Starting phenix.real_space_refine on Fri Mar 15 15:41:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjx_22216/03_2024/6xjx_22216_neut.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. 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 68 5.16 5 C 7808 2.51 5 N 2039 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 201": "NH1" <-> "NH2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "Q ARG 107": "NH1" <-> "NH2" Residue "Q ARG 221": "NH1" <-> "NH2" Residue "Q ARG 325": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 242": "NH1" <-> "NH2" Residue "R ARG 253": "NH1" <-> "NH2" Residue "R ARG 304": "NH1" <-> "NH2" Residue "R ARG 352": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12077 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1281 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "B" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "C" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1281 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "E" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1296 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1271 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "H" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2972 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 9, 'TRANS': 357} Chain: "R" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2425 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 3, 'TRANS': 287} Chain breaks: 1 Time building chain proxies: 6.55, per 1000 atoms: 0.54 Number of scatterers: 12077 At special positions: 0 Unit cell: (99.96, 128.282, 161.602, 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 68 16.00 O 2162 8.00 N 2039 7.00 C 7808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 3 sheets defined 74.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.925A pdb=" N GLN A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 removed outlier: 4.404A pdb=" N ARG A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.560A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 Processing helix chain 'A' and resid 313 through 336 removed outlier: 4.190A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 97 removed outlier: 4.123A pdb=" N ILE B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) Proline residue: B 76 - end of helix Processing helix chain 'C' and resid 192 through 257 removed outlier: 3.502A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 4.295A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 284 removed outlier: 3.592A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 311 removed outlier: 4.189A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 96 removed outlier: 4.087A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 256 Proline residue: E 216 - end of helix removed outlier: 3.696A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 249 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 285 Proline residue: E 265 - end of helix removed outlier: 3.719A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 311 Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.540A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 96 Proline residue: F 76 - end of helix removed outlier: 3.725A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 257 removed outlier: 3.879A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.610A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.973A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 310 removed outlier: 4.179A pdb=" N GLY G 306 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 340 removed outlier: 3.601A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) Proline residue: G 337 - end of helix Processing helix chain 'H' and resid 65 through 96 removed outlier: 4.027A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.506A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 122 Processing helix chain 'Q' and resid 123 through 132 Processing helix chain 'Q' and resid 148 through 157 Processing helix chain 'Q' and resid 193 through 198 Processing helix chain 'Q' and resid 205 through 217 Processing helix chain 'Q' and resid 219 through 230 removed outlier: 3.701A pdb=" N PHE Q 223 " --> pdb=" O PRO Q 219 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE Q 230 " --> pdb=" O ALA Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 251 Processing helix chain 'Q' and resid 268 through 281 Processing helix chain 'Q' and resid 292 through 314 Processing helix chain 'Q' and resid 315 through 316 No H-bonds generated for 'chain 'Q' and resid 315 through 316' Processing helix chain 'Q' and resid 317 through 321 Processing helix chain 'Q' and resid 323 through 332 Processing helix chain 'Q' and resid 338 through 350 Processing helix chain 'Q' and resid 360 through 375 removed outlier: 3.870A pdb=" N VAL Q 364 " --> pdb=" O THR Q 360 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS Q 372 " --> pdb=" O PHE Q 368 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN Q 373 " --> pdb=" O THR Q 369 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN Q 375 " --> pdb=" O LEU Q 371 " (cutoff:3.500A) Processing helix chain 'Q' and resid 377 through 387 removed outlier: 3.718A pdb=" N MET Q 386 " --> pdb=" O SER Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 404 Processing helix chain 'Q' and resid 409 through 421 removed outlier: 3.741A pdb=" N CYS Q 413 " --> pdb=" O SER Q 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 429 through 443 removed outlier: 3.553A pdb=" N PHE Q 433 " --> pdb=" O SER Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 451 through 469 removed outlier: 4.044A pdb=" N ARG Q 455 " --> pdb=" O MET Q 451 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 93 Processing helix chain 'R' and resid 105 through 115 Processing helix chain 'R' and resid 130 through 140 removed outlier: 4.143A pdb=" N LEU R 136 " --> pdb=" O ILE R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 153 Processing helix chain 'R' and resid 159 through 172 Processing helix chain 'R' and resid 177 through 184 removed outlier: 3.551A pdb=" N PHE