Starting phenix.real_space_refine on Tue Mar 3 19:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.map" model { file = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi9_21683/03_2026/6wi9_21683.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 53 5.16 5 C 5410 2.51 5 N 1526 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1646 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2706 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 11, 'TRANS': 356} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 7, 'TRP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 7, 'ASN:plan1': 6, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 1.64, per 1000 atoms: 0.19 Number of scatterers: 8550 At special positions: 0 Unit cell: (78.26, 173.72, 97.18, 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 53 16.00 O 1561 8.00 N 1526 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 345.3 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 40.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.720A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.761A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.685A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.962A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.187A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.796A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.756A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 31 through 46 removed outlier: 4.010A pdb=" N ASP R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 93 through 97 Processing helix chain 'R' and resid 131 through 165 removed outlier: 3.509A pdb=" N ARG R 135 " --> pdb=" O SER R 131 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.541A pdb=" N TYR R 176 " --> pdb=" O CYS R 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS R 180 " --> pdb=" O TYR R 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 193 " --> pdb=" O ALA R 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 3.948A pdb=" N VAL R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 229 " --> pdb=" O CYS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 265 removed outlier: 3.603A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 280 removed outlier: 4.095A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 336 through 352 removed outlier: 4.617A pdb=" N ARG R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 3.977A pdb=" N PHE R 358 " --> pdb=" O TYR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 368 removed outlier: 5.821A pdb=" N GLU R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE R 368 " --> pdb=" O ALA R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 374 removed outlier: 3.569A pdb=" N GLU R 373 " --> pdb=" O GLN R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 390 Processing helix chain 'R' and resid 393 through 408 removed outlier: 3.514A pdb=" N GLU R 398 " --> pdb=" O GLU R 394 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 399 " --> pdb=" O VAL R 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS R 401 " --> pdb=" O LEU R 397 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS R 407 " --> pdb=" O TRP R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.590A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.066A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.183A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.414A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.794A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.807A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 69 through 70 removed outlier: 3.677A pdb=" N MET R 69 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP R 76 " --> pdb=" O MET R 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 85 through 87 removed outlier: 4.269A pdb=" N LEU R 103 " --> pdb=" O VAL R 87 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2851 1.35 - 1.46: 2108 1.46 - 1.58: 3684 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8716 Sorted by residual: bond pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.37e-02 5.33e+03 1.81e+00 bond pdb=" CA ILE R 246 " pdb=" CB ILE R 246 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.19e-02 7.06e+03 9.69e-01 bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.13e-01 bond pdb=" CA ILE N 51 " pdb=" CB ILE N 51 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 7.69e-01 bond pdb=" C GLU R 67 " pdb=" N GLY R 68 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 7.03e-01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11468 1.31 - 2.61: 266 2.61 - 3.92: 51 3.92 - 5.22: 9 5.22 - 6.53: 3 Bond angle restraints: 11797 Sorted by residual: angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 114.56 109.65 4.91 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N ILE R 73 " pdb=" CA ILE R 73 " pdb=" C ILE R 73 " ideal model delta sigma weight residual 111.62 108.73 2.89 7.90e-01 1.60e+00 1.34e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 112.12 109.09 3.03 8.40e-01 1.42e+00 1.30e+01 angle pdb=" C GLU R 52 " pdb=" N GLN R 53 " pdb=" CA GLN R 53 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.20 110.06 3.14 9.60e-01 1.09e+00 1.07e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4768 17.83 - 35.67: 347 35.67 - 53.50: 39 53.50 - 71.34: 6 71.34 - 89.17: 15 Dihedral angle restraints: 5175 sinusoidal: 1970 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS R 215 " pdb=" SG CYS R 215 " pdb=" SG CYS R 285 " pdb=" CB CYS R 285 " ideal model delta sinusoidal sigma weight residual 93.00 42.54 50.46 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS R 45 " pdb=" SG CYS R 45 " pdb=" SG CYS R 75 " pdb=" CB CYS R 75 " ideal model delta sinusoidal sigma weight residual 93.00 128.25 -35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB GLU R 373 " pdb=" CG GLU R 373 " pdb=" CD GLU R 373 " pdb=" OE1 GLU R 373 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 940 0.035 - 0.071: 282 0.071 - 0.106: 87 0.106 - 0.142: 12 0.142 - 0.177: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CB ILE R 246 " pdb=" CA ILE R 246 " pdb=" CG1 ILE R 246 " pdb=" CG2 ILE R 246 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA ILE R 288 " pdb=" N ILE R 288 " pdb=" C ILE R 288 " pdb=" CB ILE R 288 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1320 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 321 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1049 2.75 - 3.29: 8547 3.29 - 3.83: 13270 3.83 - 4.36: 15713 4.36 - 4.90: 26736 Nonbonded interactions: 65315 Sorted by model distance: nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.214 3.120 nonbonded pdb=" O ASP B 76 " pdb=" OG SER B 98 " model vdw 2.236 3.040 nonbonded pdb=" O ARG R 339 " pdb=" OG SER R 343 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN R 291 " pdb=" OG SER R 293 " model vdw 2.312 3.040 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.317 3.120 ... (remaining 65310 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.002 0.020 8721 Z= 0.102 Angle : 0.502 6.528 11807 Z= 0.312 Chirality : 0.038 0.177 1323 Planarity : 0.002 0.033 1516 Dihedral : 12.848 89.170 3086 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.21), residues: 1086 helix: -2.77 (0.18), residues: 377 sheet: -1.64 (0.32), residues: 208 loop : -2.50 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.004 0.001 TYR B 124 PHE 0.013 0.001 PHE A 315 TRP 0.006 0.001 TRP A 234 HIS 0.001 0.000 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00166 ( 8716) covalent geometry : angle 0.50157 (11797) SS BOND : bond 0.00143 ( 5) SS BOND : angle 0.62532 ( 10) hydrogen bonds : bond 0.27003 ( 369) hydrogen bonds : angle 8.99390 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.273 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 217 VAL cc_start: 0.8933 (t) cc_final: 0.8615 (t) REVERT: A 374 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7523 (ttt180) REVERT: B 16 ASN cc_start: 0.9351 (m110) cc_final: 0.8822 (m110) REVERT: B 45 MET cc_start: 0.7078 (mmm) cc_final: 0.6780 (tpp) REVERT: B 78 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 145 TYR cc_start: 0.8584 (p90) cc_final: 0.8365 (p90) REVERT: B 165 THR cc_start: 0.7995 (p) cc_final: 0.7711 (t) REVERT: B 188 MET cc_start: 0.7775 (tpt) cc_final: 0.7505 (mmm) REVERT: B 220 GLN cc_start: 0.8309 (mt0) cc_final: 0.8094 (tt0) REVERT: B 339 TRP cc_start: 0.8631 (m100) cc_final: 0.8349 (m100) REVERT: G 41 CYS cc_start: 0.8871 (m) cc_final: 0.8585 (m) REVERT: G 59 ASN cc_start: 0.7332 (t0) cc_final: 0.6482 (p0) REVERT: N 61 THR cc_start: 0.8397 (p) cc_final: 0.8138 (t) REVERT: N 83 MET cc_start: 0.8048 (pmm) cc_final: 0.7847 (pmm) REVERT: P 3 ASP cc_start: 0.8242 (t0) cc_final: 0.7913 (t0) REVERT: R 132 ASN cc_start: 0.8938 (p0) cc_final: 0.8731 (p0) REVERT: R 175 ASN cc_start: 0.9107 (m-40) cc_final: 0.8701 (m-40) REVERT: R 179 MET cc_start: 0.8074 (mmm) cc_final: 0.7812 (tpp) REVERT: R 227 MET cc_start: 0.8710 (tpt) cc_final: 0.8510 (tpt) REVERT: R 230 TYR cc_start: 0.8606 (m-80) cc_final: 0.8047 (m-10) REVERT: R 256 GLN cc_start: 0.7622 (mt0) cc_final: 0.6522 (tm-30) REVERT: R 261 PHE cc_start: 0.9039 (t80) cc_final: 0.8828 (t80) REVERT: R 282 ASP cc_start: 0.7871 (t0) cc_final: 0.7609 (t0) REVERT: R 321 MET cc_start: 0.8108 (mtt) cc_final: 0.7813 (mmm) REVERT: R 354 HIS cc_start: 0.9050 (p-80) cc_final: 0.8655 (p-80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.0949 time to fit residues: 40.6594 Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 218 ASN B 17 GLN B 91 HIS N 3 GLN R 180 HIS R 223 GLN R 229 ASN R 354 HIS R 392 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086065 restraints weight = 23817.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088610 restraints weight = 14166.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090355 restraints weight = 9892.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091540 restraints weight = 7705.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092261 restraints weight = 6495.194| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8721 Z= 0.153 Angle : 0.589 6.368 11807 Z= 0.317 Chirality : 0.043 0.188 1323 Planarity : 0.004 0.037 1516 Dihedral : 3.889 16.866 1203 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.24), residues: 1086 helix: -0.51 (0.25), residues: 375 sheet: -1.11 (0.33), residues: 206 loop : -2.03 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.018 0.002 TYR R 138 PHE 0.023 0.002 PHE R 372 TRP 0.016 0.002 TRP B 297 HIS 0.007 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8716) covalent geometry : angle 0.58899 (11797) SS BOND : bond 0.00489 ( 5) SS BOND : angle 0.97837 ( 10) hydrogen bonds : bond 0.05387 ( 369) hydrogen bonds : angle 5.69797 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.346 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 221 MET cc_start: 0.8403 (tpt) cc_final: 0.8109 (tpp) REVERT: A 222 PHE cc_start: 0.7948 (m-80) cc_final: 0.7640 (m-80) REVERT: A 318 TYR cc_start: 0.7882 (t80) cc_final: 0.7138 (t80) REVERT: A 374 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7439 (ttt180) REVERT: B 9 GLN cc_start: 0.8870 (tp40) cc_final: 0.8639 (mm110) REVERT: B 78 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8473 (mmmt) REVERT: B 188 MET cc_start: 0.8213 (tpt) cc_final: 0.7811 (mmm) REVERT: B 217 MET cc_start: 0.8703 (ppp) cc_final: 0.8165 (ppp) REVERT: B 220 GLN cc_start: 0.8540 (mt0) cc_final: 0.8015 (tt0) REVERT: B 339 TRP cc_start: 0.8822 (m100) cc_final: 0.8596 (m100) REVERT: G 59 ASN cc_start: 0.7204 (t0) cc_final: 0.6917 (t0) REVERT: N 80 TYR cc_start: 0.7550 (m-80) cc_final: 0.7085 (m-80) REVERT: R 175 ASN cc_start: 0.9092 (m-40) cc_final: 0.8649 (m-40) REVERT: R 179 MET cc_start: 0.8016 (mmm) cc_final: 0.7788 (mmm) REVERT: R 230 TYR cc_start: 0.8696 (m-80) cc_final: 0.8482 (m-10) REVERT: R 251 GLU cc_start: 0.7508 (pm20) cc_final: 0.7167 (pm20) REVERT: R 321 MET cc_start: 0.8060 (mtt) cc_final: 0.7805 (mmm) REVERT: R 342 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7898 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0866 time to fit residues: 31.3669 Evaluate side-chains 201 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 0.0070 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 53 GLN R 229 ASN R 380 GLN R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.085120 restraints weight = 23740.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087645 restraints weight = 14162.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089328 restraints weight = 9870.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090362 restraints weight = 7698.