Starting phenix.real_space_refine on Thu Nov 14 20:21:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/11_2024/8szk_40919.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4749 2.51 5 N 1259 2.21 5 O 1351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7392 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 748 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "C" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1193 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3298 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Time building chain proxies: 4.62, per 1000 atoms: 0.63 Number of scatterers: 7392 At special positions: 0 Unit cell: (75.9, 113.3, 134.2, 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 33 16.00 O 1351 8.00 N 1259 7.00 C 4749 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 - 3.00 Amino acid : True - 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: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 52.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 39 through 47 Processing helix chain 'B' and resid 66 through 83 Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'C' and resid 4 through 11 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.650A pdb=" N GLN C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.926A pdb=" N GLN G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.561A pdb=" N ILE G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 removed outlier: 3.655A pdb=" N GLY G 138 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 154 removed outlier: 3.586A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 170 removed outlier: 3.657A pdb=" N LEU G 169 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G 170 " --> pdb=" O VAL G 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 165 through 170' Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 92 through 110 removed outlier: 3.859A pdb=" N ILE D 96 " --> pdb=" O LYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 119 through 132 removed outlier: 3.932A pdb=" N ASN D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 171 removed outlier: 4.476A pdb=" N LEU D 161 " --> pdb=" O PRO D 157 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 162 " --> pdb=" O HIS D 158 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.847A pdb=" N ARG D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 195 removed outlier: 3.715A pdb=" N VAL D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 200 through 218 removed outlier: 3.624A pdb=" N ARG D 204 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP D 205 " --> pdb=" O PRO D 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 238 removed outlier: 3.535A pdb=" N PHE D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.700A pdb=" N GLU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 275 removed outlier: 3.776A pdb=" N PHE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 282 Processing helix chain 'D' and resid 284 through 301 removed outlier: 4.097A pdb=" N PHE D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.754A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.549A pdb=" N GLU D 326 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 328 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 removed outlier: 3.522A pdb=" N LYS D 346 " --> pdb=" O PRO D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 360 removed outlier: 3.506A pdb=" N GLN D 355 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.527A pdb=" N ALA D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 377 removed outlier: 3.553A pdb=" N ASN D 377 " --> pdb=" O PHE D 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 377' Processing helix chain 'D' and resid 378 through 387 removed outlier: 3.675A pdb=" N GLU D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 402 Proline residue: D 393 - end of helix removed outlier: 4.543A pdb=" N ALA D 397 " --> pdb=" O PRO D 393 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 423 removed outlier: 3.555A pdb=" N ASN D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 449 removed outlier: 3.596A pdb=" N PHE D 430 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 3.543A pdb=" N ILE A 14 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 7 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 16 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 32 removed outlier: 9.586A pdb=" N VAL B 60 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS B 20 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE B 62 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE B 22 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 87 removed outlier: 3.671A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 123 " --> pdb=" O CYS C 25 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS C 25 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 