Starting phenix.real_space_refine on Thu Jan 18 03:25:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zth_14960/01_2024/7zth_14960_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 18 5.16 5 C 4622 2.51 5 N 1325 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2962 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2977 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 834 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Time building chain proxies: 4.17, per 1000 atoms: 0.55 Number of scatterers: 7620 At special positions: 0 Unit cell: (82.677, 90.678, 132.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 84 15.00 O 1571 8.00 N 1325 7.00 C 4622 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: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 6 sheets defined 30.6% alpha, 6.5% beta 12 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 121 through 124 No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.352A pdb=" N GLU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 4.151A pdb=" N GLN A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 256 through 267 removed outlier: 4.278A pdb=" N GLN A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.971A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 362 through 380 removed outlier: 4.161A pdb=" N LYS A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.895A pdb=" N GLU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 6.020A pdb=" N GLU A 452 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A 455 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 459 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 460 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 removed outlier: 4.361A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.715A pdb=" N ILE B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 228 through 231 No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.852A pdb=" N HIS B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 No H-bonds generated for 'chain 'B' and resid 292 through 295' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.843A pdb=" N HIS B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 382 removed outlier: 3.518A pdb=" N TYR B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.754A pdb=" N VAL B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 removed outlier: 5.137A pdb=" N GLU B 452 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 453 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 455 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 459 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 460 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 461 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 172 through 175 Processing sheet with id= B, first strand: chain 'A' and resid 215 through 219 removed outlier: 3.532A pdb=" N ILE A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 238 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLU A 198 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TYR A 240 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 272 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 241 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE A 274 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.544A pdb=" N ILE A 390 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 402 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.597A pdb=" N ASP B 215 " --> pdb=" O TYR B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 238 through 241 removed outlier: 6.979A pdb=" N TYR B 272 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N THR B 241 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE B 274 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 397 through 399 83 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1671 1.33 - 1.45: 2151 1.45 - 1.57: 3955 1.57 - 1.69: 164 1.69 - 1.81: 32 Bond restraints: 7973 Sorted by residual: bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.536 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.540 0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.437 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.618 -0.154 2.00e-02 2.50e+03 5.89e+01 ... (remaining 7968 not shown) Histogram of bond angle deviations from ideal: 96.99 - 104.47: 388 104.47 - 111.94: 3863 111.94 - 119.41: 2899 119.41 - 126.88: 3707 126.88 - 134.35: 295 Bond angle restraints: 11152 Sorted by residual: angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 109.01 100.06 8.95 1.13e+00 7.83e-01 6.28e+01 angle pdb=" C ASP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.62e+01 angle pdb=" CA ILE A 289 " pdb=" C ILE A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 117.00 120.72 -3.72 9.50e-01 1.11e+00 1.54e+01 angle pdb=" C ILE A 105 " pdb=" N ARG A 106 " pdb=" CA ARG A 106 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.42e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 109.29 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 11147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 3953 29.96 - 59.91: 576 59.91 - 89.87: 27 89.87 - 119.83: 0 119.83 - 149.78: 3 Dihedral angle restraints: 4559 sinusoidal: 2427 harmonic: 2132 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N LYS B 287 " pdb=" CA LYS B 287 " ideal model delta harmonic sigma weight residual 180.00 -136.34 -43.66 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA GLY B 177 " pdb=" C GLY B 177 " pdb=" N VAL B 178 " pdb=" CA VAL B 178 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" N HIS B 137 " pdb=" CA HIS B 137 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1018 0.081 - 0.161: 193 0.161 - 0.241: 8 0.241 - 0.322: 1 0.322 - 0.402: 1 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CB ILE A 446 " pdb=" CA ILE A 446 " pdb=" CG1 ILE A 446 " pdb=" CG2 ILE A 446 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU B 187 " pdb=" CB LEU B 187 " pdb=" CD1 LEU B 187 " pdb=" CD2 LEU B 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.97e-01 ... (remaining 1218 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.157 2.00e-02 2.50e+03 2.82e-01 7.96e+02 pdb=" NZ LLP A 309 " -0.384 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.132 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " -0.297 2.00e-02 2.50e+03 2.77e-01 7.65e+02 pdb=" NZ LLP B 309 " 0.311 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " -0.253 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " 0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 289 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO A 290 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.040 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1642 2.78 - 3.31: 6254 3.31 - 3.84: 12643 3.84 - 4.37: 14006 4.37 - 4.90: 22309 Nonbonded interactions: 56854 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP A 276 " model vdw 2.244 2.440 nonbonded pdb=" O SER A 314 " pdb=" OG SER A 314 " model vdw 2.261 2.440 nonbonded pdb=" OE1 GLN A 184 " pdb=" OH TYR A 330 " model vdw 2.268 2.440 nonbonded pdb=" O GLU B 453 " pdb=" OG1 THR B 457 " model vdw 2.290 2.440 nonbonded pdb=" O GLY B 177 " pdb=" OG SER B 318 " model vdw 2.294 2.440 ... (remaining 56849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 105 through 464) } 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.550 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.190 7973 Z= 0.558 Angle : 1.065 10.797 11152 Z= 0.585 Chirality : 0.060 0.402 1221 Planarity : 0.014 0.282 1133 Dihedral : 23.039 149.781 3191 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.24 % Allowed : 15.06 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -5.31 (0.24), residues: 712 helix: -4.33 (0.17), residues: 232 sheet: -3.13 (0.41), residues: 112 loop : -3.09 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 124 HIS 0.015 0.002 HIS B 113 PHE 0.025 0.004 PHE A 307 TYR 0.028 0.003 TYR B 202 ARG 0.010 0.001 ARG B 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.778 Fit side-chains REVERT: A 122 GLU cc_start: 0.7871 (mp0) cc_final: 0.6732 (pm20) REVERT: A 138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7292 (mtp180) REVERT: A 353 MET cc_start: 0.7643 (mtm) cc_final: 0.7435 (mtm) outliers start: 8 outliers final: 4 residues processed: 91 average time/residue: 0.2558 time to fit residues: 29.6486 Evaluate side-chains 60 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 146 GLN A 211 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 220 GLN B 328 HIS B 332 ASN B 438 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7973 Z= 0.243 Angle : 0.662 7.832 11152 Z= 0.366 Chirality : 0.044 0.190 1221 Planarity : 0.006 0.060 1133 Dihedral : 24.734 145.326 1750 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.73 % Allowed : 20.81 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -4.53 (0.27), residues: 712 helix: -3.40 (0.27), residues: 232 sheet: -2.43 (0.48), residues: 106 loop : -2.93 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 124 HIS 0.010 0.001 HIS B 110 PHE 0.014 0.002 PHE A 307 TYR 0.020 0.002 TYR A 157 ARG 0.002 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 0.543 Fit side-chains REVERT: A 122 GLU cc_start: 0.7866 (mp0) cc_final: 0.6786 (pm20) REVERT: A 138 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7410 (mtp180) REVERT: B 370 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7479 (ttm110) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.1585 time to fit residues: 18.7019 Evaluate side-chains 74 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.0040 