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091220 restraints weight = 6556.549| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8721 Z= 0.143 Angle : 0.563 5.867 11807 Z= 0.300 Chirality : 0.042 0.213 1323 Planarity : 0.004 0.040 1516 Dihedral : 4.037 15.841 1203 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.25), residues: 1086 helix: 0.02 (0.26), residues: 385 sheet: -0.86 (0.34), residues: 210 loop : -1.80 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.018 0.002 TYR R 138 PHE 0.017 0.001 PHE N 68 TRP 0.020 0.002 TRP A 281 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8716) covalent geometry : angle 0.56296 (11797) SS BOND : bond 0.00416 ( 5) SS BOND : angle 1.00806 ( 10) hydrogen bonds : bond 0.04538 ( 369) hydrogen bonds : angle 5.16827 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7345 (mtt180) REVERT: B 78 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8286 (mmmt) REVERT: B 188 MET cc_start: 0.8291 (tpt) cc_final: 0.7982 (mmm) REVERT: B 217 MET cc_start: 0.8622 (ppp) cc_final: 0.8246 (ppp) REVERT: B 220 GLN cc_start: 0.8228 (mt0) cc_final: 0.7934 (tt0) REVERT: B 225 HIS cc_start: 0.7438 (m-70) cc_final: 0.7218 (m-70) REVERT: B 312 ASP cc_start: 0.7642 (p0) cc_final: 0.7046 (p0) REVERT: B 339 TRP cc_start: 0.8917 (m100) cc_final: 0.8557 (m100) REVERT: G 21 MET cc_start: 0.8133 (mmm) cc_final: 0.7144 (mmm) REVERT: G 41 CYS cc_start: 0.8719 (m) cc_final: 0.8392 (m) REVERT: G 59 ASN cc_start: 0.7244 (t0) cc_final: 0.6932 (t0) REVERT: N 64 VAL cc_start: 0.7948 (m) cc_final: 0.7554 (m) REVERT: N 72 ARG cc_start: 0.6567 (ptm-80) cc_final: 0.6138 (ptt90) REVERT: N 80 TYR cc_start: 0.7586 (m-80) cc_final: 0.6569 (m-80) REVERT: R 175 ASN cc_start: 0.9088 (m-40) cc_final: 0.8661 (m-40) REVERT: R 179 MET cc_start: 0.7963 (mmm) cc_final: 0.7634 (tpp) REVERT: R 251 GLU cc_start: 0.7161 (pm20) cc_final: 0.6288 (pp20) REVERT: R 321 MET cc_start: 0.8103 (mtt) cc_final: 0.7795 (mmm) REVERT: R 342 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7863 (tmt-80) REVERT: R 355 TYR cc_start: 0.8737 (m-80) cc_final: 0.8139 (m-80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.0839 time to fit residues: 28.2880 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 80 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN N 53 GLN R 229 ASN R 332 ASN R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087172 restraints weight = 23928.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089713 restraints weight = 14167.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091436 restraints weight = 9818.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092635 restraints weight = 7610.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.093319 restraints weight = 6389.488| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8721 Z= 0.112 Angle : 0.547 7.103 11807 Z= 0.289 Chirality : 0.041 0.161 1323 Planarity : 0.003 0.042 1516 Dihedral : 3.903 16.246 1203 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1086 helix: 0.40 (0.27), residues: 385 sheet: -0.40 (0.36), residues: 205 loop : -1.64 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.017 0.001 TYR R 138 PHE 0.031 0.002 PHE A 340 TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8716) covalent geometry : angle 0.54666 (11797) SS BOND : bond 0.00160 ( 5) SS BOND : angle 0.89810 ( 10) hydrogen bonds : bond 0.04032 ( 369) hydrogen bonds : angle 4.90867 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.374 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: A 374 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7353 (mtt180) REVERT: B 78 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8314 (mmmt) REVERT: B 188 MET cc_start: 0.8275 (tpt) cc_final: 0.7961 (mmm) REVERT: B 217 MET cc_start: 0.8576 (ppp) cc_final: 0.8235 (ppp) REVERT: B 220 GLN cc_start: 0.8053 (mt0) cc_final: 0.7819 (tt0) REVERT: B 260 GLU cc_start: 0.7800 (mp0) cc_final: 0.7575 (mp0) REVERT: B 283 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7445 (tpt-90) REVERT: B 312 ASP cc_start: 0.7780 (p0) cc_final: 0.6981 (p0) REVERT: B 339 TRP cc_start: 0.8879 (m100) cc_final: 0.8580 (m100) REVERT: G 21 MET cc_start: 0.8058 (mmm) cc_final: 0.6984 (mmm) REVERT: G 41 CYS cc_start: 0.8621 (m) cc_final: 0.8380 (m) REVERT: G 59 ASN cc_start: 0.7183 (t0) cc_final: 0.6903 (t0) REVERT: N 64 VAL cc_start: 0.7988 (m) cc_final: 0.7612 (m) REVERT: N 72 ARG cc_start: 0.6498 (ptm-80) cc_final: 0.6023 (ptt90) REVERT: N 76 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8437 (mtmm) REVERT: N 104 THR cc_start: 0.8312 (p) cc_final: 0.8074 (p) REVERT: R 147 THR cc_start: 0.8793 (m) cc_final: 0.8539 (m) REVERT: R 175 ASN cc_start: 0.8949 (m-40) cc_final: 0.8482 (m-40) REVERT: R 179 MET cc_start: 0.7865 (mmm) cc_final: 0.7495 (tpp) REVERT: R 321 MET cc_start: 0.7999 (mtt) cc_final: 0.7641 (mmm) REVERT: R 342 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7809 (tmt-80) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.0869 time to fit residues: 30.7988 Evaluate side-chains 201 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083943 restraints weight = 23918.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086521 restraints weight = 13936.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088255 restraints weight = 9560.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089456 restraints weight = 7346.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090049 restraints weight = 6128.910| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8721 Z= 0.169 Angle : 0.597 6.550 11807 Z= 0.315 Chirality : 0.043 0.145 1323 Planarity : 0.004 0.045 1516 Dihedral : 4.192 17.046 1203 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.26), residues: 1086 helix: 0.37 (0.27), residues: 390 sheet: -0.33 (0.37), residues: 209 loop : -1.52 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.025 0.002 TYR G 40 PHE 0.025 0.002 PHE A 340 TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8716) covalent geometry : angle 0.59603 (11797) SS BOND : bond 0.00136 ( 5) SS BOND : angle 1.08701 ( 10) hydrogen bonds : bond 0.04132 ( 369) hydrogen bonds : angle 4.99327 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.258 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 360 TYR cc_start: 0.8897 (m-80) cc_final: 0.8687 (m-80) REVERT: A 374 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7374 (mtt180) REVERT: B 188 MET cc_start: 0.8356 (tpt) cc_final: 0.7983 (tpp) REVERT: B 217 MET cc_start: 0.8621 (ppp) cc_final: 0.8296 (ppp) REVERT: B 283 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7437 (tpt-90) REVERT: B 339 TRP cc_start: 0.8965 (m100) cc_final: 0.8624 (m100) REVERT: G 21 MET cc_start: 0.8055 (mmm) cc_final: 0.6988 (mmm) REVERT: G 59 ASN cc_start: 0.7216 (t0) cc_final: 0.6858 (t0) REVERT: N 64 VAL cc_start: 0.8105 (m) cc_final: 0.7799 (m) REVERT: N 72 ARG cc_start: 0.6395 (ptm-80) cc_final: 0.6009 (ptt90) REVERT: N 76 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8559 (mtmm) REVERT: N 78 THR cc_start: 0.7041 (p) cc_final: 0.6824 (p) REVERT: R 147 THR cc_start: 0.8796 (m) cc_final: 0.8514 (m) REVERT: R 175 ASN cc_start: 0.8997 (m-40) cc_final: 0.8574 (m-40) REVERT: R 179 MET cc_start: 0.7918 (mmm) cc_final: 0.7692 (tpp) REVERT: R 321 MET cc_start: 0.8126 (mtt) cc_final: 0.7782 (mmm) REVERT: R 342 ARG cc_start: 0.8210 (mtm180) cc_final: 0.7808 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.0820 time to fit residues: 27.6984 Evaluate side-chains 196 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083331 restraints weight = 24140.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085907 restraints weight = 14173.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087628 restraints weight = 9783.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088823 restraints weight = 7595.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089556 restraints weight = 6374.513| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8721 Z= 0.168 Angle : 0.604 9.247 11807 Z= 0.316 Chirality : 0.043 0.256 1323 Planarity : 0.004 0.044 1516 Dihedral : 4.257 16.429 1203 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.26), residues: 1086 helix: 0.37 (0.26), residues: 386 sheet: -0.14 (0.37), residues: 205 loop : -1.40 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 13 TYR 0.016 0.002 TYR R 138 PHE 0.021 0.002 PHE N 68 TRP 0.037 0.002 TRP A 281 HIS 0.007 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8716) covalent geometry : angle 0.60341 (11797) SS BOND : bond 0.00183 ( 