.7924 (mp0) REVERT: A 20 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.8024 (mtm110) REVERT: A 229 ASP cc_start: 0.8302 (t0) cc_final: 0.7771 (p0) REVERT: A 286 SER cc_start: 0.8584 (p) cc_final: 0.8029 (m) REVERT: A 343 ASP cc_start: 0.8044 (m-30) cc_final: 0.7575 (t70) REVERT: A 392 GLU cc_start: 0.7722 (pm20) cc_final: 0.7220 (mm-30) REVERT: R 46 CYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6764 (p) REVERT: R 74 ASP cc_start: 0.7692 (t0) cc_final: 0.7440 (t0) REVERT: R 215 ASP cc_start: 0.8043 (m-30) cc_final: 0.7224 (p0) REVERT: R 303 MET cc_start: 0.8625 (ptp) cc_final: 0.8044 (ptp) REVERT: R 336 LYS cc_start: 0.7474 (mmtt) cc_final: 0.6632 (mtmm) REVERT: R 397 MET cc_start: 0.6835 (mmp) cc_final: 0.5915 (mtm) REVERT: G 48 ASP cc_start: 0.5624 (t70) cc_final: 0.5315 (t0) REVERT: P 19 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6853 (mt0) outliers start: 42 outliers final: 31 residues processed: 198 average time/residue: 0.2301 time to fit residues: 61.5997 Evaluate side-chains 201 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 383 LYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 59 GLN R 182 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9420 Z= 0.202 Angle : 0.561 9.222 12770 Z= 0.288 Chirality : 0.042 0.254 1410 Planarity : 0.004 0.082 1620 Dihedral : 4.407 54.347 1267 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.18 % Allowed : 19.65 % Favored : 76.17 % 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: -0.73 (0.25), residues: 1130 helix: 0.66 (0.26), residues: 437 sheet: -1.28 (0.32), residues: 241 loop : -1.04 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 49 HIS 0.001 0.001 HIS B 188 PHE 0.023 0.001 PHE A 376 TYR 0.012 0.001 TYR N 97 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7786 (m-80) cc_final: 0.7262 (m-80) REVERT: N 89 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7237 (mtpt) REVERT: N 122 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7627 (pt0) REVERT: B 51 ARG cc_start: 0.6897 (mmp80) cc_final: 0.6493 (mtm110) REVERT: B 64 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 132 LYS cc_start: 0.8893 (pttt) cc_final: 0.8617 (pttm) REVERT: B 139 ARG cc_start: 0.6679 (ptp-170) cc_final: 0.6343 (ptm160) REVERT: B 143 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7333 (mp0) REVERT: B 174 TRP cc_start: 0.8255 (m100) cc_final: 0.8013 (m100) REVERT: B 177 GLU cc_start: 0.7329 (mp0) cc_final: 0.7071 (mp0) REVERT: B 196 SER cc_start: 0.8085 (t) cc_final: 0.7288 (t) REVERT: B 222 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6656 (pmm) REVERT: B 231 GLU cc_start: 0.7867 (pt0) cc_final: 0.6869 (pt0) REVERT: B 239 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: B 264 GLN cc_start: 0.7619 (pt0) cc_final: 0.6932 (pt0) REVERT: B 265 GLU cc_start: 0.8519 (tt0) cc_final: 0.8261 (tt0) REVERT: B 285 LYS cc_start: 0.7180 (pptt) cc_final: 0.6230 (mmmt) REVERT: A 15 GLU cc_start: 0.8423 (mp0) cc_final: 0.7952 (mp0) REVERT: A 20 ARG cc_start: 0.8300 (ptp-170) cc_final: 0.8031 (mtm110) REVERT: A 60 MET cc_start: 0.7160 (mtt) cc_final: 0.6877 (mtt) REVERT: A 229 ASP cc_start: 0.8321 (t0) cc_final: 0.7776 (p0) REVERT: A 333 ARG cc_start: 0.7764 (mmp80) cc_final: 0.7290 (mtp180) REVERT: A 343 ASP cc_start: 0.8046 (m-30) cc_final: 0.7581 (t70) REVERT: A 392 GLU cc_start: 0.7704 (pm20) cc_final: 0.7259 (mm-30) REVERT: R 33 TRP cc_start: 0.8291 (t-100) cc_final: 0.7920 (t-100) REVERT: R 74 ASP cc_start: 0.7677 (t0) cc_final: 0.7407 (t0) REVERT: R 215 ASP cc_start: 0.8074 (m-30) cc_final: 0.7286 (p0) REVERT: R 303 MET cc_start: 0.8608 (ptp) cc_final: 0.7999 (ptp) REVERT: R 336 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6457 (mtmm) REVERT: G 13 ARG cc_start: 0.9155 (mtp85) cc_final: 0.8855 (ptp-110) REVERT: G 48 ASP cc_start: 0.5666 (t70) cc_final: 0.5379 (t0) REVERT: P 19 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6804 (mt0) outliers start: 41 outliers final: 34 residues processed: 196 average time/residue: 0.2419 time to fit residues: 63.7165 Evaluate side-chains 204 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 