R 181 " --> pdb=" O PHE R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 206 removed outlier: 3.971A pdb=" N PHE R 198 " --> pdb=" O LYS R 194 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS R 199 " --> pdb=" O ARG R 195 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE R 203 " --> pdb=" O LYS R 199 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 205 " --> pdb=" O GLN R 201 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS R 206 " --> pdb=" O LYS R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 239 removed outlier: 3.640A pdb=" N MET R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE R 239 " --> pdb=" O GLN R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 272 Processing helix chain 'R' and resid 279 through 288 Processing helix chain 'R' and resid 295 through 305 removed outlier: 3.828A pdb=" N VAL R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 327 removed outlier: 3.672A pdb=" N PHE R 318 " --> pdb=" O SER R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 338 Processing helix chain 'R' and resid 346 through 359 Processing helix chain 'R' and resid 364 through 374 Processing helix chain 'R' and resid 383 through 397 removed outlier: 3.693A pdb=" N ARG R 397 " --> pdb=" O ASN R 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 134 through 138 Processing sheet with id=AA2, first strand: chain 'R' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'R' and resid 191 through 192 785 hydrogen bonds defined for protein. 2331 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: 3.24 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3727 1.34 - 1.46: 2729 1.46 - 1.58: 5759 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 12339 Sorted by residual: bond pdb=" CA THR Q 265 " pdb=" C THR Q 265 " ideal model delta sigma weight residual 1.523 1.564 -0.040 1.34e-02 5.57e+03 9.10e+00 bond pdb=" C LYS Q 161 " pdb=" N GLN Q 162 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.59e-02 3.96e+03 5.76e+00 bond pdb=" CG1 ILE Q 210 " pdb=" CD1 ILE Q 210 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.57e+00 bond pdb=" C ARG Q 263 " pdb=" N PRO Q 264 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.53e+00 bond pdb=" CB TRP C 255 " pdb=" CG TRP C 255 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.12e+00 ... (remaining 12334 not shown) Histogram of bond angle deviations from ideal: 96.56 - 104.11: 153 104.11 - 111.67: 5348 111.67 - 119.22: 4688 119.22 - 126.77: 6254 126.77 - 134.32: 144 Bond angle restraints: 16587 Sorted by residual: angle pdb=" C VAL D 74 " pdb=" N ILE D 75 " pdb=" CA ILE D 75 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" CA LEU Q 428 " pdb=" CB LEU Q 428 " pdb=" CG LEU Q 428 " ideal model delta sigma weight residual 116.30 131.10 -14.80 3.50e+00 8.16e-02 1.79e+01 angle pdb=" C LEU R 362 " pdb=" N SER R 363 " pdb=" CA SER R 363 " ideal model delta sigma weight residual 121.74 128.07 -6.33 1.58e+00 4.01e-01 1.61e+01 angle pdb=" CA LEU Q 270 " pdb=" CB LEU Q 270 " pdb=" CG LEU Q 270 " ideal model delta sigma weight residual 116.30 130.22 -13.92 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N ILE B 49 " pdb=" CA ILE B 49 " pdb=" C ILE B 49 " ideal model delta sigma weight residual 113.42 108.97 4.45 1.17e+00 7.31e-01 1.44e+01 ... (remaining 16582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 6742 14.91 - 29.82: 519 29.82 - 44.73: 151 44.73 - 59.64: 14 59.64 - 74.55: 13 Dihedral angle restraints: 7439 sinusoidal: 3151 harmonic: 4288 Sorted by residual: dihedral pdb=" CA ARG A 335 " pdb=" C ARG A 335 " pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta harmonic sigma weight residual -180.00 -146.45 -33.55 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA MET B 63 " pdb=" C MET B 63 " pdb=" N SER B 64 " pdb=" CA SER B 64 " ideal model delta harmonic sigma weight residual 180.00 148.94 31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA LEU C 253 " pdb=" C LEU C 253 " pdb=" N THR C 254 " pdb=" CA THR C 254 " ideal model delta harmonic sigma weight residual -180.00 -149.20 -30.80 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1175 0.054 - 0.108: 476 0.108 - 0.162: 123 0.162 - 0.216: 15 0.216 - 0.270: 4 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CB ILE D 97 " pdb=" CA ILE D 97 " pdb=" CG1 ILE D 97 " pdb=" CG2 ILE D 97 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB THR A 267 " pdb=" CA THR A 267 " pdb=" OG1 THR A 267 " pdb=" CG2 THR A 267 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR C 291 " pdb=" N TYR C 291 " pdb=" C TYR C 291 " pdb=" CB TYR C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1790 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 231 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C ASP Q 231 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP Q 231 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU Q 232 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN Q 162 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO Q 163 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO Q 163 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO Q 163 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 311 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLU R 311 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU R 311 " 0.016 2.00e-02 2.50e+03 pdb=" N SER R 312 " 0.014 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 67 2.48 - 3.09: 8417 3.09 - 3.69: 19382 3.69 - 4.30: 26357 4.30 - 4.90: 41408 Nonbonded interactions: 95631 Sorted by model distance: nonbonded pdb=" NZ LYS Q 341 " pdb=" OE2 GLU Q 432 " model vdw 1.876 2.520 nonbonded pdb=" OD1 ASP Q 392 " pdb=" OG1 THR Q 395 " model vdw 2.034 2.440 nonbonded pdb=" NH2 ARG R 150 " pdb=" OE1 GLU R 265 " model vdw 2.108 2.520 nonbonded pdb=" OD1 ASP Q 231 " pdb=" NH2 ARG R 352 " model vdw 2.124 2.520 nonbonded pdb=" OE2 GLU C 200 " pdb=" NH2 ARG C 335 " model vdw 2.131 2.520 ... (remaining 95626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 191 through 340) selection = (chain 'C' and resid 191 through 340) selection = (chain 'E' and