5) SS BOND : angle 1.16893 ( 10) hydrogen bonds : bond 0.04022 ( 369) hydrogen bonds : angle 4.94520 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8921 (m-80) cc_final: 0.8581 (m-80) REVERT: B 78 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7969 (mmtm) REVERT: B 188 MET cc_start: 0.8464 (tpt) cc_final: 0.8061 (tpp) REVERT: B 217 MET cc_start: 0.8556 (ppp) cc_final: 0.8277 (ppp) REVERT: B 283 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7421 (tpt-90) REVERT: B 339 TRP cc_start: 0.8965 (m100) cc_final: 0.8611 (m100) REVERT: G 21 MET cc_start: 0.8145 (mmm) cc_final: 0.7104 (mmm) REVERT: G 59 ASN cc_start: 0.7278 (t0) cc_final: 0.6884 (t0) REVERT: N 64 VAL cc_start: 0.8062 (m) cc_final: 0.7765 (m) REVERT: N 72 ARG cc_start: 0.6372 (ptm-80) cc_final: 0.6048 (ptt90) REVERT: N 76 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8482 (mtmm) REVERT: R 147 THR cc_start: 0.8787 (m) cc_final: 0.8521 (m) REVERT: R 175 ASN cc_start: 0.8984 (m-40) cc_final: 0.8536 (m-40) REVERT: R 179 MET cc_start: 0.7896 (mmm) cc_final: 0.7620 (tpp) REVERT: R 321 MET cc_start: 0.8073 (mtt) cc_final: 0.7754 (mmm) REVERT: R 342 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7828 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.0921 time to fit residues: 30.2049 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.106277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083658 restraints weight = 24069.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086216 restraints weight = 14098.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087942 restraints weight = 9699.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089143 restraints weight = 7468.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089848 restraints weight = 6244.878| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8721 Z= 0.145 Angle : 0.598 7.667 11807 Z= 0.315 Chirality : 0.043 0.218 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.308 17.503 1203 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.26), residues: 1086 helix: 0.47 (0.27), residues: 387 sheet: -0.07 (0.37), residues: 203 loop : -1.47 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.019 0.002 TYR R 150 PHE 0.022 0.002 PHE N 68 TRP 0.022 0.002 TRP A 281 HIS 0.007 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8716) covalent geometry : angle 0.59733 (11797) SS BOND : bond 0.00190 ( 5) SS BOND : angle 1.09852 ( 10) hydrogen bonds : bond 0.03971 ( 369) hydrogen bonds : angle 4.91983 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8996 (m-80) cc_final: 0.8694 (m-80) REVERT: A 374 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7557 (mtt180) REVERT: B 188 MET cc_start: 0.8403 (tpt) cc_final: 0.8013 (tpp) REVERT: B 209 LYS cc_start: 0.8853 (mttt) cc_final: 0.8551 (mttt) REVERT: B 217 MET cc_start: 0.8576 (ppp) cc_final: 0.8322 (ppp) REVERT: B 283 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7435 (tpt-90) REVERT: B 339 TRP cc_start: 0.8980 (m100) cc_final: 0.8589 (m100) REVERT: G 21 MET cc_start: 0.8165 (mmm) cc_final: 0.7169 (mmm) REVERT: G 59 ASN cc_start: 0.7344 (t0) cc_final: 0.6913 (t0) REVERT: N 64 VAL cc_start: 0.7914 (m) cc_final: 0.7382 (m) REVERT: N 72 ARG cc_start: 0.6349 (ptm-80) cc_final: 0.6024 (ptt90) REVERT: N 76 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8461 (mtmm) REVERT: N 78 THR cc_start: 0.7147 (p) cc_final: 0.6940 (p) REVERT: R 147 THR cc_start: 0.8770 (m) cc_final: 0.8514 (m) REVERT: R 175 ASN cc_start: 0.8958 (m-40) cc_final: 0.8534 (m-40) REVERT: R 221 LEU cc_start: 0.9287 (tp) cc_final: 0.9034 (pp) REVERT: R 321 MET cc_start: 0.8114 (mtt) cc_final: 0.7751 (mmm) REVERT: R 358 PHE cc_start: 0.6784 (m-80) cc_final: 0.6451 (m-10) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0843 time to fit residues: 27.8019 Evaluate side-chains 195 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS N 53 GLN R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082909 restraints weight = 23641.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085367 restraints weight = 14022.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.087070 restraints weight = 9718.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088253 restraints weight = 7521.