Starting phenix.real_space_refine on Tue Mar 3 20:07:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8r_33057/03_2026/7x8r_33057.map" } resolution = 2.61 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= 0.143 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 51 5.16 5 C 5414 2.51 5 N 1470 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 8493 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1940 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 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: "R" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2492 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 6, 'TRANS': 291} Chain breaks: 3 Chain: "R" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'BYI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8493 At special positions: 0 Unit cell: (79.254, 98.532, 155.295, 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 51 16.00 O 1558 8.00 N 1470 7.00 C 5414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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 226 " - pdb=" SG CYS R 296 " 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: 0.56 Conformation dependent library (CDL) restraints added in 261.8 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 45.4% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.966A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.636A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.567A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.531A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 138 through 170 removed outlier: 4.522A pdb=" N ARG R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 208 removed outlier: 3.708A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.921A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 275 removed outlier: 3.516A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 292 removed outlier: 3.679A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.930A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 368 removed outlier: 4.023A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 404 removed outlier: 4.348A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.412A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.093A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.563A 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: 6.247A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A 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: 3.605A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.953A 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: 6.998A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.506A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.160A 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 58 through 60 removed outlier: 6.537A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1290 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: 1.14 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1371 1.31 - 1.43: 2474 1.43 - 1.56: 4758 1.56 - 1.68: 4 1.68 - 1.81: 71 Bond restraints: 8678 Sorted by residual: bond pdb=" C42 BYI R 601 " pdb=" N41 BYI R 601 " ideal model delta sigma weight residual 1.345 1.503 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C15 BYI R 601 " pdb=" N17 BYI R 601 " ideal model delta sigma weight residual 1.345 1.486 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C51 BYI R 601 " pdb=" N50 BYI R 601 " ideal model delta sigma weight residual 1.369 1.475 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C06 BYI R 601 " pdb=" N08 BYI R 601 " ideal model delta sigma weight residual 1.367 1.473 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C51 BYI R 601 " pdb=" O53 BYI R 601 " ideal model delta sigma weight residual 1.320 1.425 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 8673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 11722 5.49 - 10.98: 31 10.98 - 16.47: 1 16.47 - 21.96: 1 21.96 - 27.45: 1 Bond angle restraints: 11756 Sorted by residual: angle pdb=" N ASN A 292 " pdb=" CA ASN A 292 " pdb=" C ASN A 292 " ideal model delta sigma weight residual 111.40 123.55 -12.15 1.22e+00 6.72e-01 9.92e+01 angle pdb=" C20 BYI R 601 " pdb=" C19 BYI R 601 " pdb=" C58 BYI R 601 " ideal model delta sigma weight residual 119.62 92.17 27.45 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C18 BYI R 601 " pdb=" C19 BYI R 601 " pdb=" C58 BYI R 601 " ideal model delta sigma weight residual 121.57 141.60 -20.03 3.00e+00 1.11e-01 4.46e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 115.07 6.07 1.75e+00 3.27e-01 1.20e+01 angle pdb=" N08 BYI R 601 " pdb=" C06 BYI R 601 " pdb=" O05 BYI R 601 " ideal model delta sigma weight residual 108.72 118.47 -9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 11751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4638 17.91 - 35.82: 425 35.82 - 53.73: 88 53.73 - 71.64: 20 71.64 - 89.56: 13 Dihedral angle restraints: 5184 sinusoidal: 2120 harmonic: 3064 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -116.40 30.40 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 5181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1211 0.087 - 0.174: 79 0.174 - 0.262: 2 0.262 - 0.349: 2 0.349 - 0.436: 2 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA ASN A 292 " pdb=" N ASN A 292 " pdb=" C ASN A 292 " pdb=" CB ASN A 292 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C18 BYI R 601 " pdb=" C19 BYI R 601 " pdb=" C21 BYI R 601 " pdb=" C74 BYI R 601 " both_signs ideal model delta sigma weight residual False -3.11 -2.77 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1293 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 BYI R 601 " -0.016 2.00e-02 2.50e+03 1.34e-02 4.07e+00 pdb=" C58 BYI R 601 " 0.035 2.00e-02 2.50e+03 pdb=" C59 BYI R 601 " -0.003 2.00e-02 2.50e+03 pdb=" C60 BYI R 601 " 0.001 2.00e-02 2.50e+03 pdb=" C61 BYI R 601 " 0.002 2.00e-02 2.50e+03 pdb=" C62 BYI R 601 " -0.001 2.00e-02 2.50e+03 pdb=" C63 BYI R 601 " -0.011 2.00e-02 2.50e+03 pdb=" O64 BYI R 601 " -0.003 2.00e-02 2.50e+03 pdb=" O72 BYI R 601 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 74 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C SER B 74 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B 74 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN B 75 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 682 2.74 - 3.28: 8482 3.28 - 3.82: 14579 3.82 - 4.36: 17817 4.36 - 4.90: 30248 Nonbonded interactions: 71808 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.201 3.040 nonbonded pdb=" ND1 HIS R 171 " pdb=" OE2 GLU R 412 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN A 23 " pdb=" N LYS B 89 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.267 3.040 ... (remaining 71803 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.006 0.158 8681 Z= 0.287 Angle : 0.789 27.449 11762 Z= 0.372 Chirality : 0.049 0.436 1296 Planarity : 0.004 0.044 1490 Dihedral : 15.070 89.556 3193 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1031 helix: 1.61 (0.25), residues: 423 sheet: 0.47 (0.33), residues: 231 loop : -0.57 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.024 0.002 TYR B 59 PHE 0.017 0.002 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.012 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 8678) covalent geometry : angle 0.78891 (11756) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.30134 ( 6) hydrogen bonds : bond 0.15271 ( 456) hydrogen bonds : angle 5.85926 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.372 Fit side-chains REVERT: A 370 GLU cc_start: 0.7557 (pm20) cc_final: 0.7334 (pm20) REVERT: R 418 GLU cc_start: 0.6225 (mm-30) cc_final: 0.5942 (mm-30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.7345 time to fit residues: 92.5270 Evaluate side-chains 92 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN N 31 ASN R 394 GLN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.199087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151386 restraints weight = 8854.824| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.73 r_work: 0.3486 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8681 Z= 0.116 Angle : 0.521 6.705 11762 Z= 0.285 Chirality : 0.041 0.157 1296 Planarity : 0.003 0.042 1490 Dihedral : 7.433 56.879 1237 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 9.58 % Favored : 88.44 % 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: 1.25 (0.26), residues: 1031 helix: 2.17 (0.25), residues: 428 sheet: 0.54 (0.32), residues: 228 loop : -0.54 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.030 0.001 TYR R 148 PHE 0.013 0.001 PHE R 390 TRP 0.013 0.001 TRP B 211 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8678) covalent geometry : angle 0.51926 (11756) SS BOND : bond 0.00239 ( 3) SS BOND : angle 2.01406 ( 6) hydrogen bonds : bond 0.04077 ( 456) hydrogen bonds : angle 4.63753 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8363 (t0) cc_final: 0.8107 (t0) REVERT: A 299 GLU cc_start: 0.7759 (pt0) cc_final: 0.7415 (pt0) REVERT: A 370 GLU cc_start: 0.8130 (pm20) cc_final: 0.7902 (pm20) REVERT: B 217 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8015 (pp-130) REVERT: B 270 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7543 (pp) REVERT: R 170 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6450 (tpt170) REVERT: R 410 GLN cc_start: 0.8032 (mt0) cc_final: 0.7800 (mt0) REVERT: R 418 GLU cc_start: 0.6448 (mm-30) cc_final: 0.6085 (mm-30) outliers start: 18 outliers final: 2 residues processed: 115 average time/residue: 0.7773 time to fit residues: 93.7381 Evaluate side-chains 106 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.197387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148769 restraints weight = 8768.319| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.76 r_work: 0.3454 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8681 Z= 0.134 Angle : 0.521 6.940 11762 Z= 0.283 Chirality : 0.042 0.176 1296 Planarity : 0.003 0.044 1490 Dihedral : 6.975 54.019 1237 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.76 % Allowed : 12.33 % Favored : 85.90 % 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: 1.38 (0.26), residues: 1031 helix: 2.34 (0.25), residues: 429 sheet: 0.57 (0.32), residues: 228 loop : -0.53 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.014 