55 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 21.024A pdb=" N TRP G 5 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 18.378A pdb=" N LYS G 91 " --> pdb=" O TRP G 5 " (cutoff:3.500A) removed outlier: 14.280A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG G 90 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS G 63 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU G 64 " --> pdb=" O HIS G 56 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE G 66 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU G 54 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR G 68 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 85 through 87 removed outlier: 18.000A pdb=" N SER G 95 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N GLN G 97 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 102 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG G 90 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS G 63 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU G 64 " --> pdb=" O HIS G 56 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N HIS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE G 66 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU G 54 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR G 68 " --> pdb=" O SER G 52 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 957 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: 1.97 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.10: 1 1.10 - 1.28: 1228 1.28 - 1.46: 2424 1.46 - 1.64: 3860 1.64 - 1.81: 51 Bond restraints: 7564 Sorted by residual: bond pdb=" CG PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 1.503 0.926 0.577 3.40e-02 8.65e+02 2.88e+02 bond pdb=" N PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 1.473 1.580 -0.107 1.40e-02 5.10e+03 5.86e+01 bond pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 1.473 1.434 0.039 1.32e-02 5.74e+03 8.85e+00 bond pdb=" CB VAL C 108 " pdb=" CG1 VAL C 108 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.17e+00 bond pdb=" CB TRP G 5 " pdb=" CG TRP G 5 " ideal model delta sigma weight residual 1.498 1.553 -0.055 3.10e-02 1.04e+03 3.12e+00 ... (remaining 7559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.35: 10177 5.35 - 10.70: 36 10.70 - 16.05: 5 16.05 - 21.40: 1 21.40 - 26.75: 1 Bond angle restraints: 10220 Sorted by residual: angle pdb=" N PRO A 39 " pdb=" CD PRO A 39 " pdb=" CG PRO A 39 " ideal model delta sigma weight residual 103.20 76.45 26.75 1.50e+00 4.44e-01 3.18e+02 angle pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" CD PRO A 39 " ideal model delta sigma weight residual 112.00 96.55 15.45 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " pdb=" CG PRO A 39 " ideal model delta sigma weight residual 104.50 84.91 19.59 1.90e+00 2.77e-01 1.06e+02 angle pdb=" N PRO A 39 " pdb=" CA PRO A 39 " pdb=" C PRO A 39 " ideal model delta sigma weight residual 113.47 123.35 -9.88 1.43e+00 4.89e-01 4.78e+01 angle pdb=" N PRO A 39 " pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " ideal model delta sigma weight residual 103.23 97.31 5.92 1.07e+00 8.73e-01 3.06e+01 ... (remaining 10215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 3875 17.90 - 35.81: 522 35.81 - 53.71: 147 53.71 - 71.62: 26 71.62 - 89.52: 11 Dihedral angle restraints: 4581 sinusoidal: 1917 harmonic: 2664 Sorted by residual: dihedral pdb=" CA TRP G 70 " pdb=" C TRP G 70 " pdb=" N GLY G 71 " pdb=" CA GLY G 71 " ideal model delta harmonic sigma weight residual 180.00 -146.54 -33.46 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 961 0.070 - 0.140: 135 0.140 - 0.211: 12 0.211 - 0.281: 4 0.281 - 0.351: 2 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB THR A 23 " pdb=" CA THR A 23 " pdb=" OG1 THR A 23 " pdb=" CG2 THR A 23 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ILE A 14 " pdb=" N ILE A 14 " pdb=" C ILE A 14 " pdb=" CB ILE A 14 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1111 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 38 " -0.108 5.00e-02 4.00e+02 1.47e-01 3.47e+01 pdb=" N PRO A 39 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 115 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C ASP C 115 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP C 115 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 116 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 15 " 0.216 9.50e-02 1.11e+02 9.67e-02 5.76e+00 pdb=" NE ARG G 15 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG G 15 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 15 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 15 " 0.009 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 921 2.75 - 3.29: 7655 3.29 - 3.83: 11653 3.83 - 4.36: 13340 4.36 - 4.90: 22349 Nonbonded interactions: 55918 Sorted by model distance: nonbonded pdb=" O THR A 63 " pdb=" OG1 THR A 66 " model vdw 2.213 