Starting phenix.real_space_refine on Wed Sep 25 10:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qau_18304/09_2024/8qau_18304.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 142 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 59 5.16 5 C 6370 2.51 5 N 1749 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10137 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3373 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain breaks: 1 Chain: "D" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3359 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1700 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 8, 'TRANS': 244} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 268 Chain: "B" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1440 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 4, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 168 Chain: "E" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 142 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.27, per 1000 atoms: 0.72 Number of scatterers: 10137 At special positions: 0 Unit cell: (171.72, 101.76, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 5 15.00 Mg 1 11.99 O 1953 8.00 N 1749 7.00 C 6370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 62.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.756A pdb=" N GLN C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.625A pdb=" N ASN C 50 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.790A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.336A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 190 through 196 removed outlier: 3.947A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.979A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.589A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.675A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 432 removed outlier: 4.001A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 46 through 49 Processing helix chain 'D' and resid 69 through 78 removed outlier: 4.627A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.637A pdb=" N ILE D 84 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 126 removed outlier: 4.230A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.536A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.643A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.823A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.739A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.670A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.601A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 4.232A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 4.373A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.538A pdb=" N ASN A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 214 through 255 removed outlier: 5.001A pdb=" N GLY A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 removed outlier: 3.933A pdb=" N LYS A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 365 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.855A pdb=" N LEU B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 37 through 53 removed outlier: 4.320A pdb=" N MET B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 70 removed outlier: 3.754A pdb=" N LEU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 101 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.774A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 140 Processing helix chain 'B' and resid 140 through 169 removed outlier: 3.577A pdb=" N ILE B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'E' and resid 257 through 267 Processing sheet with id=AA1, first strand: chain 'C' and resid 92 through 93 removed outlier: 8.036A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLU C 3 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N SER C 136 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 5 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N SER C 165 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 92 removed outlier: 7.974A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 14.092A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54 608 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1818 1.32 - 1.44: 2651 1.44 - 1.57: 5764 1.57 - 1.69: 13 1.69 - 1.81: 94 Bond restraints: 10340 Sorted by residual: bond pdb=" CG PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 1.503 1.265 0.238 3.40e-02 8.65e+02 4.91e+01 bond pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 6.02e+00 bond pdb=" CB PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.40e+00 bond pdb=" CG GLU A 131 " pdb=" CD GLU A 131 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.64e+00 bond pdb=" CD GLU A 131 " pdb=" OE1 GLU A 131 " ideal model delta sigma weight residual 1.249 1.225 0.024 1.90e-02 2.77e+03 1.58e+00 ... (remaining 10335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 13986 3.31 - 6.62: 82 6.62 - 9.92: 9 9.92 - 13.23: 0 13.23 - 16.54: 