Starting phenix.real_space_refine on Fri Jul 19 09:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/07_2024/8szk_40919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/07_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_40919/07_2024/8szk_40919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/07_2024/8szk_40919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/07_2024/8szk_40919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szk_40919/07_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 Residue "A ASP 52": "OD1" <-> "OD2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.48, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 2.05 Time building geometry restraints manager: 3.14 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: 76.45 - 87.97: 2 87.97 - 99.50: 3 99.50 - 111.03: 2751 111.03 - 122.56: 6597 122.56 - 134.08: 867 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 2.440 nonbonded pdb=" NH2 ARG A 37 " pdb=" O PRO A 38 " model vdw 2.225 2.520 nonbonded pdb=" O SER C 22 " pdb=" OG SER C 22 " model vdw 2.236 2.440 nonbonded pdb=" O ASN D 417 " pdb=" OG1 THR D 421 " model vdw 2.262 2.440 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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 0.843 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: 0.2437 time to fit residues: 87.7485 Evaluate side-chains 266 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 0.9990 chunk 66 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7008 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7564 Z= 0.237 Angle : 0.710 8.040 10220 Z= 0.371 Chirality : 0.045 0.248 1114 Planarity : 0.004 0.037 1312 Dihedral : 4.797 30.143 981 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.43 % Favored : 92.23 % Rotamer: Outliers : 5.21 % Allowed : 28.41 % Favored : 66.38 % 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: -0.32 (0.28), residues: 888 helix: 0.73 (0.26), residues: 409 sheet: 0.67 (0.53), residues: 88 loop : -1.46 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 5 HIS 0.012 0.002 HIS G 73 PHE 0.025 0.002 PHE D 396 TYR 0.018 0.002 TYR D 437 ARG 0.006 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 308 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 0.827 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: A 10 HIS cc_start: 0.6618 (m-70) cc_final: 0.5766 (m-70) REVERT: A 43 ARG cc_start: 0.5828 (tpt-90) cc_final: 0.5580 (tpt-90) REVERT: B 30 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7732 (mt) REVERT: C 91 GLU cc_start: 0.6776 (mp0) cc_final: 0.6025 (mp0) REVERT: C 104 ASN cc_start: 0.8530 (t0) cc_final: 0.8191 (t0) REVERT: C 145 GLU cc_start: 0.7377 (tp30) cc_final: 0.7121 (tp30) REVERT: G 5 TRP cc_start: 0.6983 (m-10) cc_final: 0.6762 (m-10) REVERT: D 69 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5522 (tm-30) REVERT: D 73 GLN cc_start: 0.7318 (mt0) cc_final: 0.6720 (mt0) REVERT: D 75 LEU cc_start: 0.8073 (mm) cc_final: 0.7727 (mm) REVERT: D 107 TYR cc_start: 0.7952 (t80) cc_final: 0.7751 (t80) REVERT: D 115 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8028 (tp) REVERT: D 118 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7730 (t) REVERT: D 127 ILE cc_start: 0.8260 (mm) cc_final: 0.8037 (mt) REVERT: D 161 LEU cc_start: 0.8262 (mm) cc_final: 0.7933 (mm) REVERT: D 200 ASP cc_start: 0.8337 (t0) cc_final: 0.8001 (t70) REVERT: D 208 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7746 (ttpt) REVERT: D 248 GLU cc_start: 0.6949 (mp0) cc_final: 0.6297 (mp0) REVERT: D 253 LEU cc_start: 0.8228 (mt) cc_final: 0.7935 (mm) REVERT: D 256 ILE cc_start: 0.7520 (tt) cc_final: 0.7320 (tt) REVERT: D 265 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7664 (mtmm) REVERT: D 274 LYS cc_start: 0.6538 (mmtt) cc_final: 0.6337 (mmtt) REVERT: D 283 LYS cc_start: 0.8007 (tptt) cc_final: 0.7803 (tptt) REVERT: D 285 LEU cc_start: 0.8111 (tt) cc_final: 0.7781 (tp) REVERT: D 344 GLN cc_start: 0.7088 (mm-40) cc_final: 0.6845 (mm-40) REVERT: D 348 ILE cc_start: 0.8042 (pt) cc_final: 0.7820 (pt) REVERT: D 349 GLU cc_start: 0.6793 (mp0) cc_final: 0.6547 (mp0) REVERT: D 385 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6307 (mm-30) REVERT: D 401 LYS cc_start: 0.8173 (tppt) cc_final: 0.7961 (tttp) REVERT: D 444 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7120 (tm-30) outliers start: 42 outliers final: 19 residues processed: 287 average time/residue: 0.2447 time to fit residues: 88.9889 Evaluate