resid 191 through 340) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 48 through 96) selection = (chain 'D' and resid 48 through 96) selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.680 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 32.180 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.009 0.096 12339 Z= 0.556 Angle : 1.205 14.805 16587 Z= 0.647 Chirality : 0.060 0.270 1793 Planarity : 0.007 0.065 2094 Dihedral : 12.138 74.550 4661 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.39 % Allowed : 6.01 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.41 (0.18), residues: 1440 helix: -1.84 (0.13), residues: 1028 sheet: -4.78 (0.59), residues: 15 loop : -2.85 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 255 HIS 0.014 0.003 HIS A 304 PHE 0.035 0.004 PHE H 77 TYR 0.031 0.004 TYR Q 114 ARG 0.015 0.002 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 352 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9170 (mmm) cc_final: 0.8950 (mmm) REVERT: A 276 MET cc_start: 0.9118 (ttt) cc_final: 0.8798 (ttt) REVERT: A 278 MET cc_start: 0.9006 (mtt) cc_final: 0.8636 (mtm) REVERT: A 331 LEU cc_start: 0.8833 (mt) cc_final: 0.8417 (tp) REVERT: A 335 ARG cc_start: 0.7848 (tmt170) cc_final: 0.7604 (tmt-80) REVERT: B 80 VAL cc_start: 0.9151 (t) cc_final: 0.8854 (t) REVERT: B 91 LEU cc_start: 0.8260 (tm) cc_final: 0.7595 (mp) REVERT: C 243 MET cc_start: 0.9316 (mtm) cc_final: 0.8788 (mtm) REVERT: C 246 GLN cc_start: 0.9130 (tm130) cc_final: 0.8572 (tm-30) REVERT: C 262 ILE cc_start: 0.8892 (mt) cc_final: 0.8670 (tp) REVERT: C 276 MET cc_start: 0.8561 (ttm) cc_final: 0.8335 (tmm) REVERT: C 284 MET cc_start: 0.8303 (mtp) cc_final: 0.8044 (tmm) REVERT: C 313 ASP cc_start: 0.8613 (m-30) cc_final: 0.8347 (t0) REVERT: D 77 PHE cc_start: 0.8124 (m-80) cc_final: 0.7919 (m-10) REVERT: D 79 TYR cc_start: 0.8902 (t80) cc_final: 0.8487 (t80) REVERT: D 97 ILE cc_start: 0.7980 (mt) cc_final: 0.7175 (tt) REVERT: E 202 GLU cc_start: 0.9413 (tt0) cc_final: 0.9190 (tm-30) REVERT: E 221 ARG cc_start: 0.8320 (tmt170) cc_final: 0.7695 (tmm160) REVERT: E 243 MET cc_start: 0.8061 (tpt) cc_final: 0.7375 (tpp) REVERT: E 262 ILE cc_start: 0.9574 (mt) cc_final: 0.9218 (mt) REVERT: E 263 MET cc_start: 0.8118 (mmt) cc_final: 0.7914 (mmm) REVERT: E 296 ASP cc_start: 0.9053 (m-30) cc_final: 0.8652 (m-30) REVERT: E 313 ASP cc_start: 0.9031 (m-30) cc_final: 0.8721 (p0) REVERT: E 329 MET cc_start: 0.9020 (tpt) cc_final: 0.8586 (tpp) REVERT: E 330 ASP cc_start: 0.9396 (t0) cc_final: 0.9074 (p0) REVERT: F 67 LEU cc_start: 0.7105 (tt) cc_final: 0.6694 (mt) REVERT: F 71 PHE cc_start: 0.8290 (m-80) cc_final: 0.8053 (m-80) REVERT: G 243 MET cc_start: 0.8035 (mmm) cc_final: 0.7590 (mmm) REVERT: G 276 MET cc_start: 0.8833 (mtm) cc_final: 0.8273 (mtp) REVERT: G 287 GLN cc_start: 0.8502 (tt0) cc_final: 0.8288 (tm-30) REVERT: G 316 LYS cc_start: 0.9159 (mtpm) cc_final: 0.8603 (mmmt) REVERT: G 335 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8325 (ptt90) REVERT: H 52 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7903 (mtt180) REVERT: H 67 LEU cc_start: 0.8736 (tt) cc_final: 0.8394 (tt) REVERT: H 92 LEU cc_start: 0.8189 (tp) cc_final: 0.7848 (pp) REVERT: Q 114 TYR cc_start: 0.8839 (t80) cc_final: 0.7599 (t80) REVERT: Q 204 ILE cc_start: 0.9235 (mt) cc_final: 0.9034 (tp) REVERT: Q 208 ASP cc_start: 0.8582 (m-30) cc_final: 0.8317 (m-30) REVERT: Q 213 THR cc_start: 0.9094 (m) cc_final: 0.8667 (p) REVERT: Q 228 LYS cc_start: 0.9159 (mttt) cc_final: 0.8795 (mttm) REVERT: Q 256 MET cc_start: 0.8325 (mmm) cc_final: 0.7999 (mmm) REVERT: Q 300 GLN cc_start: 0.8838 (tt0) cc_final: 0.8132 (tm-30) REVERT: Q 368 PHE cc_start: 0.9136 (m-10) cc_final: 0.8598 (m-80) REVERT: Q 375 ASN cc_start: 0.8223 (m-40) cc_final: 0.7555 (p0) REVERT: Q 386 MET cc_start: 0.8287 (mtt) cc_final: 0.7821 (ttt) REVERT: Q 445 LEU cc_start: 0.8643 (tp) cc_final: 0.8339 (tp) REVERT: R 91 MET cc_start: 0.8469 (mtp) cc_final: 0.8125 (mmm) REVERT: R 191 MET cc_start: 0.6151 (mmm) cc_final: 0.5463 (mmm) REVERT: R 278 MET cc_start: 0.7974 (mmm) cc_final: 0.7118 (tpp) REVERT: R 299 TYR cc_start: 0.8140 (m-10) cc_final: 0.7609 (m-10) REVERT: R 322 CYS cc_start: 0.8928 (m) cc_final: 0.8554 (m) REVERT: R 335 MET cc_start: 0.9037 (mmt) cc_final: 0.8724 (mmp) REVERT: R 365 ASN cc_start: 0.8314 (m-40) cc_final: 0.8100 (m-40) REVERT: R 382 LEU cc_start: 0.8312 (tp) cc_final: 0.8032 (tp) REVERT: R 396 HIS cc_start: 0.8940 (m-70) cc_final: 0.8730 (p-80) outliers start: 5 outliers final: 1 residues processed: 357 average time/residue: 0.2832 time to fit residues: 135.7228 Evaluate side-chains 197 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 HIS F 95 HIS Q 116 ASN ** Q 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN Q 260 HIS Q 295 ASN Q 352 HIS Q 366 ASN Q 425 ASN R 178 HIS R 235 GLN R 336 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12339 Z= 0.190 Angle : 0.667 10.398 16587 Z= 0.343 Chirality : 0.040 0.142 1793 Planarity : 0.005 0.050 2094 Dihedral : 5.801 26.685 1605 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.15 % Allowed : 3.08 % Favored : 96.76 % 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: -1.12 (0.20), residues: 1440 helix: -0.10 (0.15), residues: 1048 sheet: -4.41 (0.77), residues: 17 loop : -2.17 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 255 HIS 0.004 0.001 HIS E 341 PHE 0.033 0.002 PHE Q 188 TYR 0.021 0.002 TYR E 268 ARG 0.007 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 THR cc_start: 0.8693 (m) cc_final: 0.8476 (m) REVERT: A 278 MET cc_start: 0.8947 (mtt) cc_final: 0.8291 (mtm) REVERT: A 322 ASP cc_start: 0.9011 (m-30) cc_final: 0.8678 (m-30) REVERT: A 331 LEU cc_start: 0.8781 (mt) cc_final: 0.8528 (tp) REVERT: A 335 ARG cc_start: 0.7711 (tmt170) cc_final: 0.7497 (tmt-80) REVERT: B 80 VAL cc_start: 0.9388 (t) cc_final: 0.9164 (t) REVERT: B 83 LEU cc_start: 0.9140 (mm) cc_final: 0.8668 (mp) REVERT: B 91 LEU cc_start: 0.7955 (tt) cc_final: 0.7613 (mp) REVERT: C 242 TYR cc_start: 0.9008 (t80) cc_final: 0.8767 (t80) REVERT: C 243 MET cc_start: 0.9257 (mtm) cc_final: 