3.040 nonbonded pdb=" NH2 ARG A 37 " pdb=" O PRO A 38 " model vdw 2.225 3.120 nonbonded pdb=" O SER C 22 " pdb=" OG SER C 22 " model vdw 2.236 3.040 nonbonded pdb=" O ASN D 417 " pdb=" OG1 THR D 421 " model vdw 2.262 3.040 nonbonded pdb=" O ASN D 426 " pdb=" OD1 ASN D 426 " model vdw 2.274 3.040 ... (remaining 55913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.750 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.008 0.577 7564 Z= 0.551 Angle : 1.047 26.754 10220 Z= 0.584 Chirality : 0.052 0.351 1114 Planarity : 0.007 0.147 1312 Dihedral : 17.881 89.521 2841 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.00 % Favored : 91.10 % Rotamer: Outliers : 0.87 % Allowed : 30.27 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.59 (0.29), residues: 888 helix: 0.52 (0.28), residues: 374 sheet: 0.64 (0.60), residues: 81 loop : -1.43 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 5 HIS 0.013 0.002 HIS G 73 PHE 0.039 0.002 PHE A 79 TYR 0.025 0.002 TYR D 437 ARG 0.010 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 283 time to evaluate : 0.813 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: B 30 ILE cc_start: 0.7753 (tt) cc_final: 0.7430 (mt) REVERT: C 49 ARG cc_start: 0.7431 (mmm-85) cc_final: 0.6925 (mmm-85) REVERT: C 83 ARG cc_start: 0.6327 (mpp80) cc_final: 0.5606 (ptp90) REVERT: C 91 GLU cc_start: 0.6549 (mp0) cc_final: 0.5786 (mp0) REVERT: C 98 LYS cc_start: 0.7127 (tttm) cc_final: 0.6639 (tttm) REVERT: C 104 ASN cc_start: 0.8344 (t0) cc_final: 0.8053 (t0) REVERT: C 145 GLU cc_start: 0.7497 (tp30) cc_final: 0.7181 (tp30) REVERT: D 68 GLN cc_start: 0.7170 (pt0) cc_final: 0.6961 (tt0) REVERT: D 118 SER cc_start: 0.7993 (p) cc_final: 0.7769 (t) REVERT: D 126 MET cc_start: 0.7685 (tpt) cc_final: 0.7429 (tpt) REVERT: D 127 ILE cc_start: 0.8375 (mm) cc_final: 0.8169 (mt) REVERT: D 161 LEU cc_start: 0.8251 (mm) cc_final: 0.7901 (mm) REVERT: D 191 GLN cc_start: 0.8225 (mt0) cc_final: 0.7953 (mt0) REVERT: D 204 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7630 (mtm110) REVERT: D 207 LEU cc_start: 0.8968 (tp) cc_final: 0.8720 (tp) REVERT: D 208 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8113 (ttpt) REVERT: D 222 ARG cc_start: 0.8438 (mtp180) cc_final: 0.8130 (mtt180) REVERT: D 258 ASN cc_start: 0.8305 (t0) cc_final: 0.7999 (t0) REVERT: D 265 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7814 (mtmm) REVERT: D 283 LYS cc_start: 0.7994 (tptt) cc_final: 0.7777 (tptt) REVERT: D 285 LEU cc_start: 0.8081 (tt) cc_final: 0.7796 (tp) REVERT: D 348 ILE cc_start: 0.7566 (pt) cc_final: 0.7227 (pt) REVERT: D 349 GLU cc_start: 0.6462 (mp0) cc_final: 0.6071 (mp0) REVERT: D 389 ASP cc_start: 0.7496 (p0) cc_final: 0.7296 (p0) REVERT: D 398 SER cc_start: 0.8694 (m) cc_final: 0.8148 (t) REVERT: D 441 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7204 (mmm-85) outliers start: 7 outliers final: 2 residues processed: 287 average time/residue: 0.2097 time to fit residues: 75.6593 Evaluate side-chains 266 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain D residue 304 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS C 37 HIS G 28 HIS G 43 HIS G 73 HIS G 108 HIS ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 77 GLN D 212 HIS D 228 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7564 Z= 0.229 Angle : 0.721 7.889 10220 Z= 0.379 Chirality : 0.046 0.281 1114 Planarity : 0.005 0.040 1312 Dihedral : 4.852 30.263 981 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.98 % Favored : 92.68 % Rotamer: Outliers : 5.21 % Allowed : 27.79 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 888 helix: 0.73 (0.26), residues: 411 sheet: 0.68 (0.54), residues: 88 loop : -1.53 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 5 HIS 0.012 0.002 HIS G 73 PHE 0.023 0.002 PHE D 396 TYR 0.015 0.002 TYR D 437 ARG 0.007 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.829 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: B 30 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7722 (mt) REVERT: C 91 GLU cc_start: 0.6902 (mp0) cc_final: 0.6127 (mp0) REVERT: C 104 ASN cc_start: 0.8514 (t0) cc_final: 0.8141 (t0) REVERT: C 126 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5463 (mp0) REVERT: C 145 GLU cc_start: 0.7343 (tp30) cc_final: 0.7083 (tp30) REVERT: G 97 GLN cc_start: 0.8278 (mp10) cc_final: 0.7820 (mm-40) REVERT: D 75 LEU cc_start: 0.8068 (mm) cc_final: 0.7712 (mm) REVERT: D 107 TYR cc_start: 0.7937 (t80) cc_final: 0.7737 (t80) REVERT: D 115 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8029 (tp) REVERT: D 118 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7717 (t) REVERT: D 127 ILE cc_start: 0.8249 (mm) cc_final: 0.8019 (mt) REVERT: D 161 LEU cc_start: 0.8256 (mm) cc_final: 0.7930 (mm) REVERT: D 171 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6624 (mt-10) REVERT: D 194 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7160 (mm-30) REVERT: D 253 LEU cc_start: 0.8211 (mt) cc_final: 0.7917 (mm) REVERT: D 256 ILE cc_start: 0.7519 (tt) cc_final: 0.7312 (tt) REVERT: D 265 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7651 (mtmm) REVERT: D 274 LYS cc_start: 0.6566 (mmtt) cc_final: 0.6354 (mmtt) REVERT: D 283 LYS cc_start: 0.8007 (tptt) cc_final: 0.7787 (tptt) REVERT: D 285 LEU cc_start: 0.8084 (tt) cc_final: 0.7740 (tp) REVERT: D 335 GLU cc_start: 0.7303 (tp30) cc_final: 0.7070 (tp30) REVERT: D 344 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6823 (mm-40) REVERT: D 385 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6196 (mm-30) REVERT: D 401 LYS cc_start: 0.8137 (tppt) cc_final: 0.7863 (ttmm) REVERT: D 408 ASN cc_start: 0.8243 (t0) cc_final: 0.7699 (t0) REVERT: D 444 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7124 (tm-30) outliers start: 42 outliers final: 16 residues processed: 287 average time/residue: 0.2603 time to fit residues: 94.0996 Evaluate side-chains 272 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 225 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 HIS C 37 HIS G 83 GLN G 146 GLN D 212 HIS D 387 ASN D 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7564 Z= 0.283 Angle : 0.693 7.397 10220 Z= 0.362 Chirality : 0.046 0.268 1114 Planarity : 0.004 0.040 1312 Dihedral : 4.598 28.499 978 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.32 % Favored : 92.45 % Rotamer: Outliers : 5.21 % Allowed : 28.91 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 888 helix: 0.86 (0.26), residues: 414 sheet: 0.62 (0.61), residues: 67 loop : -1.69 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 5 HIS 0.007 0.001 HIS D 212 PHE 0.030 0.002 PHE A 15 TYR 0.025 0.002 TYR B 79 ARG 0.008 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7715 (mt) REVERT: C 91 GLU cc_start: 0.6944 (mp0) cc_final: 0.6189 (mp0) REVERT: C 126 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5516 (mp0) REVERT: C 149 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7962 (mtm180) REVERT: G 41 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: G 83 GLN cc_start: 0.8230 (mp-120) cc_final: 0.7936 (mp10) REVERT: G 97 GLN cc_start: 0.8414 (mp10) cc_final: 0.7943 (mm-40) REVERT: D 69 GLU cc_start: 0.6339 (tm-30) cc_final: 0.5656 (tm-30) REVERT: D 73 GLN cc_start: 0.7316 (mt0) cc_final: 0.6836 (mt0) REVERT: D 156 TRP cc_start: 0.7691 (t-100) cc_final: 0.6968 (t-100) REVERT: D 161 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7984 (mm) REVERT: D 171 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6594 (mt-10) REVERT: D 194 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7179 (mm-30) REVERT: D 202 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8297 (mtm180) REVERT: D 208 LYS cc_start: 0.8429 (ttpt) cc_final: 0.7495 (ttpt) REVERT: D 209 THR cc_start: 0.8691 (t) cc_final: 0.8333 (m) REVERT: D 222 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8112 (mtt180) REVERT: D 248 GLU cc_start: 0.6808 (mp0) cc_final: 0.6198 (mp0) REVERT: D 265 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7758 (mtmm) REVERT: D 274 LYS cc_start: 0.6713 (mmtt) cc_final: 0.6441 (mmtt) REVERT: D 283 LYS cc_start: 0.8014 (tptt) cc_final: 0.7765 (tptt) REVERT: D 285 LEU cc_start: 0.8209 (tt) cc_final: 0.7885 (tp) REVERT: D 305 THR cc_start: 0.8574 (p) cc_final: 0.8314 (m) REVERT: D 334 GLU cc_start: 0.7696 (tt0) cc_final: 0.7451 (tt0) REVERT: D 335 GLU cc_start: 0.7346 (tp30) cc_final: 0.7078 (tp30) REVERT: D 344 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6775 (mm-40) REVERT: D 347 LYS cc_start: 0.7455 (mttp) cc_final: 0.7084 (mttp) REVERT: D 373 TYR cc_start: 0.7784 (m-10) cc_final: 0.7571 (m-80) REVERT: D 408 ASN cc_start: 0.8475 (t0) cc_final: 0.8246 (t0) outliers start: 42 outliers final: 25 residues processed: 286 average time/residue: 0.2605 time to fit residues: 93.1117 Evaluate side-chains 289 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 105 GLN G 139 HIS D 68 GLN D 212 HIS D 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7564 Z= 0.243 Angle : 0.658 7.608 10220 Z= 0.344 Chirality : 0.044 0.171 1114 Planarity : 0.004 0.033 1312 Dihedral : 4.593 26.968 978 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 5.96 % Allowed : 29.65 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.36 (0.28), residues: 888 helix: 0.93 (0.26), residues: 412 sheet: 0.31 (0.57), residues: 82 loop : -1.67 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 5 HIS 0.005 0.001 HIS D 212 PHE 0.023 0.002 PHE D 396 TYR 0.022 0.002 TYR B 79 ARG 0.007 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.5992 (tp30) cc_final: 0.5782 (tp30) REVERT: C 91 GLU cc_start: 0.6896 (mp0) cc_final: 0.6115 (mp0) REVERT: C 113 TRP cc_start: 0.8268 (p-90) cc_final: 0.7620 (p-90) REVERT: C 122 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5722 (tpp) REVERT: C 149 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.8056 (mtm180) REVERT: G 41 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7185 (mmm-85) REVERT: G 70 TRP cc_start: 0.7160 (p90) cc_final: 0.6864 (p90) REVERT: G 97 GLN cc_start: 0.8383 (mp10) cc_final: 0.7927 (mm-40) REVERT: D 161 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7998 (mm) REVERT: D 171 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6620 (mt-10) REVERT: D 194 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7147 (mm-30) REVERT: D 208 LYS cc_start: 0.8389 (ttpt) cc_final: 0.8128 (ttpp) REVERT: D 209 THR cc_start: 0.8600 (t) cc_final: 0.8332 (m) REVERT: D 256 ILE cc_start: 0.7764 (tt) cc_final: 0.7432 (tt) REVERT: D 265 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7720 (mtmm) REVERT: D 274 LYS cc_start: 0.6681 (mmtt) cc_final: 0.6448 (mmtt) REVERT: D 283 LYS cc_start: 0.7900 (tptt) cc_final: 0.7698 (tptt) REVERT: D 285 LEU cc_start: 0.8241 (tt) cc_final: 0.7867 (tp) REVERT: D 305 THR cc_start: 0.8509 (p) cc_final: 0.8303 (m) REVERT: D 326 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6400 (tp30) REVERT: D 335 GLU cc_start: 0.7403 (tp30) cc_final: 0.7063 (tp30) REVERT: D 344 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6900 (mm-40) REVERT: D 395 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7059 (mtm) REVERT: D 408 ASN cc_start: 0.8475 (t0) cc_final: 0.8250 (t0) outliers start: 48 outliers final: 24 residues processed: 275 average time/residue: 0.2662 time to fit residues: 91.7453 Evaluate side-chains 277 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 404 LYS Chi-restraints excluded: chain D residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS ** D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7564 Z= 0.273 Angle : 0.665 7.899 10220 Z= 0.345 Chirality : 0.045 0.152 1114 Planarity : 0.004 0.037 1312 Dihedral : 4.648 28.913 978 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.55 % Favored : 92.34 % Rotamer: Outliers : 5.83 % Allowed : 28.91 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.24 (0.28), residues: 888 helix: 1.05 (0.26), residues: 408 sheet: 0.53 (0.58), residues: 81 loop : -1.65 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 5 HIS 0.005 0.001 HIS D 212 PHE 0.019 0.002 PHE D 396 TYR 0.030 0.002 TYR B 79 ARG 0.007 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.6771 (ptm160) cc_final: 0.6467 (ptm160) REVERT: A 29 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.2514 (mmt90) REVERT: C 24 GLU cc_start: 0.6411 (tp30) cc_final: 0.6155 (tp30) REVERT: C 113 TRP cc_start: 0.8245 (p-90) cc_final: 0.7672 (p-90) REVERT: C 122 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5725 (tpp) REVERT: C 149 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8209 (mtm180) REVERT: G 7 VAL cc_start: 0.8480 (t) cc_final: 0.8239 (m) REVERT: G 70 TRP cc_start: 0.7271 (p90) cc_final: 0.6871 (p90) REVERT: G 97 GLN cc_start: 0.8389 (mp10) cc_final: 0.7961 (mm-40) REVERT: D 78 CYS cc_start: 0.7817 (p) cc_final: 0.7613 (t) REVERT: D 161 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7963 (mm) REVERT: D 171 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6601 (mt-10) REVERT: D 190 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7534 (tm-30) REVERT: D 208 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8197 (ttpp) REVERT: D 209 THR cc_start: 0.8655 (t) cc_final: 0.8346 (m) REVERT: D 224 PHE cc_start: 0.8373 (t80) cc_final: 0.7938 (t80) REVERT: D 229 ILE cc_start: 0.7427 (mm) cc_final: 0.7216 (mt) REVERT: D 260 PHE cc_start: 0.7730 (m-10) cc_final: 0.6924 (m-80) REVERT: D 265 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7700 (mtmm) REVERT: D 274 LYS cc_start: 0.6661 (mmtt) cc_final: 0.6433 (mmtt) REVERT: D 279 MET cc_start: 0.7857 (tpp) cc_final: 0.7579 (tpp) REVERT: D 283 LYS cc_start: 0.7898 (tptt) cc_final: 0.7679 (tptt) REVERT: D 285 LEU cc_start: 0.8244 (tt) cc_final: 0.7860 (tp) REVERT: D 302 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7548 (mtpp) REVERT: D 326 GLU cc_start: 0.6601 (tt0) cc_final: 0.6371 (tp30) REVERT: D 335 GLU cc_start: 0.7423 (tp30) cc_final: 0.7008 (tp30) REVERT: D 344 GLN cc_start: 0.7263 (mm-40) cc_final: 0.7014 (mm-40) REVERT: D 395 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7092 (mtm) REVERT: D 408 ASN cc_start: 0.8493 (t0) cc_final: 0.8216 (t0) outliers start: 47 outliers final: 30 residues processed: 275 average time/residue: 0.2606 time to fit residues: 89.1135 Evaluate side-chains 282 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 212 HIS ** D 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7564 Z= 0.195 Angle : 0.633 8.054 10220 Z= 0.327 Chirality : 0.044 0.156 1114 Planarity : 0.004 0.040 1312 Dihedral : 4.559 28.683 978 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 4.47 % Allowed : 30.27 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.17 (0.28), residues: 888 helix: 1.12 (0.26), residues: 407 sheet: 0.65 (0.58), residues: 81 loop : -1.63 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.005 0.001 HIS D 212 PHE 0.025 0.002 PHE D 396 TYR 0.023 0.002 TYR D 107 ARG 0.006 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.3898 (OUTLIER) cc_final: 0.2508 (mmt90) REVERT: B 60 VAL cc_start: 0.8254 (p) cc_final: 0.8042 (p) REVERT: C 113 TRP cc_start: 0.8209 (p-90) cc_final: 0.7640 (p-90) REVERT: C 122 MET cc_start: 0.6209 (tpt) cc_final: 0.5902 (tpp) REVERT: C 149 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8204 (mtm180) REVERT: G 7 VAL cc_start: 0.8456 (t) cc_final: 0.8214 (m) REVERT: G 70 TRP cc_start: 0.6991 (p90) cc_final: 0.6642 (p90) REVERT: G 97 GLN cc_start: 0.8368 (mp10) cc_final: 0.7920 (mm-40) REVERT: D 74 LYS cc_start: 0.8454 (mttm) cc_final: 0.7795 (mttm) REVERT: D 161 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7962 (mm) REVERT: D 171 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6502 (mt-10) REVERT: D 208 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8153 (ttpp) REVERT: D 209 THR cc_start: 0.8594 (t) cc_final: 0.8268 (m) REVERT: D 224 PHE cc_start: 0.8348 (t80) cc_final: 0.7936 (t80) REVERT: D 229 ILE cc_start: 0.7427 (mm) cc_final: 0.7198 (mt) REVERT: D 234 LEU cc_start: 0.8396 (mt) cc_final: 0.8124 (mt) REVERT: D 260 PHE cc_start: 0.7685 (m-10) cc_final: 0.7018 (m-80) REVERT: D 265 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7651 (mtmm) REVERT: D 274 LYS cc_start: 0.6595 (mmtt) cc_final: 0.6379 (mmtt) REVERT: D 279 MET cc_start: 0.7829 (tpp) cc_final: 0.7593 (tpp) REVERT: D 285 LEU cc_start: 0.8239 (tt) cc_final: 0.7849 (tp) REVERT: D 302 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7694 (ttmm) REVERT: D 326 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6264 (tp30) REVERT: D 335 GLU cc_start: 0.7386 (tp30) cc_final: 0.7030 (tp30) REVERT: D 344 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6976 (mm-40) REVERT: D 374 PHE cc_start: 0.8393 (m-80) cc_final: 0.8028 (m-80) REVERT: D 408 ASN cc_start: 0.8466 (t0) cc_final: 0.8194 (t0) outliers start: 36 outliers final: 24 residues processed: 266 average time/residue: 0.2475 time to fit residues: 82.9054 Evaluate side-chains 267 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 HIS D 77 GLN D 212 HIS D 289 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7564 Z= 0.185 Angle : 0.646 8.676 10220 Z= 0.331 Chirality : 0.043 0.217 1114 Planarity : 0.004 0.040 1312 Dihedral : 4.508 26.948 978 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.87 % Favored : 93.02 % Rotamer: Outliers : 4.47 % Allowed : 29.90 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.14 (0.28), residues: 888 helix: 1.14 (0.26), residues: 408 sheet: 0.56 (0.58), residues: 81 loop : -1.59 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.011 0.001 HIS A 10 PHE 0.027 0.002 PHE D 396 TYR 0.023 0.001 TYR D 107 ARG 0.005 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.3884 (OUTLIER) cc_final: 0.2519 (mmt90) REVERT: A 85 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6466 (t80) REVERT: B 60 VAL cc_start: 0.8242 (p) cc_final: 0.8030 (p) REVERT: C 113 TRP cc_start: 0.8223 (p-90) cc_final: 0.7657 (p-90) REVERT: C 149 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8161 (mtm180) REVERT: G 7 VAL cc_start: 0.8554 (t) cc_final: 0.8288 (m) REVERT: G 70 TRP cc_start: 0.6932 (p90) cc_final: 0.6582 (p90) REVERT: G 97 GLN cc_start: 0.8376 (mp10) cc_final: 0.7883 (mm-40) REVERT: D 102 ASN cc_start: 0.7946 (m-40) cc_final: 0.7700 (m-40) REVERT: D 161 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7945 (mm) REVERT: D 171 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6498 (mt-10) REVERT: D 209 THR cc_start: 0.8609 (t) cc_final: 0.8264 (m) REVERT: D 224 PHE cc_start: 0.8372 (t80) cc_final: 0.7968 (t80) REVERT: D 234 LEU cc_start: 0.8383 (mt) cc_final: 0.8051 (mt) REVERT: D 265 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7655 (mtmm) REVERT: D 274 LYS cc_start: 0.6588 (mmtt) cc_final: 0.6366 (mmtt) REVERT: D 279 MET cc_start: 0.7794 (tpp) cc_final: 0.7591 (tpp) REVERT: D 285 LEU cc_start: 0.8095 (tt) cc_final: 0.7781 (tp) REVERT: D 302 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7754 (ttmm) REVERT: D 320 LYS cc_start: 0.8188 (tppt) cc_final: 0.7476 (tppt) REVERT: D 326 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6244 (tp30) REVERT: D 335 GLU cc_start: 0.7364 (tp30) cc_final: 0.7010 (tp30) REVERT: D 344 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6935 (mm-40) REVERT: D 385 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6330 (mm-30) REVERT: D 408 ASN cc_start: 0.8452 (t0) cc_final: 0.8191 (t0) REVERT: D 414 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7899 (mt) outliers start: 36 outliers final: 22 residues processed: 262 average