0.001 TYR R 402 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8678) covalent geometry : angle 0.51968 (11756) SS BOND : bond 0.00147 ( 3) SS BOND : angle 1.65565 ( 6) hydrogen bonds : bond 0.04140 ( 456) hydrogen bonds : angle 4.48816 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8473 (t0) cc_final: 0.8252 (t0) REVERT: A 299 GLU cc_start: 0.7822 (pt0) cc_final: 0.7482 (pt0) REVERT: A 314 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: A 370 GLU cc_start: 0.8164 (pm20) cc_final: 0.7930 (pm20) REVERT: A 392 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: B 134 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7202 (mtm110) REVERT: B 217 MET cc_start: 0.8329 (pmm) cc_final: 0.8054 (pp-130) REVERT: B 270 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7619 (pp) REVERT: R 391 THR cc_start: 0.8849 (m) cc_final: 0.8571 (p) REVERT: R 418 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6061 (mm-30) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 0.7777 time to fit residues: 94.6155 Evaluate side-chains 114 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 97 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.196945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149091 restraints weight = 8968.726| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.75 r_work: 0.3452 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8681 Z= 0.130 Angle : 0.505 6.790 11762 Z= 0.275 Chirality : 0.041 0.174 1296 Planarity : 0.003 0.044 1490 Dihedral : 6.776 52.711 1237 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.75 % Allowed : 12.67 % Favored : 84.58 % 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: 1.45 (0.26), residues: 1031 helix: 2.46 (0.25), residues: 428 sheet: 0.55 (0.33), residues: 228 loop : -0.54 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.015 0.001 TYR R 148 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8678) covalent geometry : angle 0.50452 (11756) SS BOND : bond 0.00143 ( 3) SS BOND : angle 1.38171 ( 6) hydrogen bonds : bond 0.04021 ( 456) hydrogen bonds : angle 4.39862 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8450 (t0) cc_final: 0.8237 (t0) REVERT: A 299 GLU cc_start: 0.7820 (pt0) cc_final: 0.7469 (pt0) REVERT: A 314 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 370 GLU cc_start: 0.8174 (pm20) cc_final: 0.7862 (pm20) REVERT: A 392 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 134 ARG cc_start: 0.7651 (ptp-110) cc_final: 0.7310 (mtm110) REVERT: B 217 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8056 (pp-130) REVERT: B 270 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7153 (pp) REVERT: N 103 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.6401 (p90) REVERT: R 170 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6639 (tpt170) REVERT: R 391 THR cc_start: 0.8957 (m) cc_final: 0.8650 (p) REVERT: R 418 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6079 (mm-30) outliers start: 25 outliers final: 9 residues processed: 117 average time/residue: 0.7529 time to fit residues: 92.2963 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.197019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149798 restraints weight = 8857.556| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.72 r_work: 0.3424 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8681 Z= 0.125 Angle : 0.498 6.777 11762 Z= 0.271 Chirality : 0.041 0.192 1296 Planarity : 0.003 0.045 1490 Dihedral : 6.617 51.631 1237 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.64 % Allowed : 13.66 % Favored : 83.70 % 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: 1.52 (0.26), residues: 1031 helix: 2.54 (0.25), residues: 428 sheet: 0.58 (0.32), residues: 228 loop : -0.53 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.014 0.001 TYR R 148 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8678) covalent geometry : angle 0.49738 (11756) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.27925 ( 6) hydrogen bonds : bond 0.03906 ( 456) hydrogen bonds : angle 4.31926 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8454 (t0) cc_final: 0.8253 (t0) REVERT: A 299 GLU cc_start: 0.7856 (pt0) cc_final: 0.7495 (pt0) REVERT: A 314 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: A 370 GLU cc_start: 0.8262 (pm20) cc_final: 0.7962 (pm20) REVERT: A 392 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: B 134 ARG cc_start: 0.7608 (ptp-110) cc_final: 0.7278 (mtm110) REVERT: B 217 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8054 (pp-130) REVERT: B 270 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7144 (pp) REVERT: N 103 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6296 (p90) REVERT: R 170 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6566 (tpt170) REVERT: R 418 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6138 (mm-30) outliers start: 24 outliers final: 9 residues processed: 117 average time/residue: 0.7461 time to fit residues: 91.4799 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.196512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149172 restraints weight = 8776.767| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.69 