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088938 restraints weight = 6304.518| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8721 Z= 0.182 Angle : 0.641 7.907 11807 Z= 0.337 Chirality : 0.043 0.201 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.508 18.485 1203 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.26), residues: 1086 helix: 0.52 (0.26), residues: 389 sheet: -0.32 (0.37), residues: 209 loop : -1.52 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.017 0.002 TYR A 318 PHE 0.056 0.002 PHE N 68 TRP 0.018 0.002 TRP A 281 HIS 0.008 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8716) covalent geometry : angle 0.64013 (11797) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.34035 ( 10) hydrogen bonds : bond 0.04069 ( 369) hydrogen bonds : angle 4.98642 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8994 (m-80) cc_final: 0.8756 (m-80) REVERT: A 374 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7590 (mtt180) REVERT: B 78 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8245 (mmtm) REVERT: B 82 TRP cc_start: 0.8908 (m100) cc_final: 0.8617 (m-10) REVERT: B 188 MET cc_start: 0.8390 (tpt) cc_final: 0.8022 (tpp) REVERT: B 217 MET cc_start: 0.8594 (ppp) cc_final: 0.8362 (ppp) REVERT: B 283 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7716 (tpt-90) REVERT: B 312 ASP cc_start: 0.7667 (p0) cc_final: 0.7461 (p0) REVERT: B 339 TRP cc_start: 0.9015 (m100) cc_final: 0.8639 (m100) REVERT: G 21 MET cc_start: 0.8183 (mmm) cc_final: 0.7412 (mmm) REVERT: G 59 ASN cc_start: 0.7323 (t0) cc_final: 0.6890 (t0) REVERT: N 19 ARG cc_start: 0.8497 (tpt-90) cc_final: 0.8081 (tpt90) REVERT: N 64 VAL cc_start: 0.7674 (m) cc_final: 0.7033 (m) REVERT: N 76 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8494 (mtmm) REVERT: R 147 THR cc_start: 0.8799 (m) cc_final: 0.8546 (m) REVERT: R 150 TYR cc_start: 0.7953 (m-10) cc_final: 0.7634 (m-80) REVERT: R 175 ASN cc_start: 0.9055 (m-40) cc_final: 0.8709 (m110) REVERT: R 221 LEU cc_start: 0.9298 (tp) cc_final: 0.9049 (pp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0878 time to fit residues: 26.9969 Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084928 restraints weight = 23818.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087606 restraints weight = 13851.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089419 restraints weight = 9506.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090640 restraints weight = 7330.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091519 restraints weight = 6132.488| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8721 Z= 0.127 Angle : 0.615 9.320 11807 Z= 0.319 Chirality : 0.042 0.190 1323 Planarity : 0.004 0.044 1516 Dihedral : 4.335 17.874 1203 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.26), residues: 1086 helix: 0.63 (0.26), residues: 386 sheet: 0.01 (0.37), residues: 202 loop : -1.46 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.019 0.002 TYR B 124 PHE 0.029 0.002 PHE N 68 TRP 0.015 0.002 TRP A 281 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8716) covalent geometry : angle 0.61401 (11797) SS BOND : bond 0.00250 ( 5) SS BOND : angle 1.22191 ( 10) hydrogen bonds : bond 0.03878 ( 369) hydrogen bonds : angle 4.92959 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.352 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 360 TYR cc_start: 0.8999 (m-80) cc_final: 0.8676 (m-80) REVERT: A 374 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7549 (mtt180) REVERT: B 61 MET cc_start: 0.8507 (ppp) cc_final: 0.8151 (ppp) REVERT: B 188 MET cc_start: 0.8330 (tpt) cc_final: 0.7807 (tpt) REVERT: B 217 MET cc_start: 0.8608 (ppp) cc_final: 0.8399 (ppp) REVERT: B 220 GLN cc_start: 0.8067 (tt0) cc_final: 0.7745 (tt0) REVERT: B 222 PHE cc_start: 0.8149 (m-10) cc_final: 0.7530 (m-10) REVERT: B 283 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7355 (tpt-90) REVERT: B 312 ASP cc_start: 0.7968 (p0) cc_final: 0.7583 (p0) REVERT: B 339 TRP cc_start: 0.8977 (m100) cc_final: 0.8580 (m100) REVERT: G 21 MET cc_start: 0.8150 (mmm) cc_final: 0.7339 (mmm) REVERT: G 59 ASN cc_start: 0.7239 (t0) cc_final: 0.6812 (t0) REVERT: N 19 ARG cc_start: 0.8451 (tpt-90) cc_final: 0.7879 (tpt90) REVERT: N 64 VAL cc_start: 0.7351 (m) cc_final: 0.6697 (m) REVERT: N 76 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8518 (mtmm) REVERT: N 80 TYR cc_start: 0.7273 (m-10) cc_final: 0.6990 (m-80) REVERT: R 321 MET cc_start: 0.8177 (mmm) cc_final: 0.7668 (mmm) REVERT: R 342 ARG cc_start: 0.8283 (mtm180) cc_final: 0.7774 (tmt-80) REVERT: R 406 TRP cc_start: 0.7523 (t60) cc_final: 0.6302 (m100) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0839 time to fit residues: 27.5091 Evaluate side-chains 191 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086215 restraints weight = 23872.