383 LYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.0980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9420 Z= 0.176 Angle : 0.558 9.210 12770 Z= 0.284 Chirality : 0.042 0.213 1410 Planarity : 0.004 0.082 1620 Dihedral : 4.352 53.239 1267 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.56 % Allowed : 20.57 % Favored : 75.87 % 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: -0.67 (0.25), residues: 1130 helix: 0.70 (0.26), residues: 440 sheet: -1.21 (0.33), residues: 233 loop : -1.03 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 49 HIS 0.004 0.001 HIS R 180 PHE 0.024 0.001 PHE A 376 TYR 0.014 0.001 TYR P 10 ARG 0.004 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 34 TYR cc_start: 0.7760 (m-80) cc_final: 0.7252 (m-80) REVERT: N 89 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7266 (mtpt) REVERT: N 122 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7656 (pt0) REVERT: B 51 ARG cc_start: 0.6872 (mmp80) cc_final: 0.6449 (mtm110) REVERT: B 64 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7889 (t80) REVERT: B 132 LYS cc_start: 0.8884 (pttt) cc_final: 0.8615 (pttm) REVERT: B 139 ARG cc_start: 0.6646 (ptp-170) cc_final: 0.6234 (ptm160) REVERT: B 143 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7387 (mp0) REVERT: B 177 GLU cc_start: 0.7329 (mp0) cc_final: 0.7076 (mp0) REVERT: B 196 SER cc_start: 0.8105 (t) cc_final: 0.7283 (t) REVERT: B 222 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6664 (pmm) REVERT: B 231 GLU cc_start: 0.7852 (pt0) cc_final: 0.6858 (pt0) REVERT: B 239 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: B 264 GLN cc_start: 0.7648 (pt0) cc_final: 0.6983 (pm20) REVERT: B 265 GLU cc_start: 0.8532 (tt0) cc_final: 0.8277 (tt0) REVERT: B 273 ASN cc_start: 0.8325 (t0) cc_final: 0.7988 (m110) REVERT: B 285 LYS cc_start: 0.7168 (pptt) cc_final: 0.6245 (mmmt) REVERT: A 15 GLU cc_start: 0.8382 (mp0) cc_final: 0.7925 (mp0) REVERT: A 20 ARG cc_start: 0.8295 (ptp-170) cc_final: 0.8030 (mtm110) REVERT: A 229 ASP cc_start: 0.8376 (t0) cc_final: 0.7811 (p0) REVERT: A 333 ARG cc_start: 0.7767 (mmp80) cc_final: 0.7286 (mtp180) REVERT: A 343 ASP cc_start: 0.8042 (m-30) cc_final: 0.7583 (t70) REVERT: A 392 GLU cc_start: 0.7622 (pm20) cc_final: 0.7192 (mm-30) REVERT: R 33 TRP cc_start: 0.8258 (t-100) cc_final: 0.7890 (t-100) REVERT: R 74 ASP cc_start: 0.7682 (t0) cc_final: 0.7405 (t0) REVERT: R 215 ASP cc_start: 0.8070 (m-30) cc_final: 0.7286 (p0) REVERT: R 303 MET cc_start: 0.8599 (ptp) cc_final: 0.7974 (ptp) REVERT: R 336 LYS cc_start: 0.7315 (mmtt) cc_final: 0.6474 (mtmm) REVERT: R 397 MET cc_start: 0.7318 (mmm) cc_final: 0.6015 (mtm) REVERT: G 13 ARG cc_start: 0.9159 (mtp85) cc_final: 0.8508 (ptp-110) REVERT: P 19 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6804 (mt0) outliers start: 35 outliers final: 31 residues processed: 195 average time/residue: 0.2665 time to fit residues: 69.5804 Evaluate side-chains 202 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 383 LYS Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.0470 chunk 5 optimal weight: 0.0870 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN R 182 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.159284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123975 restraints weight = 12880.191| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.52 r_work: 0.3389 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9420 Z= 0.171 Angle : 0.556 9.040 12770 Z= 0.283 Chirality : 0.041 0.208 1410 Planarity : 0.004 0.083 1620 Dihedral : 4.298 52.212 1267 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.56 % Allowed : 21.59 % Favored : 74.85 % 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: -0.60 (0.25), residues: 1130 helix: 0.74 (0.26), residues: 440 sheet: -1.09 (0.33), residues: 230 loop : -1.04 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 49 HIS 0.004 0.001 HIS R 180 PHE 0.023 0.001 PHE A 376 TYR 0.012 0.001 TYR N 97 ARG 0.004 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.02 seconds wall clock time: 45 minutes 44.30 seconds (2744.30 seconds total)