2 Bond angle restraints: 14079 Sorted by residual: angle pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 112.00 95.46 16.54 1.40e+00 5.10e-01 1.40e+02 angle pdb=" N PRO C 32 " pdb=" CD PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 103.20 89.05 14.15 1.50e+00 4.44e-01 8.89e+01 angle pdb=" CA PRO C 32 " pdb=" CB PRO C 32 " pdb=" CG PRO C 32 " ideal model delta sigma weight residual 104.50 94.58 9.92 1.90e+00 2.77e-01 2.73e+01 angle pdb=" CA MET B 108 " pdb=" CB MET B 108 " pdb=" CG MET B 108 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" N GLY C 10 " pdb=" CA GLY C 10 " pdb=" C GLY C 10 " ideal model delta sigma weight residual 113.18 122.13 -8.95 2.37e+00 1.78e-01 1.43e+01 ... (remaining 14074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 6038 32.23 - 64.46: 154 64.46 - 96.70: 29 96.70 - 128.93: 5 128.93 - 161.16: 11 Dihedral angle restraints: 6237 sinusoidal: 2318 harmonic: 3919 Sorted by residual: dihedral pdb=" C5' GDP D 501 " pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sinusoidal sigma weight residual 179.98 37.05 142.93 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" CA VAL C 9 " pdb=" C VAL C 9 " pdb=" N GLY C 10 " pdb=" CA GLY C 10 " ideal model delta harmonic sigma weight residual -180.00 -149.55 -30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -10.71 115.31 1 2.00e+01 2.50e-03 3.43e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1293 0.052 - 0.105: 255 0.105 - 0.157: 36 0.157 - 0.209: 3 0.209 - 0.262: 1 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C10 TA1 D 502 " pdb=" C02 TA1 D 502 " pdb=" C11 TA1 D 502 " pdb=" C18 TA1 D 502 " both_signs ideal model delta sigma weight residual False 2.54 2.28 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C02 TA1 D 502 " pdb=" C01 TA1 D 502 " pdb=" C10 TA1 D 502 " pdb=" O02 TA1 D 502 " both_signs ideal model delta sigma weight residual False 2.56 2.75 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ASN A 146 " pdb=" N ASN A 146 " pdb=" C ASN A 146 " pdb=" CB ASN A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 1585 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 31 " 0.092 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO C 32 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 32 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 32 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 76 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" CD GLU B 76 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 76 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 76 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 50 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" CD GLU B 50 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 50 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 50 " -0.012 2.00e-02 2.50e+03 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 95 2.56 - 3.15: 8593 3.15 - 3.73: 16539 3.73 - 4.32: 21501 4.32 - 4.90: 35889 Nonbonded interactions: 82617 Sorted by model distance: nonbonded pdb=" OD2 ASP C 98 " pdb="MG MG C 502 " model vdw 1.980 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 2.061 2.170 nonbonded pdb=" O3G GTP C 501 " pdb="MG MG C 502 " model vdw 2.152 2.170 nonbonded pdb=" OG SER C 178 " pdb=" OE1 GLU C 183 " model vdw 2.185 3.040 nonbonded pdb=" O ALA D 63 " pdb=" ND2 ASN D 89 " model vdw 2.238 3.120 ... (remaining 82612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 10340 Z= 0.277 Angle : 0.690 16.538 14079 Z= 0.365 Chirality : 0.042 0.262 1588 Planarity : 0.005 0.125 1846 Dihedral : 17.836 161.161 3703 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.50 (0.23), residues: 1333 helix: 1.34 (0.19), residues: 743 sheet: -0.49 (0.47), residues: 123 loop : -1.03 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 388 HIS 0.004 0.001 HIS C 88 PHE 0.019 0.001 PHE C 49 TYR 0.014 0.001 TYR C 282 ARG 0.011 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 MET cc_start: 0.5297 (mmm) cc_final: 0.5088 (mmm) REVERT: C 346 TRP cc_start: 0.6579 (p-90) cc_final: 0.4146 (t60) REVERT: C 352 LYS cc_start: 0.5687 (mmpt) cc_final: 0.5248 (mmtm) REVERT: A 225 MET cc_start: 0.8826 (mmp) cc_final: 0.8580 (mmm) REVERT: B 101 ILE cc_start: 0.6545 (pt) cc_final: 0.6278 (pt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2140 time to fit residues: 85.3597 Evaluate side-chains 178 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS D 414 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10340 Z= 0.234 Angle : 0.682 8.150 14079 Z= 0.343 Chirality : 0.043 0.194 1588 Planarity : 0.004 0.042 1846 Dihedral : 15.217 142.303 1571 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 13.37 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1333 helix: 1.62 (0.19), residues: 752 sheet: -0.57 (0.48), residues: 111 loop : -0.75 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 21 HIS 0.006 0.001 HIS C 88 PHE 0.019 0.002 PHE B 97 TYR 0.029 0.002 TYR B 112 ARG 0.006 0.001 