0.8752 (mtm) REVERT: C 246 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 276 MET cc_start: 0.8806 (ttm) cc_final: 0.8424 (tmm) REVERT: C 284 MET cc_start: 0.8257 (mtp) cc_final: 0.7962 (tmm) REVERT: D 79 TYR cc_start: 0.8887 (t80) cc_final: 0.8519 (t80) REVERT: D 97 ILE cc_start: 0.8163 (mt) cc_final: 0.7524 (tt) REVERT: E 201 ARG cc_start: 0.9379 (ttm110) cc_final: 0.8999 (ttm110) REVERT: E 202 GLU cc_start: 0.9433 (tt0) cc_final: 0.8519 (tm-30) REVERT: E 205 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8293 (pp20) REVERT: E 213 GLN cc_start: 0.9149 (tt0) cc_final: 0.8940 (tt0) REVERT: E 262 ILE cc_start: 0.9600 (mt) cc_final: 0.9350 (mt) REVERT: E 263 MET cc_start: 0.7915 (mmt) cc_final: 0.7692 (mmm) REVERT: E 276 MET cc_start: 0.9212 (tpp) cc_final: 0.8803 (tpp) REVERT: E 329 MET cc_start: 0.9081 (tpt) cc_final: 0.8695 (tpp) REVERT: F 71 PHE cc_start: 0.8214 (m-80) cc_final: 0.7901 (m-80) REVERT: F 83 LEU cc_start: 0.8957 (tt) cc_final: 0.8694 (mt) REVERT: G 198 ASN cc_start: 0.8653 (t0) cc_final: 0.8409 (m110) REVERT: G 224 ILE cc_start: 0.9157 (mm) cc_final: 0.8766 (pt) REVERT: G 276 MET cc_start: 0.8846 (mtm) cc_final: 0.8175 (mtp) REVERT: G 315 GLU cc_start: 0.8750 (pm20) cc_final: 0.8503 (pm20) REVERT: G 316 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8751 (mmmt) REVERT: H 52 ARG cc_start: 0.8088 (mmt180) cc_final: 0.7861 (mtt180) REVERT: H 92 LEU cc_start: 0.7890 (tp) cc_final: 0.7661 (pp) REVERT: Q 125 ASP cc_start: 0.8412 (t0) cc_final: 0.8119 (t0) REVERT: Q 176 PHE cc_start: 0.8317 (m-80) cc_final: 0.8107 (m-10) REVERT: Q 204 ILE cc_start: 0.9083 (mt) cc_final: 0.8836 (tp) REVERT: Q 208 ASP cc_start: 0.8533 (m-30) cc_final: 0.8252 (m-30) REVERT: Q 228 LYS cc_start: 0.9101 (mttt) cc_final: 0.8896 (mttm) REVERT: Q 229 MET cc_start: 0.8008 (mmm) cc_final: 0.7405 (mmp) REVERT: Q 256 MET cc_start: 0.8123 (mmm) cc_final: 0.7797 (mmm) REVERT: Q 300 GLN cc_start: 0.9049 (tt0) cc_final: 0.8838 (tm-30) REVERT: Q 330 MET cc_start: 0.8259 (tmm) cc_final: 0.7885 (tmm) REVERT: Q 386 MET cc_start: 0.8384 (mtt) cc_final: 0.8119 (ttt) REVERT: R 91 MET cc_start: 0.8174 (mtp) cc_final: 0.7935 (mmt) REVERT: R 118 MET cc_start: 0.4482 (mmm) cc_final: 0.3899 (mtm) REVERT: R 256 MET cc_start: 0.8159 (mtp) cc_final: 0.7809 (mtp) REVERT: R 278 MET cc_start: 0.7450 (mmm) cc_final: 0.7150 (mmt) REVERT: R 293 THR cc_start: 0.7681 (p) cc_final: 0.6861 (p) REVERT: R 321 PHE cc_start: 0.9000 (t80) cc_final: 0.8768 (t80) REVERT: R 322 CYS cc_start: 0.8911 (m) cc_final: 0.8705 (m) REVERT: R 335 MET cc_start: 0.8916 (mmt) cc_final: 0.8682 (mmp) REVERT: R 382 LEU cc_start: 0.8289 (tp) cc_final: 0.8016 (tp) outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.2444 time to fit residues: 100.8197 Evaluate side-chains 204 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN D 87 ASN ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 HIS Q 362 GLN Q 373 ASN Q 397 GLN R 178 HIS R 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12339 Z= 0.358 Angle : 0.755 8.503 16587 Z= 0.397 Chirality : 0.043 0.191 1793 Planarity : 0.005 0.048 2094 Dihedral : 5.655 25.051 1605 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: -0.38 (0.21), residues: 1440 helix: 0.47 (0.15), residues: 1051 sheet: -4.74 (0.59), residues: 17 loop : -1.97 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 260 HIS 0.012 0.002 HIS R 178 PHE 0.022 0.002 PHE C 247 TYR 0.030 0.003 TYR G 289 ARG 0.011 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9229 (mmm) cc_final: 0.8992 (mmm) REVERT: A 267 THR cc_start: 0.8622 (m) cc_final: 0.8392 (m) REVERT: A 278 MET cc_start: 0.8876 (mtt) cc_final: 0.8169 (mtm) REVERT: A 331 LEU cc_start: 0.8816 (mt) cc_final: 0.8571 (tp) REVERT: A 335 ARG cc_start: 0.7342 (tmt170) cc_final: 0.6926 (tmt-80) REVERT: B 83 LEU cc_start: 0.9018 (mm) cc_final: 0.8722 (mm) REVERT: B 91 LEU cc_start: 0.7959 (tt) cc_final: 0.7624 (mp) REVERT: C 243 MET cc_start: 0.9308 (mtm) cc_final: 0.8658 (mtm) REVERT: C 246 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 276 MET cc_start: 0.8881 (ttm) cc_final: 0.8571 (tmm) REVERT: C 284 MET cc_start: 0.8604 (mtp) cc_final: 0.8019 (tmm) REVERT: D 79 TYR cc_start: 0.8928 (t80) cc_final: 0.8532 (t80) REVERT: D 97 ILE cc_start: 0.7879 (mt) cc_final: 0.7189 (tt) REVERT: E 201 ARG cc_start: 0.9518 (ttm110) cc_final: 0.8771 (ptp-110) REVERT: E 202 GLU cc_start: 0.9442 (tt0) cc_final: 0.8623 (tm-30) REVERT: E 205 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8272 (pp20) REVERT: E 221 ARG cc_start: 0.8424 (tmt170) cc_final: 0.7939 (tmm160) REVERT: E 243 MET cc_start: 0.8590 (ttm) cc_final: 0.7996 (ttt) REVERT: E 246 GLN cc_start: 0.9147 (tt0) cc_final: 0.8805 (tm-30) REVERT: E 262 ILE cc_start: 0.9576 (mt) cc_final: 0.9364 (mt) REVERT: E 263 MET cc_start: 0.8160 (mmt) cc_final: 0.7909 (mmm) REVERT: E 311 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8307 (mtm-85) REVERT: E 329 MET cc_start: 0.9017 (tpt) cc_final: 0.8676 (tpp) REVERT: F 63 MET cc_start: 0.7466 (ttt) cc_final: 0.7182 (ttt) REVERT: F 83 LEU cc_start: 0.9174 (tt) cc_final: 0.8888 (mt) REVERT: G 198 ASN cc_start: 0.8475 (t0) cc_final: 0.8192 (m110) REVERT: G 213 GLN cc_start: 0.9431 (mt0) cc_final: 0.9173 (mt0) REVERT: G 243 MET cc_start: 0.7564 (mtt) cc_final: 0.7273 (mtp) REVERT: G 276 MET cc_start: 0.9093 (mtm) cc_final: 0.8399 (mtp) REVERT: H 52 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7933 (mtt180) REVERT: H 92 LEU cc_start: 0.7890 (tp) cc_final: 0.7666 (pp) REVERT: Q 147 MET cc_start: 0.7840 (ptp) cc_final: 0.7569 (ptp) REVERT: Q 176 PHE cc_start: 0.8150 (m-80) cc_final: 0.7679 (m-10) REVERT: Q 208 ASP cc_start: 0.8574 (m-30) cc_final: 0.8352 (m-30) REVERT: Q 228 LYS cc_start: 0.9312 (mttt) cc_final: 0.8983 (mttm) REVERT: Q 256 MET cc_start: 0.8329 (mmm) cc_final: 0.7923 (mmm) REVERT: Q 260 HIS cc_start: 0.7997 (m-70) cc_final: 0.7710 (m90) REVERT: Q 300 GLN cc_start: 0.9079 (tt0) cc_final: 0.8720 (tm-30) REVERT: Q 330 MET cc_start: 0.8339 (tmm) cc_final: 0.7909 (tmm) REVERT: Q 386 MET cc_start: 0.8543 (mtt) cc_final: 0.8218 (ttt) REVERT: R 91 