time/residue: 0.2542 time to fit residues: 84.1404 Evaluate side-chains 264 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7564 Z= 0.248 Angle : 0.681 9.617 10220 Z= 0.349 Chirality : 0.045 0.204 1114 Planarity : 0.005 0.046 1312 Dihedral : 4.563 27.136 978 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.32 % Favored : 92.57 % Rotamer: Outliers : 4.96 % Allowed : 30.15 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 888 helix: 1.12 (0.26), residues: 402 sheet: 0.58 (0.59), residues: 81 loop : -1.60 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 5 HIS 0.014 0.001 HIS A 10 PHE 0.016 0.002 PHE B 77 TYR 0.030 0.002 TYR B 79 ARG 0.007 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.4372 (OUTLIER) cc_final: 0.3022 (mmt90) REVERT: B 60 VAL cc_start: 0.8274 (p) cc_final: 0.8066 (p) REVERT: C 113 TRP cc_start: 0.8168 (p-90) cc_final: 0.7632 (p-90) REVERT: C 140 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8034 (mt0) REVERT: C 149 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.8199 (mtm180) REVERT: G 7 VAL cc_start: 0.8378 (t) cc_final: 0.8138 (m) REVERT: G 70 TRP cc_start: 0.7112 (p90) cc_final: 0.6703 (p90) REVERT: D 74 LYS cc_start: 0.8290 (mttm) cc_final: 0.7877 (tttm) REVERT: D 77 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: D 102 ASN cc_start: 0.8021 (m-40) cc_final: 0.7746 (m-40) REVERT: D 103 GLU cc_start: 0.6665 (tt0) cc_final: 0.6410 (tt0) REVERT: D 161 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7994 (mm) REVERT: D 171 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6543 (mt-10) REVERT: D 208 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8150 (ttpt) REVERT: D 209 THR cc_start: 0.8663 (t) cc_final: 0.8336 (m) REVERT: D 224 PHE cc_start: 0.8382 (t80) cc_final: 0.8013 (t80) REVERT: D 234 LEU cc_start: 0.8433 (mt) cc_final: 0.8092 (mt) REVERT: D 260 PHE cc_start: 0.7649 (m-10) cc_final: 0.7264 (m-80) REVERT: D 265 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7659 (mtmm) REVERT: D 274 LYS cc_start: 0.6639 (mmtt) cc_final: 0.6437 (mmtt) REVERT: D 279 MET cc_start: 0.7755 (tpp) cc_final: 0.7502 (tpp) REVERT: D 285 LEU cc_start: 0.8117 (tt) cc_final: 0.7803 (tp) REVERT: D 302 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7801 (ttmm) REVERT: D 315 LEU cc_start: 0.8503 (mm) cc_final: 0.8302 (mm) REVERT: D 326 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6267 (tp30) REVERT: D 335 GLU cc_start: 0.7374 (tp30) cc_final: 0.7018 (tp30) REVERT: D 344 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7075 (mm-40) REVERT: D 374 PHE cc_start: 0.8406 (m-80) cc_final: 0.8034 (m-80) REVERT: D 398 SER cc_start: 0.8721 (t) cc_final: 0.8504 (t) REVERT: D 408 ASN cc_start: 0.8492 (t0) cc_final: 0.8103 (t0) REVERT: D 414 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7952 (mt) outliers start: 40 outliers final: 25 residues processed: 271 average time/residue: 0.2455 time to fit residues: 83.9669 Evaluate side-chains 271 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS D 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7564 Z= 0.225 Angle : 0.693 10.117 10220 Z= 0.351 Chirality : 0.044 0.192 1114 Planarity : 0.005 0.042 1312 Dihedral : 4.571 27.366 978 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 3.72 % Allowed : 31.51 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.19 (0.28), residues: 888 helix: 1.07 (0.26), residues: 410 sheet: 0.55 (0.59), residues: 81 loop : -1.59 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 5 HIS 0.014 0.001 HIS A 10 PHE 0.022 0.002 PHE D 243 TYR 0.031 0.002 TYR G 94 ARG 0.007 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.4433 (OUTLIER) cc_final: 0.3113 (mmt90) REVERT: B 60 VAL cc_start: 0.8238 (p) cc_final: 0.8037 (p) REVERT: C 113 TRP cc_start: 0.8158 (p-90) cc_final: 0.7658 (p-90) REVERT: C 149 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8190 (mtm180) REVERT: G 7 VAL cc_start: 0.8338 (t) cc_final: 0.8089 (m) REVERT: G 70 TRP cc_start: 0.7068 (p90) cc_final: 0.6699 (p90) REVERT: D 74 LYS cc_start: 0.8345 (mttm) cc_final: 0.7956 (tttm) REVERT: D 102 ASN cc_start: 0.8007 (m-40) cc_final: 0.7754 (m-40) REVERT: D 161 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8010 (mm) REVERT: D 171 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6579 (mt-10) REVERT: D 208 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8099 (ttpt) REVERT: D 209 THR cc_start: 0.8649 (t) cc_final: 0.8319 (m) REVERT: D 224 PHE cc_start: 0.8453 (t80) cc_final: 0.8152 (t80) REVERT: D 234 LEU cc_start: 0.8443 (mt) cc_final: 0.8154 (mt) REVERT: D 241 GLU cc_start: 0.5201 (mm-30) cc_final: 0.4520 (mm-30) REVERT: D 260 PHE cc_start: 0.7590 (m-10) cc_final: 0.7263 (m-80) REVERT: D 265 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7631 (mtmm) REVERT: D 274 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6441 (mmtt) REVERT: D 285 LEU cc_start: 