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 346 TRP cc_start: 0.6865 (p-90) cc_final: 0.4113 (t60) REVERT: A 225 MET cc_start: 0.8410 (mmp) cc_final: 0.8190 (mtp) outliers start: 19 outliers final: 11 residues processed: 208 average time/residue: 0.1940 time to fit residues: 58.4798 Evaluate side-chains 181 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain B residue 39 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 40.0000 chunk 106 optimal weight: 50.0000 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10340 Z= 0.228 Angle : 0.649 10.630 14079 Z= 0.324 Chirality : 0.044 0.247 1588 Planarity : 0.004 0.045 1846 Dihedral : 13.471 141.482 1571 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 2.06 % Allowed : 15.84 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1333 helix: 1.79 (0.19), residues: 758 sheet: -0.63 (0.47), residues: 116 loop : -0.63 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 21 HIS 0.004 0.001 HIS C 139 PHE 0.013 0.001 PHE C 267 TYR 0.020 0.002 TYR C 172 ARG 0.004 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 ASP cc_start: 0.5448 (p0) cc_final: 0.4960 (p0) REVERT: C 346 TRP cc_start: 0.6921 (p-90) cc_final: 0.4268 (t-100) REVERT: D 257 MET cc_start: 0.5991 (mmt) cc_final: 0.5652 (mmt) REVERT: A 226 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8018 (t) outliers start: 20 outliers final: 11 residues processed: 196 average time/residue: 0.1927 time to fit residues: 55.0662 Evaluate side-chains 173 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 39 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 50.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10340 Z= 0.206 Angle : 0.635 9.469 14079 Z= 0.321 Chirality : 0.044 0.456 1588 Planarity : 0.004 0.043 1846 Dihedral : 9.636 141.127 1571 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 2.78 % Allowed : 17.18 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1333 helix: 1.86 (0.19), residues: 757 sheet: -0.63 (0.46), residues: 116 loop : -0.63 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 21 HIS 0.005 0.001 HIS C 139 PHE 0.017 0.001 PHE A 153 TYR 0.025 0.001 TYR C 172 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.170 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: D 293 MET cc_start: 0.6527 (mmt) cc_final: 0.5792 (tpt) REVERT: D 404 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6705 (t0) REVERT: A 186 GLU cc_start: 0.7713 (tt0) cc_final: 0.7242 (tt0) REVERT: A 226 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (t) REVERT: B 58 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8139 (mp0) outliers start: 27 outliers final: 17 residues processed: 193 average time/residue: 0.1877 time to fit residues: 53.5974 Evaluate side-chains 172 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN C 372 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 298 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 10340 Z= 0.491 Angle : 0.803 8.305 14079 Z= 0.412 Chirality : 0.048 0.299 1588 Planarity : 0.005 0.048 1846 Dihedral : 9.725 156.734 1571 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.13 % Favored : 95.72 % Rotamer: Outliers : 3.60 % Allowed : 18.83 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.80 (0.23), residues: 1333 helix: 1.49 (0.19), residues: 766 sheet: -0.23 (0.47), residues: 114 loop : -0.90 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 21 HIS 0.009 0.002 HIS C 192 PHE 0.018 0.002 PHE D 167 TYR 0.028 0.003 TYR C 172 ARG 0.007 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 293 MET cc_start: 0.6022 (mmt) cc_final: 0.5796 (tpt) REVERT: B 58 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8444 (mp0) outliers start: 35 outliers final: 18 residues processed: 176 average time/residue: 0.1999 time to fit residues: 51.7263 Evaluate side-chains 159 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10340 Z= 0.215 Angle : 0.668 8.846 14079 Z= 0.341 Chirality : 0.044 0.222 1588 Planarity : 0.004 0.044 1846 Dihedral : 9.219 152.462 1571 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 2.06 % Allowed : 20.68 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1333 helix: 1.70 (0.19), residues: 762 sheet: -0.29 (0.47), residues: 109 loop : -0.63 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 21 HIS 0.004 0.001 HIS C 8 PHE 0.024 0.001 PHE A 153 TYR 0.022 0.002 TYR C 172 ARG 0.006 0.001 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8376 (mmp) cc_final: 0.7950 (mmp) REVERT: A 226 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 58 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8478 (mp0) outliers start: 20 outliers final: 15 residues processed: 176 average time/residue: 0.1972 time to fit residues: 51.6255 Evaluate side-chains 160 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 40.0000 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10340 Z= 0.209 Angle : 0.694 16.416 14079 Z= 0.353 Chirality : 0.045 0.330 1588 Planarity : 0.004 