side-chains 276 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 254 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP 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 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 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 205 ASP Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS G 105 GLN G 146 GLN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS ** D 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7564 Z= 0.335 Angle : 0.712 7.033 10220 Z= 0.377 Chirality : 0.047 0.273 1114 Planarity : 0.005 0.093 1312 Dihedral : 4.772 29.208 978 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.55 % Favored : 92.23 % Rotamer: Outliers : 6.58 % Allowed : 27.30 % Favored : 66.13 % 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: -0.47 (0.28), residues: 888 helix: 0.80 (0.26), residues: 413 sheet: 0.30 (0.55), residues: 82 loop : -1.69 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 5 HIS 0.010 0.002 HIS A 10 PHE 0.033 0.003 PHE A 15 TYR 0.032 0.002 TYR B 79 ARG 0.017 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 319 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 266 time to evaluate : 0.892 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: 0.8025 (OUTLIER) cc_final: 0.7796 (mt) REVERT: B 83 TYR cc_start: 0.7727 (m-10) cc_final: 0.7497 (m-10) REVERT: C 24 GLU cc_start: 0.6285 (tp30) cc_final: 0.6083 (tp30) REVERT: C 122 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5877 (tpp) REVERT: C 149 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8114 (mtm180) REVERT: G 7 VAL cc_start: 0.8508 (t) cc_final: 0.8262 (m) REVERT: D 66 GLU cc_start: 0.6813 (pp20) cc_final: 0.6533 (pp20) REVERT: D 78 CYS cc_start: 0.7919 (p) cc_final: 0.7581 (t) REVERT: D 107 TYR cc_start: 0.8111 (t80) cc_final: 0.7855 (t80) REVERT: D 161 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (mm) REVERT: D 171 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: D 208 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7997 (ttpt) REVERT: D 222 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8126 (mtt180) REVERT: D 229 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6965 (mt) REVERT: D 248 GLU cc_start: 0.6824 (mp0) cc_final: 0.6523 (mp0) REVERT: D 265 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7795 (mtmm) REVERT: D 274 LYS cc_start: 0.6665 (mmtt) cc_final: 0.6446 (mmtt) REVERT: D 283 LYS cc_start: 0.8009 (tptt) cc_final: 0.7744 (tptt) REVERT: D 285 LEU cc_start: 0.8305 (tt) cc_final: 0.7965 (tp) REVERT: D 344 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6785 (mm-40) REVERT: D 347 LYS cc_start: 0.7437 (mttp) cc_final: 0.6875 (mttp) REVERT: D 348 ILE cc_start: 0.8099 (pt) cc_final: 0.7850 (pt) REVERT: D 349 GLU cc_start: 0.6928 (mp0) cc_final: 0.6618 (mp0) REVERT: D 385 GLU cc_start: 0.6599 (mm-30) cc_final: 0.5903 (mm-30) REVERT: D 415 VAL cc_start: 0.8356 (t) cc_final: 0.8147 (p) outliers start: 53 outliers final: 31 residues processed: 288 average time/residue: 0.2524 time to fit residues: 90.7705 Evaluate side-chains 300 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 22 SER 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 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 C residue 26 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 62 THR 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 3 ASN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE 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 171 GLU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 404 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS D 387 ASN D 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7564 Z= 0.213 Angle : 0.633 7.307 10220 Z= 0.329 Chirality : 0.043 0.167 1114 Planarity : 0.005 0.067 1312 Dihedral : 4.648 27.417 978 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.98 % Favored : 92.79 % Rotamer: Outliers : 4.71 % Allowed : 30.40 % 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: -0.31 (0.28), residues: 888 helix: 0.93 (0.26), residues: 414 sheet: 0.48 (0.56), residues: 82 loop : -1.64 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.006 0.001 HIS D 406 PHE 0.019 0.002 PHE A 15 TYR 0.017 0.002 TYR B 79 ARG 0.008 0.001 ARG D 370 *********************** 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 288 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 250 time to evaluate : 0.902 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: 0.7966 (OUTLIER) cc_final: 0.7739 (mt) REVERT: C 24 GLU cc_start: 0.6188 (tp30) cc_final: 0.5982 (tp30) REVERT: C 113 TRP cc_start: 0.8250 (p-90) cc_final: 0.7606 (p-90) REVERT: C 149 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.8087 (mtm180) REVERT: G 70 TRP cc_start: 0.6937 (p90) cc_final: 0.6511 (p90) REVERT: D 66 GLU cc_start: 0.6972 (pp20) cc_final: 0.6586 (pp20) REVERT: D 75 LEU cc_start: 0.8166 (mm) cc_final: 0.7790 (mm) REVERT: D 78 CYS cc_start: 0.7952 (p) cc_final: 0.7520 (t) REVERT: D 161 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7957 (mm) REVERT: D 194 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7056 (mm-30) REVERT: D 203 GLU cc_start: 0.7735 (tt0) cc_final: 0.7507 (tt0) REVERT: D 208 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7818 (ttpt) REVERT: D 229 ILE cc_start: 0.7314 (mm) cc_final: 0.7015 (mt) REVERT: D 256 ILE cc_start: 0.7736 (tt) cc_final: 0.7441 (tt) REVERT: D 265 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7671 (mtmm) REVERT: D 274 LYS cc_start: 0.6634 (mmtt) cc_final: 0.6400 (mmtt) REVERT: D 283 LYS cc_start: 0.7965 (tptt) cc_final: 0.7726 (tptt) REVERT: D 285 LEU cc_start: 0.8226 (tt) cc_final: 0.7896 (tp) REVERT: D 344 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6943 (mm-40) outliers start: 38 outliers final: 28 residues processed: 264 average time/residue: 0.2422 time to fit residues: 82.2102 Evaluate side-chains 277 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 35 LEU 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 17 PHE Chi-restraints excluded: chain C residue 28 LYS 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 8 MET Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU 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 328 MET Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 404 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** C 140 GLN G 83 GLN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7564 Z= 0.204 Angle : 0.640 9.738 10220 Z= 0.328 Chirality : 0.044 0.191 1114 Planarity : 0.004 0.038 1312 Dihedral : 4.524 27.663 978 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 6.33 % Allowed : 28.29 % Favored : 65.38 % 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 (0.29), residues: 888 helix: 1.10 (0.26), residues: 407 sheet: 0.53 (0.57), residues: 82 loop : -1.59 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 5 HIS 0.004 0.001 HIS D 212 PHE 0.015 0.002 PHE A 15 TYR 0.020 0.001 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 303 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 252 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7383 (tmt170) cc_final: 0.7179 (ttt180) REVERT: A 29 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.2546 (mmt90) REVERT: B 30 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7755 (mt) REVERT: C 113 TRP cc_start: 0.8257 (p-90) cc_final: 0.7609 (p-90) REVERT: C 122 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5726 (mmm) REVERT: C 140 GLN cc_start: 0.8160 (mm110) cc_final: 0.7908 (mt0) REVERT: C 149 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8139 (mtm180) REVERT: D 66 GLU cc_start: 0.6892 (pp20) cc_final: 0.6501 (pp20) REVERT: D 75 LEU cc_start: 0.8146 (mm) cc_final: 0.7825 (mm) REVERT: D 77 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: D 161 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (mm) REVERT: D 172 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7802 (p) REVERT: D 194 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6986 (mm-30) REVERT: D 208 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7747 (ttpt) REVERT: D 229 ILE cc_start: 0.7372 (mm) cc_final: 0.7110 (mt) REVERT: D 234 LEU cc_start: 0.8385 (mt) cc_final: 0.8064 (mt) REVERT: D 265 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7689 (mtmm) REVERT: D 274 LYS cc_start: 0.6588 (mmtt) cc_final: 0.6375 (mmtt) REVERT: D 279 MET cc_start: 0.7868 (tpp) cc_final: 0.7612 (tpp) REVERT: D 283 LYS cc_start: 0.7908 (tptt) cc_final: 0.7689 (tptt) REVERT: D 285 LEU cc_start: 0.8235 (tt) cc_final: 0.7786 (tp) REVERT: D 302 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7588 (ttmm) REVERT: D 320 LYS cc_start: 0.8205 (tppt) cc_final: 0.7531 (tppt) REVERT: D 326 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: D 335 GLU cc_start: 0.7379 (tp30) cc_final: 0.7065 (tp30) REVERT: D 344 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6896 (mm-40) outliers start: 51 outliers final: 28 residues processed: 