Starting phenix.real_space_refine on Sat Aug 23 01:36:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3x_27872/08_2025/8e3x_27872.cif" } resolution = 2.3 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= 0.002 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 61 5.16 5 C 5692 2.51 5 N 1558 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1921 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} 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: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2841 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'HIS:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 8979 At special positions: 0 Unit cell: (92.96, 94.62, 159.36, 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 61 16.00 O 1668 8.00 N 1558 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 34 " - pdb=" SG CYS R 63 " distance=2.04 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 77 " - pdb=" SG CYS R 134 " 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: 0.64 Conformation dependent library (CDL) restraints added in 317.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 41.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 61 removed outlier: 4.009A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.514A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.708A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (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 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.542A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix 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 25 through 45 removed outlier: 3.620A pdb=" N GLN R 31 " --> pdb=" O PHE R 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS R 34 " --> pdb=" O GLU R 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 35 " --> pdb=" O GLN R 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 177 Processing helix chain 'R' and resid 183 through 211 Processing helix chain 'R' and resid 211 through 218 removed outlier: 3.614A pdb=" N SER R 216 " --> pdb=" O ALA R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.658A pdb=" N LYS R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 291 Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.779A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 346 through 363 removed outlier: 3.556A pdb=" N ARG R 350 " --> pdb=" O SER R 346 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 357 " --> pdb=" O ARG R 353 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 366 through 371 removed outlier: 4.506A pdb=" N PHE R 371 " --> pdb=" O THR R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 386 Processing helix chain 'R' and resid 388 through 390 No H-bonds generated for 'chain 'R' and resid 388 through 390' Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 7.259A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.172A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.582A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.841A 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: 3.509A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.279A 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: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.694A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.708A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.375A 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: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1317 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: 1.01 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1541 1.32 - 1.45: 2519 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9159 Sorted by residual: bond pdb=" CA SER R 316 " pdb=" CB SER R 316 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.59e-02 3.96e+03 9.20e+00 bond pdb=" C LEU R 251 " pdb=" O LEU R 251 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.04e+00 bond pdb=" N LEU R 361 " pdb=" CA LEU R 361 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.31e-02 5.83e+03 7.72e+00 bond pdb=" C LEU R 249 " pdb=" O LEU R 249 " ideal model delta sigma weight residual 1.237 1.207 0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N TYR R 400 " pdb=" CA TYR R 400 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.53e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12168 1.85 - 3.70: 195 3.70 - 5.55: 26 5.55 - 7.40: 9 7.40 - 9.25: 2 Bond angle restraints: 12400 Sorted by residual: angle pdb=" N ASN R 320 " pdb=" CA ASN R 320 " pdb=" C ASN R 320 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 angle pdb=" N SER R 316 " pdb=" CA SER R 316 " pdb=" C SER R 316 " ideal model delta sigma weight residual 