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088625 restraints weight = 14457.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090311 restraints weight = 10206.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091339 restraints weight = 8004.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092212 restraints weight = 6823.826| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8721 Z= 0.135 Angle : 0.643 12.140 11807 Z= 0.326 Chirality : 0.044 0.283 1323 Planarity : 0.004 0.041 1516 Dihedral : 4.321 17.909 1203 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 1086 helix: 0.67 (0.26), residues: 386 sheet: -0.19 (0.38), residues: 190 loop : -1.41 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 67 TYR 0.026 0.001 TYR A 318 PHE 0.029 0.002 PHE A 340 TRP 0.016 0.002 TRP R 232 HIS 0.005 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8716) covalent geometry : angle 0.64261 (11797) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.20358 ( 10) hydrogen bonds : bond 0.03823 ( 369) hydrogen bonds : angle 4.89557 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.8986 (m-80) cc_final: 0.8674 (m-80) REVERT: B 61 MET cc_start: 0.8518 (ppp) cc_final: 0.8186 (ppp) REVERT: B 78 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8564 (mmmt) REVERT: B 82 TRP cc_start: 0.8872 (m100) cc_final: 0.8640 (m-10) REVERT: B 188 MET cc_start: 0.8340 (tpt) cc_final: 0.7985 (tpp) REVERT: B 217 MET cc_start: 0.8448 (ppp) cc_final: 0.8196 (ppp) REVERT: B 339 TRP cc_start: 0.8961 (m100) cc_final: 0.8607 (m100) REVERT: G 21 MET cc_start: 0.8177 (mmm) cc_final: 0.7362 (mmm) REVERT: G 59 ASN cc_start: 0.7230 (t0) cc_final: 0.6817 (t0) REVERT: N 64 VAL cc_start: 0.7420 (m) cc_final: 0.7168 (m) REVERT: N 76 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8477 (mtmm) REVERT: N 123 GLN cc_start: 0.8062 (pp30) cc_final: 0.7841 (tm-30) REVERT: R 147 THR cc_start: 0.8786 (m) cc_final: 0.8577 (m) REVERT: R 175 ASN cc_start: 0.8616 (m-40) cc_final: 0.8342 (m-40) REVERT: R 321 MET cc_start: 0.8121 (mmm) cc_final: 0.7628 (mmm) REVERT: R 342 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7758 (tmt-80) REVERT: R 406 TRP cc_start: 0.7499 (t60) cc_final: 0.6326 (m100) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0792 time to fit residues: 25.4090 Evaluate side-chains 186 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 0.0060 chunk 56 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085456 restraints weight = 24303.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087852 restraints weight = 14962.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089478 restraints weight = 10720.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090560 restraints weight = 8516.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091165 restraints weight = 7299.705| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8721 Z= 0.140 Angle : 0.630 8.510 11807 Z= 0.322 Chirality : 0.043 0.184 1323 Planarity : 0.004 0.041 1516 Dihedral : 4.334 17.947 1203 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1086 helix: 0.66 (0.26), residues: 385 sheet: -0.15 (0.37), residues: 206 loop : -1.48 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.022 0.001 TYR A 318 PHE 0.021 0.001 PHE A 340 TRP 0.023 0.002 TRP R 232 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8716) covalent geometry : angle 0.62885 (11797) SS BOND : bond 0.00233 ( 5) SS BOND : angle 1.22149 ( 10) hydrogen bonds : bond 0.03816 ( 369) hydrogen bonds : angle 4.80209 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.86 seconds wall clock time: 26 minutes 32.43 seconds (1592.43 seconds total)