r_work: 0.3428 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8681 Z= 0.133 Angle : 0.503 6.768 11762 Z= 0.274 Chirality : 0.042 0.192 1296 Planarity : 0.003 0.044 1490 Dihedral : 6.579 51.399 1237 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.31 % Allowed : 14.54 % Favored : 83.15 % 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: 1.52 (0.26), residues: 1031 helix: 2.56 (0.25), residues: 428 sheet: 0.55 (0.33), residues: 229 loop : -0.53 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.015 0.001 TYR R 402 PHE 0.016 0.001 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8678) covalent geometry : angle 0.50272 (11756) SS BOND : bond 0.00172 ( 3) SS BOND : angle 1.25045 ( 6) hydrogen bonds : bond 0.03971 ( 456) hydrogen bonds : angle 4.32934 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8237 (pm20) cc_final: 0.7990 (pm20) REVERT: A 392 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: B 134 ARG cc_start: 0.7740 (ptp-110) cc_final: 0.7425 (mtm110) REVERT: B 217 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8045 (pp-130) REVERT: B 270 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7739 (pp) REVERT: R 170 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6710 (tpt170) REVERT: R 391 THR cc_start: 0.8836 (m) cc_final: 0.8561 (p) REVERT: R 412 GLU cc_start: 0.7111 (tp30) cc_final: 0.6544 (tp30) REVERT: R 418 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6185 (mm-30) outliers start: 21 outliers final: 10 residues processed: 117 average time/residue: 0.7558 time to fit residues: 92.7943 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.197036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149598 restraints weight = 8941.262| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.72 r_work: 0.3438 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8681 Z= 0.121 Angle : 0.489 6.757 11762 Z= 0.267 Chirality : 0.041 0.197 1296 Planarity : 0.003 0.044 1490 Dihedral : 6.494 51.132 1237 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.53 % Allowed : 15.09 % Favored : 82.38 % 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: 1.53 (0.26), residues: 1031 helix: 2.57 (0.25), residues: 428 sheet: 0.50 (0.33), residues: 231 loop : -0.49 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.016 0.001 TYR A 311 PHE 0.016 0.001 PHE B 151 TRP 0.014 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8678) covalent geometry : angle 0.48827 (11756) SS BOND : bond 0.00172 ( 3) SS BOND : angle 1.14077 ( 6) hydrogen bonds : bond 0.03817 ( 456) hydrogen bonds : angle 4.27736 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (m) REVERT: A 370 GLU cc_start: 0.8245 (pm20) cc_final: 0.7983 (pm20) REVERT: B 134 ARG cc_start: 0.7647 (ptp-110) cc_final: 0.7355 (mtm110) REVERT: B 217 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8041 (pp-130) REVERT: B 270 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7164 (pp) REVERT: N 103 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.6349 (p90) REVERT: R 170 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6631 (tpt170) REVERT: R 364 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7438 (mm-30) REVERT: R 391 THR cc_start: 0.8874 (m) cc_final: 0.8579 (p) REVERT: R 412 GLU cc_start: 0.7115 (tp30) cc_final: 0.6547 (tp30) REVERT: R 418 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6155 (mm-30) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 0.7196 time to fit residues: 88.4006 Evaluate side-chains 119 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 103 PHE Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.197948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149987 restraints weight = 8789.601| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.69 r_work: 0.3492 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8681 Z= 0.107 Angle : 0.473 6.744 11762 Z= 0.259 Chirality : 0.041 0.201 1296 Planarity : 0.003 0.045 1490 Dihedral : 6.376 50.734 1237 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 15.97 % Favored : 82.05 % 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: 1.61 (0.26), residues: 1031 helix: 2.66 (0.25), residues: 428 sheet: 0.52 (0.33), residues: 230 loop : -0.48 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.016 0.001 TYR A 311 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8678) covalent geometry : angle 0.47293 (11756) SS BOND : bond 0.00136 ( 3) SS BOND : angle 1.06755 ( 6) hydrogen bonds : bond 0.03615 ( 456) hydrogen bonds : angle 4.19376 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.8254 (pm20) cc_final: 0.7998 (pm20) REVERT: A 392 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: B 134 ARG cc_start: 0.7665 (ptp-110) cc_final: 0.7348 (mtm110) REVERT: B 217 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8055 (pp-130) REVERT: B 270 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7666 (pp) REVERT: R 170 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6664 (tpt170) REVERT: R 364 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7394 (mm-30) REVERT: R 391 THR cc_start: 0.8929 (m) cc_final: 0.8621 (p) REVERT: R 412 GLU cc_start: 