111.36 105.78 5.58 1.09e+00 8.42e-01 2.62e+01 angle pdb=" N ILE R 188 " pdb=" CA ILE R 188 " pdb=" C ILE R 188 " ideal model delta sigma weight residual 110.62 105.82 4.80 1.02e+00 9.61e-01 2.21e+01 angle pdb=" N PHE R 362 " pdb=" CA PHE R 362 " pdb=" C PHE R 362 " ideal model delta sigma weight residual 114.12 107.73 6.39 1.39e+00 5.18e-01 2.11e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 111.36 106.63 4.73 1.09e+00 8.42e-01 1.89e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4879 16.07 - 32.13: 428 32.13 - 48.20: 92 48.20 - 64.26: 16 64.26 - 80.33: 8 Dihedral angle restraints: 5423 sinusoidal: 2113 harmonic: 3310 Sorted by residual: dihedral pdb=" CB CYS R 77 " pdb=" SG CYS R 77 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 150.58 -57.58 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS R 34 " pdb=" SG CYS R 34 " pdb=" SG CYS R 63 " pdb=" CB CYS R 63 " ideal model delta sinusoidal sigma weight residual -86.00 -127.56 41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -122.59 36.59 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 5420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1116 0.050 - 0.101: 204 0.101 - 0.151: 46 0.151 - 0.202: 4 0.202 - 0.252: 3 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ASN R 186 " pdb=" N ASN R 186 " pdb=" C ASN R 186 " pdb=" CB ASN R 186 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA PHE R 242 " pdb=" N PHE R 242 " pdb=" C PHE R 242 " pdb=" CB PHE R 242 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN R 191 " pdb=" N ASN R 191 " pdb=" C ASN R 191 " pdb=" CB ASN R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1370 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 315 " 0.013 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C GLY R 315 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY R 315 " 0.018 2.00e-02 2.50e+03 pdb=" N SER R 316 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 319 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C VAL R 319 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL R 319 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN R 320 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1681 2.77 - 3.30: 8600 3.30 - 3.84: 15318 3.84 - 4.37: 17983 4.37 - 4.90: 31029 Nonbonded interactions: 74611 Sorted by model distance: nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU B 12 " pdb=" ND2 ASN B 16 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.334 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.344 3.040 ... (remaining 74606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.400 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.003 0.048 9165 Z= 0.197 Angle : 0.583 9.249 12412 Z= 0.389 Chirality : 0.042 0.252 1373 Planarity : 0.003 0.045 1585 Dihedral : 13.023 80.331 3267 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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 aren not related in a simple way. whole: 1.49 (0.25), residues: 1120 helix: 2.27 (0.25), residues: 434 sheet: 0.92 (0.32), residues: 222 loop : -0.19 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.025 0.001 TYR B 59 PHE 0.016 0.001 PHE R 252 TRP 0.016 0.001 TRP B 339 HIS 0.005 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9159) covalent geometry : angle 0.58223 (12400) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.10862 ( 12) hydrogen bonds : bond 0.14015 ( 458) hydrogen bonds : angle 5.56695 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 134 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7556 (ptp-170) REVERT: B 340 ASN cc_start: 0.7767 (t0) cc_final: 0.7566 (t0) REVERT: R 33 MET cc_start: 0.7147 (pmm) cc_final: 0.6896 (pmm) REVERT: R 82 ARG cc_start: 0.7318 (tpt-90) cc_final: 0.6845 (mtp85) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.6679 time to fit residues: 103.2694 Evaluate side-chains 109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 54 ASN A 292 ASN B 268 ASN N 13 GLN N 77 ASN R 189 HIS R 336 GLN R 365 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072136 restraints weight = 14685.487| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.57 r_work: 0.2825 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9165 Z= 0.182 Angle : 0.551 7.991 12412 Z= 0.298 Chirality : 0.042 0.149 1373 Planarity : 0.004 0.051 1585 Dihedral : 4.012 18.407 1241 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.16 % Allowed : 7.91 % Favored : 90.93 % 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 aren not related in a simple way. whole: 1.65 (0.25), residues: 1120 helix: 2.50 (0.25), residues: 434 sheet: 0.99 (0.32), residues: 225 loop : -0.21 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.036 