0.8102 (tt) cc_final: 0.7794 (tp) REVERT: D 302 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7821 (ttmm) REVERT: D 326 GLU cc_start: 0.6469 (tt0) cc_final: 0.6245 (tp30) REVERT: D 335 GLU cc_start: 0.7369 (tp30) cc_final: 0.7082 (tp30) REVERT: D 344 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7056 (mm-40) REVERT: D 398 SER cc_start: 0.8708 (t) cc_final: 0.8499 (t) REVERT: D 408 ASN cc_start: 0.8440 (t0) cc_final: 0.8142 (t0) REVERT: D 414 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7961 (mt) REVERT: D 437 TYR cc_start: 0.5832 (t80) cc_final: 0.5600 (t80) outliers start: 30 outliers final: 25 residues processed: 265 average time/residue: 0.2570 time to fit residues: 85.5103 Evaluate side-chains 269 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 80 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.0370 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 212 HIS D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 7564 Z= 0.430 Angle : 0.791 10.123 10220 Z= 0.409 Chirality : 0.049 0.202 1114 Planarity : 0.007 0.139 1312 Dihedral : 4.916 28.260 978 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 3.97 % Allowed : 31.27 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 888 helix: 0.82 (0.25), residues: 411 sheet: 0.43 (0.60), residues: 81 loop : -1.66 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 5 HIS 0.013 0.002 HIS A 10 PHE 0.030 0.003 PHE D 243 TYR 0.045 0.003 TYR B 79 ARG 0.019 0.001 ARG D 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.3191 (mmt90) REVERT: C 113 TRP cc_start: 0.8160 (p-90) cc_final: 0.7736 (p-90) REVERT: C 149 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8267 (mtm180) REVERT: G 7 VAL cc_start: 0.8311 (t) cc_final: 0.8083 (m) REVERT: G 41 ARG cc_start: 0.7532 (mmm-85) cc_final: 0.7060 (mtm-85) REVERT: G 69 TYR cc_start: 0.8204 (m-10) cc_final: 0.7960 (m-80) REVERT: G 70 TRP cc_start: 0.7661 (p90) cc_final: 0.7440 (p90) REVERT: D 102 ASN cc_start: 0.8155 (m-40) cc_final: 0.7885 (m-40) REVERT: D 132 PHE cc_start: 0.8640 (m-10) cc_final: 0.8318 (m-10) REVERT: D 133 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7754 (ptt90) REVERT: D 161 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8053 (mm) REVERT: D 171 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6693 (mt-10) REVERT: D 208 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8167 (ttpt) REVERT: D 209 THR cc_start: 0.8664 (t) cc_final: 0.8366 (m) REVERT: D 224 PHE cc_start: 0.8546 (t80) cc_final: 0.8252 (t80) REVERT: D 231 ASN cc_start: 0.7602 (m-40) cc_final: 0.7340 (m110) REVERT: D 234 LEU cc_start: 0.8492 (mt) cc_final: 0.8231 (mt) REVERT: D 260 PHE cc_start: 0.7528 (m-10) cc_final: 0.7323 (m-10) REVERT: D 265 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7734 (mtmm) REVERT: D 274 LYS cc_start: 0.6735 (mmtt) cc_final: 0.6528 (mmtt) REVERT: D 285 LEU cc_start: 0.8176 (tt) cc_final: 0.7878 (tp) REVERT: D 302 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7871 (ttmm) REVERT: D 326 GLU cc_start: 0.6602 (tt0) cc_final: 0.6372 (tp30) REVERT: D 335 GLU cc_start: 0.7468 (tp30) cc_final: 0.7091 (tp30) REVERT: D 344 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7152 (mm-40) REVERT: D 398 SER cc_start: 0.8726 (t) cc_final: 0.8521 (t) REVERT: D 399 LEU cc_start: 0.8427 (mt) cc_final: 0.8203 (mt) REVERT: D 408 ASN cc_start: 0.8458 (t0) cc_final: 0.8112 (t0) outliers start: 32 outliers final: 26 residues processed: 279 average time/residue: 0.2597 time to fit residues: 89.6927 Evaluate side-chains 281 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 17 PHE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain G residue 5 TRP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 288 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS ** D 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114573 restraints weight = 12379.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118790 restraints weight = 6710.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121674 restraints weight = 4330.992| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.152 7564 Z= 0.495 Angle : 1.142 59.199 10220 Z= 0.643 Chirality : 0.055 0.927 1114 Planarity : 0.007 0.138 1312 Dihedral : 4.930 28.360 978 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.89 % Rotamer: Outliers : 3.35 % Allowed : 32.38 % Favored : 64.27 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.65 % 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: -0.43 (0.28), residues: 888 helix: 0.82 (0.26), residues: 408 sheet: 0.41 (0.60), residues: 81 loop : -1.64 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.004 TRP G 89 HIS 0.012 0.002 HIS A 10 PHE 0.053 0.003 PHE C 143 TYR 0.051 0.004 TYR D 400 ARG 0.013 0.001 ARG D 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.12 seconds wall clock time: 41 minutes 44.30 seconds (2504.30 seconds total)