275 average time/residue: 0.2362 time to fit residues: 81.8995 Evaluate side-chains 283 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET 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 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 52 ARG Chi-restraints excluded: chain C residue 54 GLU 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 3 ASN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4227 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= 0.202 Angle : 0.648 10.251 10220 Z= 0.331 Chirality : 0.045 0.292 1114 Planarity : 0.004 0.042 1312 Dihedral : 4.533 25.786 978 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 5.96 % Allowed : 27.79 % Favored : 66.25 % 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: -0.16 (0.28), residues: 888 helix: 1.14 (0.26), residues: 408 sheet: 0.57 (0.58), residues: 82 loop : -1.64 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.007 0.001 HIS A 10 PHE 0.018 0.002 PHE D 243 TYR 0.022 0.001 TYR B 79 ARG 0.008 0.001 ARG A 8 *********************** 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 298 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 250 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.3861 (OUTLIER) cc_final: 0.2467 (mmt90) REVERT: B 30 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7757 (mt) REVERT: B 60 VAL cc_start: 0.8209 (p) cc_final: 0.7995 (p) REVERT: C 113 TRP cc_start: 0.8246 (p-90) cc_final: 0.7640 (p-90) REVERT: C 149 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8097 (mtm180) REVERT: G 7 VAL cc_start: 0.8447 (t) cc_final: 0.8205 (m) REVERT: G 135 TYR cc_start: 0.7411 (t80) cc_final: 0.7193 (t80) REVERT: G 139 HIS cc_start: 0.6979 (m90) cc_final: 0.6714 (m90) REVERT: D 66 GLU cc_start: 0.6925 (pp20) cc_final: 0.6517 (pp20) REVERT: D 75 LEU cc_start: 0.8000 (mm) cc_final: 0.7783 (mm) REVERT: D 161 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7930 (mm) REVERT: D 172 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7779 (p) REVERT: D 194 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6944 (mm-30) REVERT: D 208 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7687 (ttpt) REVERT: D 229 ILE cc_start: 0.7431 (mm) cc_final: 0.7218 (mt) REVERT: D 234 LEU cc_start: 0.8404 (mt) cc_final: 0.8094 (mt) REVERT: D 265 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7697 (mtmm) REVERT: D 279 MET cc_start: 0.7830 (tpp) cc_final: 0.7576 (tpp) REVERT: D 285 LEU cc_start: 0.8230 (tt) cc_final: 0.7862 (tp) REVERT: D 302 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7634 (ttmm) REVERT: D 335 GLU cc_start: 0.7386 (tp30) cc_final: 0.7047 (tp30) REVERT: D 344 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6911 (mm-40) REVERT: D 374 PHE cc_start: 0.8364 (m-80) cc_final: 0.8008 (m-80) outliers start: 48 outliers final: 33 residues processed: 275 average time/residue: 0.2298 time to fit residues: 80.2521 Evaluate side-chains 285 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET 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 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 54 GLU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 193 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 394 ILE Chi-restraints excluded: chain D residue 404 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 G 105 GLN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.4441 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= 0.189 Angle : 0.661 11.371 10220 Z= 0.333 Chirality : 0.044 0.269 1114 Planarity : 0.004 0.044 1312 Dihedral : 4.403 26.387 978 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.87 % Favored : 93.02 % Rotamer: Outliers : 4.09 % Allowed : 30.15 % Favored : 65.76 % 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: -0.11 (0.29), residues: 888 helix: 1.19 (0.26), residues: 408 sheet: 0.68 (0.59), residues: 82 loop : -1.65 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.006 0.001 HIS G 139 PHE 0.014 0.001 PHE D 243 TYR 0.020 0.001 TYR B 79 ARG 0.006 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 285 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7241 (ttt180) cc_final: 0.7034 (ttt180) REVERT: A 24 VAL cc_start: 0.6284 (OUTLIER) cc_final: 0.5944 (t) REVERT: A 29 ARG cc_start: 0.3852 (OUTLIER) cc_final: 0.2476 (mmt90) REVERT: A 85 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.6389 (t80) REVERT: B 30 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (mt) REVERT: B 60 VAL cc_start: 0.8185 (p) cc_final: 0.7953 (p) REVERT: B 74 CYS cc_start: 0.7547 (t) cc_final: 0.7323 (t) REVERT: C 122 MET cc_start: 0.5748 (tpp) cc_final: 0.5266 (tpp) REVERT: C 140 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7998 (mt0) REVERT: C 149 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8107 (mtm180) REVERT: G 7 VAL cc_start: 0.8502 (t) cc_final: 0.8246 (m) REVERT: D 66 GLU cc_start: 0.6910 (pp20) cc_final: 0.6498 (pp20) REVERT: D 73 GLN cc_start: 0.7213 (mt0) cc_final: 0.6950 (mt0) REVERT: D 102 ASN cc_start: 0.8052 (m-40) cc_final: 0.7771 (m-40) REVERT: D 132 PHE cc_start: 0.8596 (m-10) cc_final: 0.8294 (m-10) REVERT: D 161 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7941 (mm) REVERT: D 172 SER cc_start: 0.8182 (t) cc_final: 0.7760 (p) REVERT: D 194 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6997 (mm-30) REVERT: D 208 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7497 (ttpt) REVERT: D 229 ILE cc_start: 0.7415 (mm) cc_final: 0.7190 (mt) REVERT: D 234 LEU cc_start: 0.8375 (mt) cc_final: 0.8098 (mt) REVERT: D 260 PHE cc_start: 0.7617 (m-10) cc_final: 0.7175 (m-80) REVERT: D 265 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7659 (mtmm) REVERT: D 285 LEU cc_start: 0.8088 (tt) cc_final: 0.7781 (tp) REVERT: D 302 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7486 (mtpp) REVERT: D 320 LYS cc_start: 0.8218 (tppt) cc_final: 0.7555 (tppt) REVERT: D 335 GLU cc_start: 0.7401 (tp30) cc_final: 0.7022 (tp30) REVERT: D 344 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6912 (mm-40) REVERT: D 374 PHE cc_start: 0.8384 (m-80) cc_final: 0.7987 (m-80) outliers start: 33 outliers final: 25 residues processed: 271 average time/residue: 0.2420 time to fit residues: 82.7888 Evaluate side-chains 275 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET 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 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 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 62 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 3 ASN 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 D residue 104 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU 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 394 ILE Chi-restraints excluded: chain D residue 448 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.0270 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4661 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= 0.235 Angle : 0.686 11.455 10220 Z= 0.348 Chirality : 0.045 0.296 1114 Planarity : 0.004 0.045 1312 Dihedral : 4.440 25.109 978 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.32 % Favored : 92.57 % Rotamer: Outliers : 4.34 % Allowed : 30.77 % 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: -0.13 (0.29), residues: 888 helix: 1.22 (0.26), residues: 406 sheet: 0.63 (0.59), residues: 82 loop : -1.68 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 5 HIS 0.007 0.001 HIS G 139 PHE 0.017 0.002 PHE D 243 TYR 0.027 0.002 TYR B 79 ARG 0.007 0.001 ARG D 182 *********************** 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 279 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 24 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6102 (t) REVERT: A 29 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.2998 (mmt90) REVERT: A 75 VAL cc_start: 0.7970 (m) cc_final: 0.7635 (p) REVERT: B 30 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 60 VAL cc_start: 0.8217 (p) cc_final: 0.7987 (p) REVERT: B 74 CYS cc_start: 0.7576 (t) cc_final: 0.7368 (t) REVERT: C 113 TRP cc_start: 0.8216 (p-90) cc_final: 0.7618 (p-90) REVERT: C 122 MET cc_start: 0.6105 (tpp) cc_final: 0.5679 (mmp) REVERT: C 140 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8026 (mt0) REVERT: C 149 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.8148 (mtm180) REVERT: G 7 VAL cc_start: 0.8447 (t) cc_final: 0.8200 (m) REVERT: D 66 GLU cc_start: 0.6949 (pp20) cc_final: 0.6569 (pp20) REVERT: D 73 GLN cc_start: 0.7060 (mt0) cc_final: 0.6860 (mt0) REVERT: D 102 ASN cc_start: 0.8084 (m-40) cc_final: 0.7804 (m-40) REVERT: D 132 PHE cc_start: 0.8607 (m-10) cc_final: 0.8277 (m-10) REVERT: D 161 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7948 (mm) REVERT: D 171 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: D 172 SER cc_start: 0.8222 (t) cc_final: 0.7813 (p) REVERT: D 194 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6999 (mm-30) REVERT: D 208 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7705 (ttmt) REVERT: D 229 ILE cc_start: 0.7491 (mm) cc_final: 0.7276 (mt) REVERT: D 234 LEU cc_start: 0.8341 (mt) cc_final: 0.8074 (mt) REVERT: D 260 PHE cc_start: 0.7653 (m-10) cc_final: 0.7300 (m-80) REVERT: D 265 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7658 (mtmm) REVERT: D 285 LEU cc_start: 0.8111 (tt) cc_final: 0.7797 (tp) REVERT: D 302 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7503 (mtpp) REVERT: D 335 GLU cc_start: 0.7396 (tp30) cc_final: 0.7037 (tp30) REVERT: D 344 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7045 (mm-40) REVERT: D 374 PHE cc_start: 0.8404 (m-80) cc_final: 0.7998 (m-80) REVERT: D 414 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8005 (mt) outliers start: 35 outliers final: 28 residues processed: 263 average time/residue: 0.2298 time to fit residues: 76.4268 Evaluate side-chains 276 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET 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 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 25 CYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 5 TRP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 207 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 394 ILE Chi-restraints excluded: chain D residue 404 LYS 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: 0.0770 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 71 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 83 optimal weight: 0.0060 overall best weight: 0.1030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** 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: 0.7070 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7564 Z= 0.178 Angle : 0.680 10.396 10220 Z= 0.341 Chirality : 0.043 0.216 1114 Planarity : 0.004 0.045 1312 Dihedral : 4.396 25.018 978 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 3.60 % Allowed : 32.01 % 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: -0.07 (0.29), residues: 888 helix: 1.23 (0.26), residues: 405 sheet: 0.84 (0.60), residues: 82 loop : -1.65 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.007 0.001 HIS A 10 PHE 0.014 0.001 PHE D 353 TYR 0.012 0.001 TYR G 111 ARG 0.009 0.001 ARG A 37 *********************** 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 280 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 4 PHE cc_start: 0.7169 (m-80) cc_final: 0.6866 (m-80) REVERT: A 8 ARG cc_start: 0.7372 (mtp-110) cc_final: 0.7141 (mtm110) REVERT: A 29 ARG cc_start: 0.4404 (OUTLIER) cc_final: 0.3113 (mmt90) REVERT: B 30 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7621 (mt) REVERT: B 74 CYS cc_start: 0.7540 (t) cc_final: 0.7233 (t) REVERT: C 113 TRP cc_start: 0.8171 (p-90) cc_final: 0.7583 (p-90) REVERT: C 122 MET cc_start: 0.6115 (tpp) cc_final: 0.5475 (mmp) REVERT: C 149 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8076 (mtm180) REVERT: G 7 VAL cc_start: 0.8352 (t) cc_final: 0.8082 (m) REVERT: G 139 HIS cc_start: 0.6754 (m-70) cc_final: 0.6443 (m90) REVERT: D 66 GLU cc_start: 0.6938 (pp20) cc_final: 0.6541 (pp20) REVERT: D 102 ASN cc_start: 0.8049 (m-40) cc_final: 0.7768 (m-40) REVERT: D 132 PHE cc_start: 0.8537 (m-10) cc_final: 0.8233 (m-10) REVERT: D 161 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7927 (mm) REVERT: D 171 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: D 172 SER cc_start: 0.8045 (t) cc_final: 0.7632 (p) REVERT: D 194 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6962 (mm-30) REVERT: D 208 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7470 (ttpt) REVERT: D 234 LEU cc_start: 0.8292 (mt) cc_final: 0.8054 (mt) REVERT: D 285 LEU cc_start: 0.8019 (tt) cc_final: 0.7731 (tp) REVERT: D 302 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7567 (ttmm) REVERT: D 335 GLU cc_start: 0.7422 (tp30) cc_final: 0.6996 (tp30) REVERT: D 344 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6961 (mm-40) REVERT: D 374 PHE cc_start: 0.8369 (m-80) cc_final: 0.7894 (m-80) REVERT: D 414 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 437 TYR cc_start: 0.5715 (t80) cc_final: 0.5477 (t80) REVERT: D 441 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7400 (mmm-85) outliers start: 29 outliers final: 20 residues processed: 265 average time/residue: 0.2536 time to fit residues: 84.1232 Evaluate side-chains 269 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET 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 30 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 ILE 