0.002 TYR R 157 PHE 0.018 0.002 PHE G 61 TRP 0.019 0.002 TRP R 243 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9159) covalent geometry : angle 0.55085 (12400) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.00860 ( 12) hydrogen bonds : bond 0.04702 ( 458) hydrogen bonds : angle 4.38383 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8468 (pm20) cc_final: 0.8125 (pm20) REVERT: G 42 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: R 82 ARG cc_start: 0.7472 (tpt-90) cc_final: 0.7000 (mtp85) REVERT: R 174 ILE cc_start: 0.7965 (tt) cc_final: 0.7667 (tp) REVERT: R 197 MET cc_start: 0.7782 (mpt) cc_final: 0.7553 (mmm) REVERT: R 412 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7620 (mmtt) outliers start: 11 outliers final: 2 residues processed: 117 average time/residue: 0.6005 time to fit residues: 73.9447 Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073631 restraints weight = 14673.041| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.57 r_work: 0.2864 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9165 Z= 0.111 Angle : 0.479 8.176 12412 Z= 0.259 Chirality : 0.039 0.140 1373 Planarity : 0.003 0.048 1585 Dihedral : 3.757 16.726 1241 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.27 % Allowed : 9.39 % Favored : 89.35 % 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 aren not related in a simple way. whole: 1.74 (0.25), residues: 1120 helix: 2.64 (0.25), residues: 435 sheet: 1.11 (0.32), residues: 222 loop : -0.27 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.027 0.001 TYR R 157 PHE 0.011 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9159) covalent geometry : angle 0.47850 (12400) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.62536 ( 12) hydrogen bonds : bond 0.04010 ( 458) hydrogen bonds : angle 4.16470 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8419 (pm20) cc_final: 0.8063 (pm20) REVERT: B 134 ARG cc_start: 0.8583 (ptp-110) cc_final: 0.8275 (ptp-110) REVERT: R 174 ILE cc_start: 0.8082 (tt) cc_final: 0.7780 (tp) REVERT: R 197 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7631 (mmm) REVERT: R 412 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7634 (mmtt) outliers start: 12 outliers final: 1 residues processed: 110 average time/residue: 0.6613 time to fit residues: 76.5704 Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain R residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.072167 restraints weight = 14790.996| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.57 r_work: 0.2831 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9165 Z= 0.129 Angle : 0.487 7.561 12412 Z= 0.265 Chirality : 0.040 0.142 1373 Planarity : 0.004 0.049 1585 Dihedral : 3.854 17.729 1241 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.05 % Allowed : 10.76 % Favored : 88.19 % 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 aren not related in a simple way. whole: 1.69 (0.25), residues: 1120 helix: 2.61 (0.25), residues: 435 sheet: 1.00 (0.32), residues: 225 loop : -0.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.027 0.001 TYR R 157 PHE 0.012 0.001 PHE G 61 TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9159) covalent geometry : angle 0.48671 (12400) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.58972 ( 12) hydrogen bonds : bond 0.04165 ( 458) hydrogen bonds : angle 4.14077 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8415 (pm20) cc_final: 0.8057 (pm20) REVERT: B 134 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.8172 (ptp-110) REVERT: B 334 SER cc_start: 0.7968 (m) cc_final: 0.7280 (t) REVERT: R 82 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7436 (mtp85) REVERT: R 174 ILE cc_start: 0.8168 (tt) cc_final: 0.7869 (tp) REVERT: R 412 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7610 (mmtt) outliers start: 10 outliers final: 2 residues processed: 111 average time/residue: 0.6602 time to fit residues: 77.1323 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072439 restraints weight = 14641.655| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.56 r_work: 0.2838 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9165 Z= 0.119 Angle : 0.486 9.316 12412 Z= 0.262 Chirality : 0.039 0.139 1373 Planarity : 0.003 0.049 1585 Dihedral : 3.807 17.308 1241 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.74 % Allowed : 12.03 % Favored : 87.24 % 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 aren not related in a simple way. whole: 1.71 (0.25), residues: 1120 helix: 2.67 (0.25), residues: 435 sheet: 1.01 (0.32), residues: 223 loop : -0.30 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 105 TYR 0.025 0.001 TYR R 157 PHE 0.011 