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7973 Z= 0.182 Angle : 0.586 7.508 11152 Z= 0.321 Chirality : 0.041 0.165 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.381 144.339 1750 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.35 % Allowed : 22.20 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.90 (0.28), residues: 712 helix: -2.83 (0.29), residues: 234 sheet: -1.89 (0.50), residues: 106 loop : -2.63 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.006 0.001 HIS B 110 PHE 0.011 0.001 PHE A 307 TYR 0.017 0.001 TYR A 157 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 0.714 Fit side-chains REVERT: A 114 ILE cc_start: 0.6303 (tt) cc_final: 0.5969 (tt) REVERT: A 122 GLU cc_start: 0.7894 (mp0) cc_final: 0.6736 (pm20) REVERT: A 138 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7329 (mtp180) REVERT: B 110 HIS cc_start: 0.7706 (t-90) cc_final: 0.7398 (t-170) outliers start: 28 outliers final: 18 residues processed: 92 average time/residue: 0.1595 time to fit residues: 21.0300 Evaluate side-chains 78 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.0060 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7973 Z= 0.188 Angle : 0.583 8.220 11152 Z= 0.317 Chirality : 0.042 0.211 1221 Planarity : 0.005 0.052 1133 Dihedral : 24.334 145.305 1748 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.43 % Allowed : 23.29 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.65 (0.29), residues: 712 helix: -2.62 (0.30), residues: 239 sheet: -1.71 (0.50), residues: 106 loop : -2.49 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.007 0.001 HIS B 110 PHE 0.011 0.001 PHE A 334 TYR 0.022 0.001 TYR A 157 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 64 time to evaluate : 0.591 Fit side-chains REVERT: A 122 GLU cc_start: 0.7889 (mp0) cc_final: 0.6759 (pm20) REVERT: A 138 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7486 (mtp180) outliers start: 35 outliers final: 28 residues processed: 92 average time/residue: 0.1268 time to fit residues: 17.0624 Evaluate side-chains 88 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 60 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.0030 chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 0.0010 chunk 26 optimal weight: 4.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7973 Z= 0.208 Angle : 0.594 10.277 11152 Z= 0.321 Chirality : 0.042 0.162 1221 Planarity : 0.005 0.051 1133 Dihedral : 24.288 145.712 1748 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.28 % Allowed : 23.60 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.45 (0.29), residues: 712 helix: -2.43 (0.31), residues: 237 sheet: -1.63 (0.51), residues: 106 loop : -2.38 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.004 0.001 HIS B 113 PHE 0.011 0.001 PHE A 307 TYR 0.019 0.001 TYR A 157 ARG 0.001 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 62 time to evaluate : 0.666 Fit side-chains REVERT: A 122 GLU cc_start: 0.7888 (mp0) cc_final: 0.6779 (pm20) REVERT: A 138 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7322 (mtp180) outliers start: 34 outliers final: 30 residues processed: 88 average time/residue: 0.1571 time to fit residues: 20.1459 Evaluate side-chains 88 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 58 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7973 Z= 0.192 Angle : 0.589 9.687 11152 Z= 0.316 Chirality : 0.042 0.161 1221 Planarity : 0.005 0.051 1133 Dihedral : 24.240 146.192 1748 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.90 % Allowed : 24.53 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.30 (0.30), residues: 712 helix: -2.36 (0.32), residues: 237 sheet: -1.50 (0.51), residues: 106 loop : -2.27 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 PHE 0.010 0.001 PHE A 307 TYR 0.017 0.001 TYR A 157 ARG 0.002 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 63 time to evaluate : 0.739 Fit side-chains REVERT: A 122 GLU cc_start: 0.7875 (mp0) cc_final: 0.6755 (pm20) REVERT: A 138 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7308 (mtp180) REVERT: B 353 MET cc_start: 0.8190 (mtm) cc_final: 0.7968 (ttm) outliers start: 38 outliers final: 35 residues processed: 92 average time/residue: 0.1537 time to fit residues: 20.8188 Evaluate side-chains 94 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 59 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7973 Z= 0.182 Angle : 0.579 9.476 11152 Z= 0.311 Chirality : 0.042 0.185 1221 Planarity : 0.005 0.051 1133 Dihedral : 24.196 146.856 1748 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.52 % Allowed : 24.22 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.18 (0.30), residues: 712 helix: -2.26 (0.32), residues: 237 sheet: -1.40 (0.51), residues: 106 loop : -2.21 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 PHE 0.011 0.001 PHE A 307 TYR 0.024 0.001 TYR A 157 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 65 time to evaluate : 0.758 Fit side-chains REVERT: A 122 GLU cc_start: 0.7859 (mp0) cc_final: 0.6745 (pm20) REVERT: A 138 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7295 (mtp180) REVERT: B 353 MET cc_start: 0.8210 (mtm) cc_final: 0.7932 (ttm) outliers start: 42 outliers final: 40 residues processed: 97 average time/residue: 0.1523 time to fit residues: 21.5661 Evaluate side-chains 103 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 63 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 0.0670 overall best weight: 1.