0.046 1846 Dihedral : 8.747 151.847 1571 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 2.16 % Allowed : 21.81 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1333 helix: 1.80 (0.19), residues: 760 sheet: -0.20 (0.47), residues: 109 loop : -0.61 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 21 HIS 0.003 0.001 HIS C 88 PHE 0.011 0.001 PHE A 198 TYR 0.027 0.002 TYR A 196 ARG 0.006 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 ASP cc_start: 0.5854 (p0) cc_final: 0.5469 (p0) REVERT: A 226 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 58 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8409 (mp0) outliers start: 21 outliers final: 13 residues processed: 173 average time/residue: 0.1812 time to fit residues: 47.0301 Evaluate side-chains 160 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10340 Z= 0.211 Angle : 0.707 12.230 14079 Z= 0.357 Chirality : 0.045 0.332 1588 Planarity : 0.004 0.046 1846 Dihedral : 8.550 151.600 1571 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.26 % Allowed : 22.94 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1333 helix: 1.78 (0.19), residues: 763 sheet: -0.02 (0.48), residues: 107 loop : -0.54 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 21 HIS 0.004 0.001 HIS D 190 PHE 0.009 0.001 PHE D 167 TYR 0.024 0.001 TYR B 40 ARG 0.007 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.291 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 226 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (t) outliers start: 22 outliers final: 16 residues processed: 177 average time/residue: 0.1931 time to fit residues: 50.5404 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 128 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 71 optimal weight: 0.0060 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10340 Z= 0.289 Angle : 0.750 12.985 14079 Z= 0.380 Chirality : 0.046 0.329 1588 Planarity : 0.004 0.045 1846 Dihedral : 8.704 153.904 1571 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 2.37 % Allowed : 23.66 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1333 helix: 1.84 (0.19), residues: 757 sheet: 0.02 (0.47), residues: 113 loop : -0.60 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 21 HIS 0.004 0.001 HIS C 8 PHE 0.026 0.001 PHE A 153 TYR 0.023 0.002 TYR B 40 ARG 0.009 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 PHE cc_start: 0.8038 (t80) cc_final: 0.7766 (t80) REVERT: A 225 MET cc_start: 0.8343 (mmp) cc_final: 0.8004 (ttt) REVERT: A 226 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8281 (t) outliers start: 23 outliers final: 19 residues processed: 160 average time/residue: 0.1894 time to fit residues: 45.1023 Evaluate side-chains 161 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 128 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10340 Z= 0.240 Angle : 0.739 12.093 14079 Z= 0.375 Chirality : 0.046 0.351 1588 Planarity : 0.004 0.044 1846 Dihedral : 8.594 152.151 1571 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 1.75 % Allowed : 24.38 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1333 helix: 1.76 (0.19), residues: 759 sheet: -0.03 (0.47), residues: 118 loop : -0.51 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 21 HIS 0.004 0.001 HIS A 223 PHE 0.026 0.001 PHE A 153 TYR 0.023 0.002 TYR B 40 ARG 0.005 0.001 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.211 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: C 313 MET cc_start: 0.6519 (tpt) cc_final: 0.6262 (tpt) REVERT: A 136 LEU cc_start: 0.8298 (tp) cc_final: 0.7964 (tp) REVERT: A 226 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8278 (t) outliers start: 17 outliers final: 16 residues processed: 157 average time/residue: 0.1858 time to fit residues: 43.5045 Evaluate side-chains 157 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 363 MET Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 128 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.103560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074261 restraints weight = 37392.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076281 restraints weight = 18235.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.077719 restraints weight = 11292.207| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10340 Z= 0.219 Angle : 0.728 11.473 14079 Z= 0.368 Chirality : 0.045 0.338 1588 Planarity : 0.004 0.044 1846 Dihedral : 8.391 151.230 1571 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.15 % Favored : 96.77 % Rotamer: Outliers : 1.85 % Allowed : 24.38 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1333 helix: 1.81 (0.19), residues: 758 sheet: 0.02 (0.47), residues: 118 loop : -0.49 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 21 HIS 0.003 0.001 HIS A 223 PHE 0.041 0.001 PHE A 153 TYR 0.021 0.001 TYR B 40 ARG 0.007 0.000 ARG A 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.23 seconds wall clock time: 38 minutes 40.71 seconds (2320.71 seconds total)