0.001 PHE G 61 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9159) covalent geometry : angle 0.48624 (12400) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.49675 ( 12) hydrogen bonds : bond 0.04003 ( 458) hydrogen bonds : angle 4.12946 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8433 (pm20) cc_final: 0.8062 (pm20) REVERT: B 134 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.8173 (ptp-110) REVERT: B 217 MET cc_start: 0.9132 (pmm) cc_final: 0.8897 (pmm) REVERT: B 334 SER cc_start: 0.7920 (m) cc_final: 0.7238 (t) REVERT: P 21 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8522 (tmtt) REVERT: R 82 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7402 (mtp85) REVERT: R 174 ILE cc_start: 0.8128 (tt) cc_final: 0.7828 (tp) REVERT: R 412 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7665 (mmtt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.6678 time to fit residues: 74.6906 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069313 restraints weight = 14562.236| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.57 r_work: 0.2747 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9165 Z= 0.198 Angle : 0.539 9.045 12412 Z= 0.293 Chirality : 0.042 0.153 1373 Planarity : 0.004 0.053 1585 Dihedral : 4.201 20.956 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.95 % Allowed : 12.87 % Favored : 86.18 % 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 aren not related in a simple way. whole: 1.50 (0.25), residues: 1120 helix: 2.40 (0.24), residues: 442 sheet: 0.79 (0.32), residues: 233 loop : -0.32 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.028 0.001 TYR R 157 PHE 0.018 0.001 PHE G 61 TRP 0.019 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9159) covalent geometry : angle 0.53870 (12400) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.75071 ( 12) hydrogen bonds : bond 0.04865 ( 458) hydrogen bonds : angle 4.35736 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8447 (pm20) cc_final: 0.8081 (pm20) REVERT: B 134 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8121 (ptp-110) REVERT: N 89 GLU cc_start: 0.8700 (pm20) cc_final: 0.8431 (pm20) REVERT: R 174 ILE cc_start: 0.8265 (tt) cc_final: 0.7968 (tp) REVERT: R 412 LYS cc_start: 0.8123 (ptpt) cc_final: 0.7676 (mmtt) outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.6947 time to fit residues: 81.0982 Evaluate side-chains 108 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN N 13 GLN ** R 234 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.113806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071800 restraints weight = 14641.936| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.56 r_work: 0.2796 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9165 Z= 0.117 Angle : 0.507 11.356 12412 Z= 0.272 Chirality : 0.039 0.140 1373 Planarity : 0.004 0.053 1585 Dihedral : 3.918 18.340 1241 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.53 % Allowed : 13.71 % Favored : 85.76 % 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 aren not related in a simple way. whole: 1.58 (0.25), residues: 1120 helix: 2.55 (0.24), residues: 442 sheet: 0.92 (0.33), residues: 223 loop : -0.40 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.024 0.001 TYR R 157 PHE 0.010 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9159) covalent geometry : angle 0.50687 (12400) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.44988 ( 12) hydrogen bonds : bond 0.04114 ( 458) hydrogen bonds : angle 4.19741 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8440 (pm20) cc_final: 0.8073 (pm20) REVERT: B 134 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8143 (ptp-110) REVERT: B 334 SER cc_start: 0.8038 (m) cc_final: 0.7498 (t) REVERT: N 89 GLU cc_start: 0.8656 (pm20) cc_final: 0.8395 (pm20) REVERT: R 174 ILE cc_start: 0.8252 (tt) cc_final: 0.7956 (tp) REVERT: R 412 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7676 (mmtt) outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 0.6307 time to fit residues: 74.6561 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073263 restraints weight = 14645.475| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.56 r_work: 0.2830 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9165 Z= 0.107 Angle : 0.497 10.807 12412 Z= 0.266 Chirality : 0.039 0.136 1373 Planarity : 0.004 0.055 1585 Dihedral : 3.741 16.990 1241 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.53 % Allowed : 13.82 % Favored : 85.65 % 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 aren not related in a simple way. whole: 1.72 (0.25), residues: 1120 helix: 2.75 (0.25), residues: 435 sheet: 0.88 (0.33), residues: 223 loop : -0.31 