MET cc_start: 0.8264 (mtp) cc_final: 0.7943 (mmt) REVERT: R 118 MET cc_start: 0.4591 (mmm) cc_final: 0.4131 (mtm) REVERT: R 191 MET cc_start: 0.6631 (mmm) cc_final: 0.6033 (mmm) REVERT: R 299 TYR cc_start: 0.8511 (m-80) cc_final: 0.8040 (m-10) REVERT: R 321 PHE cc_start: 0.9025 (t80) cc_final: 0.8714 (t80) REVERT: R 322 CYS cc_start: 0.8997 (m) cc_final: 0.8744 (m) REVERT: R 382 LEU cc_start: 0.8414 (tp) cc_final: 0.8170 (tp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2389 time to fit residues: 80.4502 Evaluate side-chains 177 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12339 Z= 0.218 Angle : 0.628 8.293 16587 Z= 0.326 Chirality : 0.040 0.144 1793 Planarity : 0.004 0.047 2094 Dihedral : 5.259 23.427 1605 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1440 helix: 1.00 (0.16), residues: 1054 sheet: -4.49 (0.67), residues: 17 loop : -1.82 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 255 HIS 0.004 0.001 HIS R 323 PHE 0.016 0.001 PHE R 197 TYR 0.018 0.002 TYR E 268 ARG 0.010 0.001 ARG Q 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9182 (mmm) cc_final: 0.8920 (mmm) REVERT: A 267 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8505 (m) REVERT: A 278 MET cc_start: 0.8748 (mtt) cc_final: 0.8424 (mmt) REVERT: A 332 LYS cc_start: 0.9202 (tptt) cc_final: 0.8945 (tppt) REVERT: A 335 ARG cc_start: 0.7319 (tmt170) cc_final: 0.6679 (tmt-80) REVERT: B 83 LEU cc_start: 0.8960 (mm) cc_final: 0.8727 (tp) REVERT: B 91 LEU cc_start: 0.7912 (tt) cc_final: 0.7586 (mp) REVERT: C 243 MET cc_start: 0.9360 (mtm) cc_final: 0.8887 (ttp) REVERT: C 246 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8433 (tm-30) REVERT: C 276 MET cc_start: 0.8832 (ttm) cc_final: 0.8509 (tmm) REVERT: C 284 MET cc_start: 0.8638 (mtp) cc_final: 0.7947 (tmm) REVERT: D 79 TYR cc_start: 0.8889 (t80) cc_final: 0.8531 (t80) REVERT: D 97 ILE cc_start: 0.8210 (mt) cc_final: 0.7679 (tt) REVERT: E 213 GLN cc_start: 0.9187 (tt0) cc_final: 0.8985 (tt0) REVERT: E 243 MET cc_start: 0.8272 (ttm) cc_final: 0.7812 (ttt) REVERT: E 246 GLN cc_start: 0.9138 (tt0) cc_final: 0.8794 (tm-30) REVERT: E 263 MET cc_start: 0.8174 (mmt) cc_final: 0.7956 (mmm) REVERT: E 276 MET cc_start: 0.9055 (tpp) cc_final: 0.8012 (tpp) REVERT: E 329 MET cc_start: 0.8987 (tpt) cc_final: 0.8664 (tpt) REVERT: F 83 LEU cc_start: 0.9146 (tt) cc_final: 0.8874 (mt) REVERT: F 88 PHE cc_start: 0.8555 (t80) cc_final: 0.8227 (t80) REVERT: F 92 LEU cc_start: 0.8928 (pp) cc_final: 0.8723 (pp) REVERT: G 198 ASN cc_start: 0.8666 (t0) cc_final: 0.8433 (m110) REVERT: G 276 MET cc_start: 0.9125 (mtm) cc_final: 0.8678 (tmm) REVERT: H 67 LEU cc_start: 0.8703 (mt) cc_final: 0.8138 (pt) REVERT: Q 125 ASP cc_start: 0.8512 (t0) cc_final: 0.8279 (t0) REVERT: Q 147 MET cc_start: 0.8211 (ptp) cc_final: 0.7973 (ptp) REVERT: Q 176 PHE cc_start: 0.7867 (m-80) cc_final: 0.7336 (m-10) REVERT: Q 208 ASP cc_start: 0.8576 (m-30) cc_final: 0.8349 (m-30) REVERT: Q 228 LYS cc_start: 0.9274 (mttt) cc_final: 0.9068 (mttm) REVERT: Q 229 MET cc_start: 0.8468 (mmp) cc_final: 0.8065 (mmp) REVERT: Q 256 MET cc_start: 0.8135 (mmm) cc_final: 0.7766 (mmm) REVERT: Q 260 HIS cc_start: 0.7963 (m-70) cc_final: 0.7637 (m90) REVERT: Q 300 GLN cc_start: 0.9111 (tt0) cc_final: 0.8696 (tm-30) REVERT: Q 330 MET cc_start: 0.8348 (tmm) cc_final: 0.7879 (tmm) REVERT: Q 386 MET cc_start: 0.8558 (mtt) cc_final: 0.8164 (ttt) REVERT: Q 396 MET cc_start: 0.8843 (mtt) cc_final: 0.8633 (mtt) REVERT: R 91 MET cc_start: 0.7957 (mtp) cc_final: 0.7494 (mmt) REVERT: R 278 MET cc_start: 0.7220 (mmt) cc_final: 0.6632 (mmt) REVERT: R 299 TYR cc_start: 0.8491 (m-80) cc_final: 0.8027 (m-10) REVERT: R 321 PHE cc_start: 0.9011 (t80) cc_final: 0.8720 (t80) REVERT: R 322 CYS cc_start: 0.8936 (m) cc_final: 0.8717 (m) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.2339 time to fit residues: 79.7242 Evaluate side-chains 183 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 0.0870 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 339 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12339 Z= 0.369 Angle : 0.737 8.542 16587 Z= 0.388 Chirality : 0.043 0.152 1793 Planarity : 0.005 0.062 2094 Dihedral : 5.406 23.653 1605 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 0.23 (0.22), residues: 1440 helix: 0.93 (0.16), residues: 1052 sheet: -4.00 (0.91), residues: 12 loop : -1.85 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 255 HIS 0.007 0.001 HIS D 95 PHE 0.020 0.002 PHE H 88 TYR 0.019 0.002 TYR E 268 ARG 0.006 0.001 ARG Q 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 THR cc_start: 0.8633 (m) cc_final: 0.8359 (m) REVERT: A 278 MET cc_start: 0.8756 (mtt) cc_final: 0.8128 (mtm) REVERT: A 332 LYS cc_start: 0.9115 (tptt) cc_final: 0.8873 (tppt) REVERT: B 83 LEU cc_start: 0.8989 (mm) cc_final: 0.8709 (mm) REVERT: B 91 LEU cc_start: 0.7893 (tt) cc_final: 0.7540 (mp) REVERT: C 243 MET cc_start: 0.9295 (mtm) cc_final: 0.8794 (ttp) REVERT: C 246 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 276 MET cc_start: 0.8896 (ttm) cc_final: 0.8631 (tmm) REVERT: C 278 MET cc_start: 0.7644 (mmt) cc_final: 0.7008 (mmp) REVERT: C 284 MET cc_start: 0.8822 (mtp) cc_final: 0.8094 (tmm) REVERT: D 79 TYR cc_start: 0.8978 (t80) cc_final: 0.8597 (t80) REVERT: D 97 ILE cc_start: 0.8259 (mt) cc_final: 0.7648 (tt) REVERT: E 205 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8278 (pp20) REVERT: E 243 MET cc_start: 0.8329 (ttm) cc_final: 0.7974 (ttt) REVERT: E 246 GLN cc_start: 0.9144 (tt0) cc_final: 0.8797 (tm-30) REVERT: E 262 ILE cc_start: 0.9593 (mt) cc_final: 0.9376 (mt) REVERT: E 263 MET cc_start: 0.8268 (mmt) cc_final: 0.8062 (mmm) REVERT: E 311 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8271 (mtm-85) REVERT: E 329 MET cc_start: 0.8968 (tpt) cc_final: 0.8710 (tpp) REVERT: F 83 LEU cc_start: 0.9158 (tt) cc_final: 0.8881 (mt) REVERT: G 198 ASN cc_start: 0.8536 (t0) cc_final: 0.8285 (m110) REVERT: G 276 MET cc_start: 0.9173 (mtm) cc_final: 0.8752 (tmm) REVERT: G 287 GLN cc_start: 0.8503 (tt0) cc_final: 0.8133 (tm-30) REVERT: G 335 ARG cc_start: 0.8736 (mmt180) cc_final: 0.8450 (ptt90) REVERT: H 67 LEU cc_start: 0.8675 (mt) cc_final: 0.8141 (pt) REVERT: Q 118 ILE cc_start: 0.9452 (mt) cc_final: 0.8850 (mt) REVERT: Q 125 ASP cc_start: 0.8473 (t0) cc_final: 0.8273 (t0) REVERT: Q 147 MET cc_start: 0.8252 (ptp) cc_final: 0.7922 (ptp) REVERT: Q 228 LYS cc_start: 0.9271 (mttt) cc_final: 0.9065 (mttm) REVERT: Q 256 MET cc_start: 0.8358 (mmm) cc_final: 0.7950 (mmm) REVERT: Q 330 MET cc_start: 0.8437 (tmm) cc_final: 0.7993 (tmm) REVERT: Q 386 MET cc_start: 0.8509 (mtt) cc_final: 0.8080 (ttt) REVERT: R 91 MET cc_start: 0.8050 (mtp) cc_final: 0.7518 (mmt) REVERT: R 178 HIS cc_start: 0.7746 (t70) cc_final: 0.7491 (t70) REVERT: R 191 MET cc_start: 0.6520 (mmm) cc_final: 0.5737 (mmm) REVERT: R 299 TYR cc_start: 0.8444 (m-80) cc_final: 0.7959 (m-10) REVERT: R 321 PHE cc_start: 0.9011 (t80) cc_final: 0.8737 (t80) REVERT: R 322 CYS cc_start: 0.9001 (m) cc_final: 0.8779 (m) REVERT: R 382 LEU cc_start: 0.8481 (tp) cc_final: 0.8205 (tp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2504 time to fit residues: 77.1617 Evaluate side-chains 167 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 HIS ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 235 GLN R 384 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12339 Z= 0.163 Angle : 0.610 7.841 16587 Z= 0.310 Chirality : 0.039 0.127 1793 Planarity : 0.004 0.077 2094 Dihedral : 5.046 21.597 1605 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 (0.22), residues: 1440 helix: 1.32 (0.16), residues: 1060 sheet: -4.23 (0.78), residues: 17 loop : -1.76 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 256 HIS 0.004 0.001 HIS G 195 PHE 0.024 0.001 PHE H 77 TYR 0.020 0.001 TYR E 268 ARG 0.013 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9147 (mmm) cc_final: 0.8738 (mmm) REVERT: A 267 THR cc_start: 0.8713 (m) cc_final: 0.8437 (m) REVERT: A 322 ASP cc_start: 0.9106 (m-30) cc_final: 0.8798 (m-30) REVERT: B 63 MET cc_start: 0.6365 (ptm) cc_final: 0.5879 (ptm) REVERT: B 77 PHE cc_start: 0.8326 (m-80) cc_final: 0.7999 (m-80) REVERT: B 83 LEU cc_start: 0.9094 (mm) cc_final: 0.8709 (tp) REVERT: B 91 LEU cc_start: 0.7755 (tt) cc_final: 0.7406 (mp) REVERT: C 243 MET cc_start: 0.9310 (mtm) cc_final: 0.8896 (ttp) REVERT: C 246 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8036 (tm-30) REVERT: C 284 MET cc_start: 0.8686 (mtp) cc_final: 0.7993 (tmm) REVERT: D 77 PHE cc_start: 0.8383 (m-80) cc_final: 0.8148 (m-80) REVERT: D 79 TYR cc_start: 0.8928 (t80) cc_final: 0.8590 (t80) REVERT: D 97 ILE cc_start: 0.8289 (mt) cc_final: 0.7653 (tt) REVERT: E 205 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8271 (pp20) REVERT: E 243 MET cc_start: 0.8386 (ttm) cc_final: 0.7886 (ttt) REVERT: E 263 MET cc_start: 0.8207 (mmt) cc_final: 0.7716 (tpp) REVERT: E 276 MET cc_start: 0.9034 (mmt) cc_final: 0.8357 (mmt) REVERT: E 329 MET cc_start: 0.8986 (tpt) cc_final: 0.8740 (tpt) REVERT: F 83 LEU cc_start: 0.9118 (tt) cc_final: 0.8889 (mt) REVERT: F 88 PHE cc_start: 0.8488 (t80) cc_final: 0.8287 (t80) REVERT: G 198 ASN cc_start: 0.8660 (t0) cc_final: 0.8455 (m110) REVERT: G 276 MET cc_start: 0.9085 (mtm) cc_final: 0.8662 (tmm) REVERT: G 287 GLN cc_start: 0.8611 (tt0) cc_final: 0.8390 (tm-30) REVERT: H 57 LEU cc_start: 0.8671 (mt) cc_final: 0.8460 (mt) REVERT: H 67 LEU cc_start: 0.8611 (mt) cc_final: 0.8061 (pt) REVERT: Q 118 ILE cc_start: 0.9458 (mt) cc_final: 0.8846 (mt) REVERT: Q 125 ASP cc_start: 0.8407 (t0) cc_final: 0.8202 (t0) REVERT: Q 208 ASP cc_start: 0.8739 (m-30) cc_final: 0.8506 (m-30) REVERT: Q 256 MET cc_start: 0.8139 (mmm) cc_final: 0.7899 (mmm) REVERT: Q 300 GLN cc_start: 0.8943 (tt0) cc_final: 0.8735 (tm-30) REVERT: Q 330 MET cc_start: 0.8252 (tmm) cc_final: 0.7900 (tmm) REVERT: Q 386 MET cc_start: 0.8492 (mtt) cc_final: 0.8125 (ttt) REVERT: Q 445 LEU cc_start: 0.8510 (tp) cc_final: 0.7257 (tp) REVERT: R 91 MET cc_start: 0.7911 (mtp) cc_final: 0.7420 (mmt) REVERT: R 178 HIS cc_start: 0.7586 (t70) cc_final: 0.7343 (t70) REVERT: R 191 MET cc_start: 0.6439 (mmm) cc_final: 0.5751 (mmm) REVERT: R 299 TYR cc_start: 0.8412 (m-80) cc_final: 0.7880 (m-10) REVERT: R 321 PHE cc_start: 0.8953 (t80) cc_final: 0.8687 (t80) REVERT: R 322 CYS cc_start: 0.8965 (m) cc_final: 0.8717 (m) REVERT: R 382 LEU cc_start: 0.8446 (tp) cc_final: 0.8134 (tp) REVERT: R 387 PHE cc_start: 0.9056 (t80) cc_final: 0.8845 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2286 time to fit residues: 78.9187 Evaluate side-chains 178 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.0070 chunk 116 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 ASN Q 260 HIS Q 366 ASN Q 373 ASN ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12339 Z= 0.190 Angle : 0.621 9.906 16587 Z= 0.314 Chirality : 0.039 0.131 1793 Planarity : 0.004 0.055 2094 Dihedral : 4.927 22.067 1605 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.85 (0.22), residues: 1440 helix: 1.39 (0.16), residues: 1053 sheet: -4.32 (0.69), residues: 17 loop : -1.59 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 256 HIS 0.005 0.001 HIS R 98 PHE 0.021 0.001 PHE H 77 TYR 0.027 0.001 TYR A 289 ARG 0.011 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.9399 (tp) cc_final: 0.9057 (tp) REVERT: A 263 MET cc_start: 0.9127 (mmm) cc_final: 0.8839 (mmm) REVERT: A 267 THR cc_start: 0.8739 (m) cc_final: 0.8505 (m) REVERT: B 63 MET cc_start: 0.6404 (ptm) cc_final: 0.5866 (ptm) REVERT: B 83 LEU cc_start: 0.8958 (mm) cc_final: 0.8751 (tp) REVERT: B 91 LEU cc_start: 0.7920 (tt) cc_final: 0.7628 (mp) REVERT: C 243 MET cc_start: 0.9233 (mtm) cc_final: 0.8800 (ttp) REVERT: C 246 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 284 MET cc_start: 0.8769 (mtp) cc_final: 0.8028 (tmm) REVERT: D 79 TYR cc_start: 0.8894 (t80) cc_final: 0.8586 (t80) REVERT: D 97 ILE cc_start: 0.8315 (mt) cc_final: 0.7731 (tt) REVERT: E 205 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8241 (pp20) REVERT: E 243 MET cc_start: 0.8117 (ttm) cc_final: 0.7761 (ttt) REVERT: E 263 MET cc_start: 0.8188 (mmt) cc_final: 0.7745 (tpp) REVERT: E 276 MET cc_start: 0.8834 (mmt) cc_final: 0.8139 (mmt) REVERT: E 329 MET