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 155 ASP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 271 PHE Chi-restraints excluded: chain D residue 288 PHE 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 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS ** D 268 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: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7564 Z= 0.264 Angle : 0.731 10.655 10220 Z= 0.368 Chirality : 0.045 0.221 1114 Planarity : 0.005 0.055 1312 Dihedral : 4.464 22.548 978 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 3.10 % Allowed : 32.75 % Favored : 64.14 % 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: -0.15 (0.28), residues: 888 helix: 1.18 (0.26), residues: 407 sheet: 0.75 (0.61), residues: 82 loop : -1.72 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 5 HIS 0.006 0.001 HIS D 212 PHE 0.042 0.002 PHE D 260 TYR 0.031 0.002 TYR B 79 ARG 0.013 0.001 ARG D 370 ********************** 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 273 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.7223 (m-80) cc_final: 0.6984 (m-80) REVERT: A 29 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3017 (mmt90) REVERT: A 75 VAL cc_start: 0.8014 (m) cc_final: 0.7665 (p) REVERT: B 30 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7775 (mt) REVERT: B 74 CYS cc_start: 0.7535 (t) cc_final: 0.7283 (t) REVERT: C 113 TRP cc_start: 0.8163 (p-90) cc_final: 0.7619 (p-90) REVERT: C 122 MET cc_start: 0.6255 (tpp) cc_final: 0.6010 (mmp) REVERT: C 149 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8187 (mtm180) REVERT: G 7 VAL cc_start: 0.8386 (t) cc_final: 0.8105 (m) REVERT: D 66 GLU cc_start: 0.6942 (pp20) cc_final: 0.6593 (pp20) REVERT: D 102 ASN cc_start: 0.8127 (m-40) cc_final: 0.7854 (m-40) REVERT: D 132 PHE cc_start: 0.8589 (m-10) cc_final: 0.8253 (m-10) REVERT: D 161 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8041 (mm) REVERT: D 171 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6380 (mp0) REVERT: D 172 SER cc_start: 0.8112 (t) cc_final: 0.7692 (p) REVERT: D 194 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6976 (mm-30) REVERT: D 203 GLU cc_start: 0.7674 (tt0) cc_final: 0.7379 (mt-10) REVERT: D 208 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7567 (ttpt) REVERT: D 234 LEU cc_start: 0.8348 (mt) cc_final: 0.8130 (mt) REVERT: D 285 LEU cc_start: 0.8109 (tt) cc_final: 0.7805 (tp) REVERT: D 302 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7569 (ttmm) REVERT: D 335 GLU cc_start: 0.7402 (tp30) cc_final: 0.6985 (tp30) REVERT: D 344 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7150 (mm-40) REVERT: D 414 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8021 (mt) REVERT: D 437 TYR cc_start: 0.5801 (t80) cc_final: 0.5469 (t80) REVERT: D 441 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7522 (mmm-85) outliers start: 25 outliers final: 20 residues processed: 262 average time/residue: 0.2480 time to fit residues: 81.3658 Evaluate side-chains 269 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 29 ARG 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 155 ASP Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 5 TRP Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 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 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 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS ** D 268 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.146464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122457 restraints weight = 12209.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126734 restraints weight = 6599.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129586 restraints weight = 4210.483| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7564 Z= 0.196 Angle : 0.706 10.703 10220 Z= 0.354 Chirality : 0.044 0.212 1114 Planarity : 0.005 0.045 1312 Dihedral : 4.423 25.026 978 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.13 % Rotamer: Outliers : 3.35 % Allowed : 32.51 % Favored : 64.14 % 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 (0.29), residues: 888 helix: 1.18 (0.26), residues: 412 sheet: 0.74 (0.63), residues: 77 loop : -1.75 (0.30), residues: 399 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 0.045 0.002 PHE D 260 TYR 0.016 0.001 TYR B 79 ARG 0.009 0.001 ARG D 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.49 seconds wall clock time: 38 minutes 50.36 seconds (2330.36 seconds total)