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.023 0.001 TYR R 157 PHE 0.010 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9159) covalent geometry : angle 0.49694 (12400) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.44627 ( 12) hydrogen bonds : bond 0.03822 ( 458) hydrogen bonds : angle 4.05111 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8420 (pm20) cc_final: 0.8045 (pm20) REVERT: B 134 ARG cc_start: 0.8504 (ptp-110) cc_final: 0.8155 (ptp-110) REVERT: B 334 SER cc_start: 0.7856 (m) cc_final: 0.7259 (t) REVERT: R 28 LYS cc_start: 0.5710 (mppt) cc_final: 0.5430 (mtmm) REVERT: R 174 ILE cc_start: 0.8211 (tt) cc_final: 0.7915 (tp) REVERT: R 412 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7683 (mmtt) outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 0.5906 time to fit residues: 67.4836 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 13 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069571 restraints weight = 14569.670| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.54 r_work: 0.2752 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9165 Z= 0.200 Angle : 0.568 12.196 12412 Z= 0.305 Chirality : 0.041 0.152 1373 Planarity : 0.004 0.058 1585 Dihedral : 4.163 20.716 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.42 % Allowed : 14.24 % Favored : 85.34 % 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 aren not related in a simple way. whole: 1.51 (0.25), residues: 1120 helix: 2.43 (0.24), residues: 442 sheet: 0.70 (0.33), residues: 233 loop : -0.28 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.028 0.001 TYR R 157 PHE 0.017 0.001 PHE G 61 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9159) covalent geometry : angle 0.56783 (12400) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.65876 ( 12) hydrogen bonds : bond 0.04796 ( 458) hydrogen bonds : angle 4.36289 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8470 (pm20) cc_final: 0.8103 (pm20) REVERT: B 134 ARG cc_start: 0.8486 (ptp-110) cc_final: 0.8129 (ptp-110) REVERT: R 174 ILE cc_start: 0.8278 (tt) cc_final: 0.7973 (tp) outliers start: 4 outliers final: 4 residues processed: 102 average time/residue: 0.6525 time to fit residues: 69.9628 Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 13 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.071832 restraints weight = 14559.525| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.54 r_work: 0.2795 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9165 Z= 0.124 Angle : 0.527 12.189 12412 Z= 0.280 Chirality : 0.039 0.141 1373 Planarity : 0.004 0.062 1585 Dihedral : 3.922 18.276 1241 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.32 % Allowed : 14.14 % Favored : 85.55 % 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 aren not related in a simple way. whole: 1.61 (0.25), residues: 1120 helix: 2.56 (0.24), residues: 441 sheet: 0.82 (0.33), residues: 229 loop : -0.31 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.024 0.001 TYR R 157 PHE 0.010 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9159) covalent geometry : angle 0.52734 (12400) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.45142 ( 12) hydrogen bonds : bond 0.04099 ( 458) hydrogen bonds : angle 4.18668 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8444 (pm20) cc_final: 0.8079 (pm20) REVERT: B 134 ARG cc_start: 0.8493 (ptp-110) cc_final: 0.8147 (ptp-110) REVERT: B 334 SER cc_start: 0.8043 (m) cc_final: 0.7473 (t) outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 0.6589 time to fit residues: 70.8809 Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069824 restraints weight = 14474.612| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.56 r_work: 0.2780 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9165 Z= 0.151 Angle : 0.537 12.409 12412 Z= 0.287 Chirality : 0.040 0.146 1373 Planarity : 0.004 0.062 1585 Dihedral : 4.023 19.524 1241 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.53 % Allowed : 14.56 % Favored : 84.92 % 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 aren not related in a simple way. whole: 1.55 (0.25), residues: 1120 helix: 2.51 (0.24), residues: 442 sheet: 0.74 (0.33), residues: 231 loop : -0.32 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.026 0.001 TYR R 157 PHE 0.012 0.001 PHE G 61 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9159) covalent geometry : angle 0.53747 (12400) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.54643 ( 12) hydrogen bonds : bond 0.04369 ( 458) hydrogen bonds : angle 4.24252 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4377.03 seconds wall clock time: 74 minutes 52.72 seconds (4492.72 seconds total)