cc_start: 0.8991 (tpt) cc_final: 0.8706 (tpp) REVERT: F 71 PHE cc_start: 0.8279 (m-80) cc_final: 0.8076 (m-80) REVERT: F 83 LEU cc_start: 0.9104 (tt) cc_final: 0.8900 (mt) REVERT: G 198 ASN cc_start: 0.8733 (t0) cc_final: 0.8511 (m110) REVERT: G 276 MET cc_start: 0.9108 (mtm) cc_final: 0.8650 (tmm) REVERT: G 287 GLN cc_start: 0.8636 (tt0) cc_final: 0.8399 (tm-30) REVERT: H 57 LEU cc_start: 0.8716 (mt) cc_final: 0.8510 (mt) REVERT: H 67 LEU cc_start: 0.8626 (mt) cc_final: 0.8068 (pt) REVERT: Q 118 ILE cc_start: 0.9484 (mt) cc_final: 0.8854 (mt) REVERT: Q 125 ASP cc_start: 0.8373 (t0) cc_final: 0.8154 (t0) REVERT: Q 147 MET cc_start: 0.7061 (ptp) cc_final: 0.6817 (ptp) REVERT: Q 256 MET cc_start: 0.8180 (mmm) cc_final: 0.7894 (mmm) REVERT: Q 300 GLN cc_start: 0.8954 (tt0) cc_final: 0.8752 (tm-30) REVERT: Q 330 MET cc_start: 0.8149 (tmm) cc_final: 0.7756 (tmm) REVERT: Q 386 MET cc_start: 0.8536 (mtt) cc_final: 0.8137 (ttt) REVERT: Q 445 LEU cc_start: 0.7867 (tp) cc_final: 0.7511 (tp) REVERT: R 91 MET cc_start: 0.7927 (mtp) cc_final: 0.7420 (mmt) REVERT: R 178 HIS cc_start: 0.7599 (t70) cc_final: 0.7344 (t70) REVERT: R 278 MET cc_start: 0.7249 (mmt) cc_final: 0.6691 (mmt) REVERT: R 299 TYR cc_start: 0.8423 (m-80) cc_final: 0.7891 (m-10) REVERT: R 321 PHE cc_start: 0.8962 (t80) cc_final: 0.8714 (t80) REVERT: R 322 CYS cc_start: 0.8941 (m) cc_final: 0.8702 (m) REVERT: R 382 LEU cc_start: 0.8972 (tp) cc_final: 0.8681 (tp) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2205 time to fit residues: 72.5261 Evaluate side-chains 179 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 27 optimal weight: 0.0010 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 260 HIS ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12339 Z= 0.195 Angle : 0.623 7.869 16587 Z= 0.318 Chirality : 0.040 0.183 1793 Planarity : 0.004 0.051 2094 Dihedral : 4.882 22.010 1605 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.90 (0.22), residues: 1440 helix: 1.45 (0.16), residues: 1055 sheet: -4.35 (0.67), residues: 17 loop : -1.66 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 256 HIS 0.004 0.001 HIS G 195 PHE 0.023 0.002 PHE H 88 TYR 0.024 0.001 TYR A 289 ARG 0.010 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9127 (mmm) cc_final: 0.8893 (mmm) REVERT: A 267 THR cc_start: 0.8753 (m) cc_final: 0.8494 (m) REVERT: B 63 MET cc_start: 0.6405 (ptm) cc_final: 0.5862 (ptm) REVERT: B 80 VAL cc_start: 0.9148 (m) cc_final: 0.8888 (m) REVERT: B 83 LEU cc_start: 0.8949 (mm) cc_final: 0.8622 (mp) REVERT: B 91 LEU cc_start: 0.7917 (tt) cc_final: 0.7624 (mp) REVERT: C 243 MET cc_start: 0.9196 (mtm) cc_final: 0.8810 (ttp) REVERT: C 246 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8281 (tm-30) REVERT: C 284 MET cc_start: 0.8806 (mtp) cc_final: 0.8090 (tmm) REVERT: C 324 ILE cc_start: 0.9468 (tp) cc_final: 0.9113 (tp) REVERT: D 79 TYR cc_start: 0.9002 (t80) cc_final: 0.8690 (t80) REVERT: D 97 ILE cc_start: 0.7886 (mt) cc_final: 0.7579 (tt) REVERT: E 205 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8211 (pp20) REVERT: E 243 MET cc_start: 0.8569 (ttm) cc_final: 0.8285 (ttt) REVERT: E 263 MET cc_start: 0.8211 (mmt) cc_final: 0.7782 (tpp) REVERT: E 329 MET cc_start: 0.8996 (tpt) cc_final: 0.8711 (tpp) REVERT: F 71 PHE cc_start: 0.8306 (m-80) cc_final: 0.8097 (m-80) REVERT: F 83 LEU cc_start: 0.9100 (tt) cc_final: 0.8895 (mt) REVERT: G 198 ASN cc_start: 0.8735 (t0) cc_final: 0.8520 (m110) REVERT: G 276 MET cc_start: 0.9132 (mtm) cc_final: 0.8652 (tmm) REVERT: G 287 GLN cc_start: 0.8631 (tt0) cc_final: 0.8430 (tm-30) REVERT: H 57 LEU cc_start: 0.8737 (mt) cc_final: 0.8449 (mt) REVERT: H 67 LEU cc_start: 0.8615 (mt) cc_final: 0.8093 (pt) REVERT: Q 118 ILE cc_start: 0.9493 (mt) cc_final: 0.8915 (mt) REVERT: Q 125 ASP cc_start: 0.8389 (t0) cc_final: 0.8156 (t0) REVERT: Q 147 MET cc_start: 0.7617 (ptp) cc_final: 0.7229 (ptp) REVERT: Q 256 MET cc_start: 0.8155 (mmm) cc_final: 0.7890 (mmm) REVERT: Q 330 MET cc_start: 0.8235 (tmm) cc_final: 0.7829 (tmm) REVERT: Q 386 MET cc_start: 0.8558 (mtt) cc_final: 0.8148 (ttt) REVERT: Q 445 LEU cc_start: 0.8049 (tp) cc_final: 0.7783 (tp) REVERT: R 178 HIS cc_start: 0.7307 (t70) cc_final: 0.7019 (t70) REVERT: R 191 MET cc_start: 0.6334 (mmm) cc_final: 0.5013 (mmm) REVERT: R 266 MET cc_start: 0.9082 (mmp) cc_final: 0.8874 (mmp) REVERT: R 278 MET cc_start: 0.7865 (mmt) cc_final: 0.7416 (mmt) REVERT: R 299 TYR cc_start: 0.8445 (m-80) cc_final: 0.7907 (m-10) REVERT: R 321 PHE cc_start: 0.8983 (t80) cc_final: 0.8731 (t80) REVERT: R 322 CYS cc_start: 0.8958 (m) cc_final: 0.8735 (m) REVERT: R 382 LEU cc_start: 0.8972 (tp) cc_final: 0.8689 (tp) REVERT: R 387 PHE cc_start: 0.8972 (t80) cc_final: 0.8723 (t80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2291 time to fit residues: 75.6519 Evaluate side-chains 177 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12339 Z= 0.240 Angle : 0.654 8.132 16587 Z= 0.337 Chirality : 0.041 0.198 1793 Planarity : 0.004 0.055 2094 Dihedral : 4.947 21.765 1605 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.87 (0.22), residues: 1440 helix: 1.41 (0.16), residues: 1055 sheet: -3.66 (0.91), residues: 12 loop : -1.69 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 255 HIS 0.004 0.001 HIS G 195 PHE 0.026 0.002 PHE F 88 TYR 0.026 0.002 TYR A 289 ARG 0.009 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9100 (mmm) cc_final: 0.8878 (mmm) REVERT: A 267 THR cc_start: 0.8792 (m) cc_final: 0.8549 (m) REVERT: B 59 LYS cc_start: 0.9064 (tptt) cc_final: 0.8447 (tppt) REVERT: B 63 MET cc_start: 0.6387 (ptm) cc_final: 0.5838 (ptm) REVERT: B 80 VAL cc_start: 0.9137 (m) cc_final: 0.8922 (m) REVERT: B 83 LEU cc_start: 0.8957 (mm) cc_final: 0.8645 (mm) REVERT: B 91 LEU cc_start: 0.7935 (tt) cc_final: 0.7632 (mp) REVERT: C 243 MET cc_start: 0.9214 (mtm) cc_final: 0.8809 (ttp) REVERT: C 246 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 259 SER cc_start: 0.7815 (t) cc_final: 0.7562 (t) REVERT: C 284 MET cc_start: 0.8832 (mtp) cc_final: 0.8071 (tmm) REVERT: D 79 TYR cc_start: 0.8923 (t80) cc_final: 0.8620 (t80) REVERT: D 97 ILE