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7973 Z= 0.189 Angle : 0.582 9.406 11152 Z= 0.312 Chirality : 0.042 0.224 1221 Planarity : 0.005 0.051 1133 Dihedral : 24.185 147.173 1748 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.52 % Allowed : 24.38 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -3.05 (0.30), residues: 712 helix: -2.13 (0.32), residues: 237 sheet: -1.35 (0.51), residues: 106 loop : -2.14 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 264 HIS 0.005 0.001 HIS B 110 PHE 0.010 0.001 PHE A 307 TYR 0.022 0.001 TYR A 157 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 63 time to evaluate : 0.676 Fit side-chains REVERT: A 122 GLU cc_start: 0.7852 (mp0) cc_final: 0.6750 (pm20) REVERT: A 138 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7300 (mtp180) outliers start: 42 outliers final: 39 residues processed: 96 average time/residue: 0.1554 time to fit residues: 21.7721 Evaluate side-chains 101 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 62 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7973 Z= 0.154 Angle : 0.550 9.207 11152 Z= 0.295 Chirality : 0.040 0.188 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.042 149.324 1748 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.50 % Allowed : 26.24 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.30), residues: 712 helix: -1.74 (0.34), residues: 231 sheet: -1.13 (0.51), residues: 108 loop : -1.94 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 264 HIS 0.003 0.001 HIS B 110 PHE 0.008 0.001 PHE B 352 TYR 0.022 0.001 TYR A 157 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7880 (mp0) cc_final: 0.6768 (pm20) REVERT: A 138 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7258 (mtp180) REVERT: A 343 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7489 (ttt180) outliers start: 29 outliers final: 27 residues processed: 92 average time/residue: 0.1700 time to fit residues: 22.3427 Evaluate side-chains 89 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 62 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7973 Z= 0.171 Angle : 0.564 9.191 11152 Z= 0.302 Chirality : 0.040 0.161 1221 Planarity : 0.005 0.059 1133 Dihedral : 24.009 149.338 1748 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.81 % Allowed : 26.09 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.31), residues: 712 helix: -1.60 (0.34), residues: 228 sheet: -0.93 (0.51), residues: 104 loop : -1.84 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 264 HIS 0.004 0.001 HIS B 110 PHE 0.010 0.001 PHE B 358 TYR 0.022 0.001 TYR A 157 ARG 0.002 0.000 ARG B 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 63 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 122 GLU cc_start: 0.7813 (mp0) cc_final: 0.6775 (pm20) REVERT: A 138 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7263 (mtp180) REVERT: B 353 MET cc_start: 0.8137 (mtm) cc_final: 0.7935 (ttm) outliers start: 31 outliers final: 31 residues processed: 88 average time/residue: 0.1657 time to fit residues: 21.2564 Evaluate side-chains 92 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 61 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.166345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130308 restraints weight = 14501.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132047 restraints weight = 12268.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132769 restraints weight = 7984.223| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7973 Z= 0.231 Angle : 0.614 8.663 11152 Z= 0.329 Chirality : 0.042 0.168 1221 Planarity : 0.005 0.061 1133 Dihedral : 24.083 148.809 1748 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.43 % Allowed : 25.00 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.31), residues: 712 helix: -1.70 (0.33), residues: 235 sheet: -1.01 (0.52), residues: 104 loop : -1.92 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 264 HIS 0.004 0.001 HIS A 338 PHE 0.010 0.002 PHE A 307 TYR 0.023 0.002 TYR A 157 ARG 0.002 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1484.69 seconds wall clock time: 30 minutes 45.33 seconds (1845.33 seconds total)