0.7076 (tp30) cc_final: 0.6502 (tp30) REVERT: R 418 GLU cc_start: 0.6480 (mm-30) cc_final: 0.6125 (mm-30) outliers start: 18 outliers final: 9 residues processed: 116 average time/residue: 0.7330 time to fit residues: 89.2507 Evaluate side-chains 118 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.194319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145786 restraints weight = 8794.913| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.69 r_work: 0.3417 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8681 Z= 0.203 Angle : 0.575 6.808 11762 Z= 0.312 Chirality : 0.045 0.194 1296 Planarity : 0.004 0.043 1490 Dihedral : 6.744 52.297 1237 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 15.75 % Favored : 82.16 % 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: 1.42 (0.26), residues: 1031 helix: 2.43 (0.25), residues: 427 sheet: 0.49 (0.33), residues: 228 loop : -0.51 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.021 0.002 TYR R 402 PHE 0.019 0.002 PHE B 151 TRP 0.019 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8678) covalent geometry : angle 0.57405 (11756) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.43409 ( 6) hydrogen bonds : bond 0.04569 ( 456) hydrogen bonds : angle 4.51147 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (m) REVERT: A 370 GLU cc_start: 0.8190 (pm20) cc_final: 0.7955 (pm20) REVERT: A 392 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: B 134 ARG cc_start: 0.7636 (ptp-110) cc_final: 0.7334 (mtm110) REVERT: B 217 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8098 (pmm) REVERT: B 270 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7838 (pp) REVERT: R 170 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6672 (tpt170) REVERT: R 364 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7422 (mm-30) REVERT: R 412 GLU cc_start: 0.7131 (tp30) cc_final: 0.6564 (tp30) REVERT: R 418 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6163 (mm-30) outliers start: 19 outliers final: 9 residues processed: 115 average time/residue: 0.7517 time to fit residues: 90.5087 Evaluate side-chains 117 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.195886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147449 restraints weight = 8797.428| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.71 r_work: 0.3420 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8681 Z= 0.141 Angle : 0.514 6.780 11762 Z= 0.281 Chirality : 0.042 0.200 1296 Planarity : 0.003 0.043 1490 Dihedral : 6.596 52.055 1237 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.65 % Allowed : 16.08 % Favored : 82.27 % 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: 1.44 (0.26), residues: 1031 helix: 2.49 (0.25), residues: 428 sheet: 0.44 (0.33), residues: 231 loop : -0.51 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.016 0.001 TYR R 402 PHE 0.017 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8678) covalent geometry : angle 0.51387 (11756) SS BOND : bond 0.00206 ( 3) SS BOND : angle 1.22603 ( 6) hydrogen bonds : bond 0.04053 ( 456) hydrogen bonds : angle 4.36903 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8350 (m) REVERT: A 370 GLU cc_start: 0.8159 (pm20) cc_final: 0.7942 (pm20) REVERT: A 392 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 134 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.7268 (mtm110) REVERT: B 217 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8100 (pmm) REVERT: B 270 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7754 (pp) REVERT: R 170 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6781 (tpt170) REVERT: R 364 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7364 (mm-30) REVERT: R 391 THR cc_start: 0.8737 (m) cc_final: 0.8444 (p) REVERT: R 412 GLU cc_start: 0.7021 (tp30) cc_final: 0.6603 (tp30) REVERT: R 418 GLU cc_start: 0.6478 (mm-30) cc_final: 0.6119 (mm-30) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.7556 time to fit residues: 90.4419 Evaluate side-chains 119 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 170 ARG Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN ** R 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150501 restraints weight = 8797.534| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.86 r_work: 0.3460 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8681 Z= 0.106 Angle : 0.479 6.729 11762 Z= 0.262 Chirality : 0.041 0.199 1296 Planarity : 0.003 0.044 1490 Dihedral : 6.403 51.421 1237 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 16.08 % Favored : 82.05 % 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: 1.58 (0.26), residues: 1031 helix: 2.66 (0.25), residues: 427 sheet: 0.51 (0.33), residues: 230 loop : -0.51 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.015 0.001 TYR A 311 PHE 0.014 0.001 PHE B 151 TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8678) covalent geometry : angle 0.47811 (11756) SS BOND : bond 0.00119 ( 3) SS BOND : angle 1.06172 ( 6) hydrogen bonds : bond 0.03608 ( 456) hydrogen bonds : angle 4.20407 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.82 seconds wall clock time: 66 minutes 27.09 seconds (3987.09 seconds total)