cc_start: 0.7868 (mt) cc_final: 0.7476 (tt) REVERT: E 205 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8206 (pp20) REVERT: E 221 ARG cc_start: 0.8366 (tmt170) cc_final: 0.7931 (tmm160) REVERT: E 243 MET cc_start: 0.8490 (ttm) cc_final: 0.7739 (ttt) REVERT: E 246 GLN cc_start: 0.8938 (tt0) cc_final: 0.8611 (tm-30) REVERT: E 263 MET cc_start: 0.8265 (mmt) cc_final: 0.7891 (tpp) REVERT: E 329 MET cc_start: 0.8997 (tpt) cc_final: 0.8714 (tpp) REVERT: F 71 PHE cc_start: 0.8451 (m-80) cc_final: 0.8226 (m-80) REVERT: F 83 LEU cc_start: 0.9092 (tt) cc_final: 0.8882 (mt) REVERT: G 198 ASN cc_start: 0.8758 (t0) cc_final: 0.8540 (m110) REVERT: G 276 MET cc_start: 0.9309 (mtm) cc_final: 0.8644 (tmm) REVERT: H 67 LEU cc_start: 0.8623 (mt) cc_final: 0.8110 (pt) REVERT: Q 118 ILE cc_start: 0.9467 (mt) cc_final: 0.8996 (mt) REVERT: Q 125 ASP cc_start: 0.8399 (t0) cc_final: 0.8164 (t0) REVERT: Q 147 MET cc_start: 0.7799 (ptp) cc_final: 0.7356 (ptp) REVERT: Q 229 MET cc_start: 0.8395 (mmp) cc_final: 0.8094 (mmp) REVERT: Q 256 MET cc_start: 0.8220 (mmm) cc_final: 0.7946 (mmm) REVERT: Q 330 MET cc_start: 0.8276 (tmm) cc_final: 0.7870 (tmm) REVERT: Q 386 MET cc_start: 0.8525 (mtt) cc_final: 0.8071 (ttt) REVERT: Q 445 LEU cc_start: 0.8108 (tp) cc_final: 0.7842 (tp) REVERT: R 178 HIS cc_start: 0.7450 (t70) cc_final: 0.7219 (t70) REVERT: R 191 MET cc_start: 0.6429 (mmm) cc_final: 0.5256 (mmm) REVERT: R 266 MET cc_start: 0.8980 (mmp) cc_final: 0.8707 (mmp) REVERT: R 299 TYR cc_start: 0.8478 (m-80) cc_final: 0.7948 (m-10) REVERT: R 321 PHE cc_start: 0.8971 (t80) cc_final: 0.8678 (t80) REVERT: R 322 CYS cc_start: 0.8970 (m) cc_final: 0.8740 (m) REVERT: R 382 LEU cc_start: 0.9011 (tp) cc_final: 0.8671 (tp) REVERT: R 387 PHE cc_start: 0.9005 (t80) cc_final: 0.8755 (t80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2202 time to fit residues: 71.7480 Evaluate side-chains 175 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN R 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12339 Z= 0.159 Angle : 0.618 8.561 16587 Z= 0.314 Chirality : 0.040 0.189 1793 Planarity : 0.004 0.044 2094 Dihedral : 4.802 21.577 1605 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 1.01 (0.22), residues: 1440 helix: 1.54 (0.16), residues: 1064 sheet: -4.29 (0.70), residues: 17 loop : -1.73 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 256 HIS 0.004 0.001 HIS G 195 PHE 0.027 0.001 PHE H 88 TYR 0.018 0.001 TYR E 268 ARG 0.006 0.000 ARG C 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.9158 (ttp) cc_final: 0.8453 (tmm) REVERT: A 246 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 263 MET cc_start: 0.9083 (mmm) cc_final: 0.8802 (mmm) REVERT: A 267 THR cc_start: 0.8714 (m) cc_final: 0.8358 (m) REVERT: A 279 TYR cc_start: 0.7427 (t80) cc_final: 0.6589 (t80) REVERT: B 59 LYS cc_start: 0.8954 (tptt) cc_final: 0.8563 (tppt) REVERT: B 80 VAL cc_start: 0.9249 (m) cc_final: 0.8998 (m) REVERT: B 83 LEU cc_start: 0.8914 (mm) cc_final: 0.8561 (mp) REVERT: B 91 LEU cc_start: 0.7897 (tt) cc_final: 0.7617 (mt) REVERT: C 243 MET cc_start: 0.9101 (mtm) cc_final: 0.8612 (ttp) REVERT: C 246 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 281 TYR cc_start: 0.9387 (t80) cc_final: 0.9131 (t80) REVERT: C 284 MET cc_start: 0.8737 (mtp) cc_final: 0.8164 (tmm) REVERT: D 79 TYR cc_start: 0.8955 (t80) cc_final: 0.8627 (t80) REVERT: D 97 ILE cc_start: 0.8440 (mt) cc_final: 0.8163 (tt) REVERT: E 205 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8201 (pp20) REVERT: E 243 MET cc_start: 0.8474 (ttm) cc_final: 0.8121 (ttt) REVERT: E 276 MET cc_start: 0.9004 (mmt) cc_final: 0.8463 (mmt) REVERT: E 322 ASP cc_start: 0.9310 (t0) cc_final: 0.8895 (m-30) REVERT: E 329 MET cc_start: 0.8995 (tpt) cc_final: 0.8738 (tpp) REVERT: F 71 PHE cc_start: 0.8432 (m-80) cc_final: 0.8196 (m-80) REVERT: G 276 MET cc_start: 0.9329 (mtm) cc_final: 0.8636 (tmm) REVERT: H 57 LEU cc_start: 0.8722 (mt) cc_final: 0.8477 (mt) REVERT: H 67 LEU cc_start: 0.8590 (mt) cc_final: 0.8064 (pt) REVERT: Q 118 ILE cc_start: 0.9486 (mt) cc_final: 0.8822 (mt) REVERT: Q 125 ASP cc_start: 0.8310 (t0) cc_final: 0.8089 (t0) REVERT: Q 147 MET cc_start: 0.7765 (ptp) cc_final: 0.7324 (ptp) REVERT: Q 229 MET cc_start: 0.8388 (mmp) cc_final: 0.8102 (mmp) REVERT: Q 256 MET cc_start: 0.8123 (mmm) cc_final: 0.7842 (mmm) REVERT: Q 300 GLN cc_start: 0.8885 (tt0) cc_final: 0.8683 (tm-30) REVERT: Q 330 MET cc_start: 0.8263 (tmm) cc_final: 0.7838 (tmm) REVERT: Q 386 MET cc_start: 0.8525 (mtt) cc_final: 0.8084 (ttt) REVERT: Q 442 MET cc_start: 0.7656 (ppp) cc_final: 0.7425 (ppp) REVERT: R 178 HIS cc_start: 0.7355 (t70) cc_final: 0.7093 (t70) REVERT: R 191 MET cc_start: 0.6324 (mmm) cc_final: 0.4987 (mmm) REVERT: R 266 MET cc_start: 0.9164 (mmp) cc_final: 0.8893 (mmp) REVERT: R 299 TYR cc_start: 0.8451 (m-80) cc_final: 0.7895 (m-10) REVERT: R 321 PHE cc_start: 0.8970 (t80) cc_final: 0.8754 (t80) REVERT: R 322 CYS cc_start: 0.8949 (m) cc_final: 0.8709 (m) REVERT: R 382 LEU cc_start: 0.8945 (tp) cc_final: 0.8667 (tp) REVERT: R 387 PHE cc_start: 0.8990 (t80) cc_final: 0.8739 (t80) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2266 time to fit residues: 77.5064 Evaluate side-chains 181 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.045173 restraints weight = 74317.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046552 restraints weight = 42960.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.047535 restraints weight = 29465.442| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12339 Z= 0.158 Angle : 0.613 8.300 16587 Z= 0.311 Chirality : 0.040 0.177 1793 Planarity : 0.003 0.042 2094 Dihedral : 4.702 21.174 1605 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.12 (0.22), residues: 1440 helix: 1.61 (0.16), residues: 1064 sheet: -4.28 (0.71), residues: 17 loop : -1.67 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 256 HIS 0.003 0.001 HIS G 195 PHE 0.028 0.001 PHE H 88 TYR 0.015 0.001 TYR E 268 ARG 0.005 0.000 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.86 seconds wall clock time: 44 minutes 23.01 seconds (2663.01 seconds total)