Starting phenix.real_space_refine on Thu Mar 13 15:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3x_27872/03_2025/8e3x_27872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3x_27872/03_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_27872/03_2025/8e3x_27872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3x_27872/03_2025/8e3x_27872.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3x_27872/03_2025/8e3x_27872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3x_27872/03_2025/8e3x_27872.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} 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: 5.26, per 1000 atoms: 0.59 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: 2.13 Conformation dependent library (CDL) restraints added in 987.4 milliseconds 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: 0.87 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: 2.47 Time building geometry restraints manager: 2.56 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: 1.120 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.930 ------------------------------------------------------------------------------- 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 9159 Z= 0.197 Angle : 0.582 9.249 12400 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (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 TRP 0.016 0.001 TRP B 339 HIS 0.005 0.001 HIS A 387 PHE 0.016 0.001 PHE R 252 TYR 0.025 0.001 TYR B 59 ARG 0.003 0.000 ARG A 389 *********************** 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 : 1.053 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: 0.6857 (mtp85) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.6906 time to fit residues: 261.4374 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 : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 100 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: A 31 GLN A 54 ASN A 292 ASN B 268 ASN N 13 GLN N 77 ASN R 189 HIS R 336 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.117314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076305 restraints weight = 14542.021| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.56 r_work: 0.2915 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9159 Z= 0.181 Angle : 0.498 7.414 12400 Z= 0.268 Chirality : 0.040 0.139 1373 Planarity : 0.004 0.053 1585 Dihedral : 3.607 15.418 1241 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.84 % Allowed : 8.12 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1120 helix: 2.62 (0.25), residues: 435 sheet: 1.13 (0.33), residues: 219 loop : -0.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.031 0.001 TYR R 157 ARG 0.007 0.000 ARG N 105 *********************** 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 121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8443 (pm20) cc_final: 0.8122 (pm20) REVERT: A 370 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: R 82 ARG cc_start: 0.7528 (tpt-90) cc_final: 0.7052 (mtp85) REVERT: R 174 ILE cc_start: 0.7962 (tt) cc_final: 0.7641 (tp) REVERT: R 412 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7616 (mmtt) outliers start: 8 outliers final: 0 residues processed: 116 average time/residue: 1.3983 time to fit residues: 172.0653 Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 0.0000 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 268 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 = 0.3727 r_free = 0.3727 target = 0.116692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075572 restraints weight = 14767.605| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.56 r_work: 0.2904 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9159 Z= 0.156 Angle : 0.474 7.939 12400 Z= 0.255 Chirality : 0.039 0.202 1373 Planarity : 0.003 0.046 1585 Dihedral : 3.591 15.619 1241 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.84 % Allowed : 9.28 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1120 helix: 2.71 (0.25), residues: 434 sheet: 1.26 (0.33), residues: 218 loop : -0.24 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 243 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.027 0.001 TYR R 157 ARG 0.006 0.000 ARG N 105 *********************** 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 117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8447 (pm20) cc_final: 0.8149 (pm20) REVERT: B 134 ARG cc_start: 0.8591 (ptp-110) cc_final: 0.8305 (ptp-110) REVERT: R 82 ARG cc_start: 0.7555 (tpt-90) cc_final: 0.7074 (mtp85) REVERT: R 174 ILE cc_start: 0.8015 (tt) cc_final: 0.7699 (tp) REVERT: R 412 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7632 (mmtt) outliers start: 8 outliers final: 0 residues processed: 112 average time/residue: 1.6786 time to fit residues: 198.8276 Evaluate side-chains 100 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.071780 restraints weight = 14534.379| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.55 r_work: 0.2821 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9159 Z= 0.213 Angle : 0.499 6.894 12400 Z= 0.271 Chirality : 0.041 0.180 1373 Planarity : 0.004 0.049 1585 Dihedral : 3.924 18.290 1241 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.48 % Allowed : 10.13 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1120 helix: 2.64 (0.25), residues: 435 sheet: 1.08 (0.32), residues: 224 loop : -0.25 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE G 61 TYR 0.028 0.001 TYR R 157 ARG 0.009 0.000 ARG N 105 *********************** 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 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7936 (mtm-85) REVERT: A 314 GLU cc_start: 0.8453 (pm20) cc_final: 0.8091 (pm20) REVERT: B 134 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8170 (ptp-110) REVERT: B 334 SER cc_start: 0.8058 (m) cc_final: 0.7374 (t) REVERT: R 174 ILE cc_start: 0.8108 (tt) cc_final: 0.7797 (tp) REVERT: R 412 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7606 (mmtt) outliers start: 14 outliers final: 3 residues processed: 116 average time/residue: 1.6116 time to fit residues: 197.5396 Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 138 GLU 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 32 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.111214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068550 restraints weight = 14614.453| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.58 r_work: 0.2742 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9159 Z= 0.313 Angle : 0.545 7.875 12400 Z= 0.297 Chirality : 0.042 0.153 1373 Planarity : 0.004 0.053 1585 Dihedral : 4.215 20.756 1241 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.16 % Allowed : 11.08 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1120 helix: 2.35 (0.24), residues: 442 sheet: 0.88 (0.32), residues: 232 loop : -0.36 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.019 0.001 PHE G 61 TYR 0.030 0.001 TYR R 157 ARG 0.011 0.000 ARG N 105 *********************** 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 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8466 (pm20) cc_final: 0.8110 (pm20) REVERT: B 134 ARG cc_start: 0.8487 (ptp-110) cc_final: 0.8146 (ptp-110) REVERT: P 21 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8514 (tmmt) REVERT: R 412 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7666 (mmtt) outliers start: 11 outliers final: 4 residues processed: 115 average time/residue: 1.5184 time to fit residues: 184.4607 Evaluate side-chains 110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 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 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 = 0.3683 r_free = 0.3683 target = 0.113805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071982 restraints weight = 14429.540| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.55 r_work: 0.2804 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9159 Z= 0.179 Angle : 0.494 9.611 12400 Z= 0.266 Chirality : 0.039 0.140 1373 Planarity : 0.003 0.048 1585 Dihedral : 3.919 18.226 1241 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1120 helix: 2.54 (0.24), residues: 441 sheet: 0.91 (0.32), residues: 229 loop : -0.33 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE G 61 TYR 0.025 0.001 TYR R 157 ARG 0.011 0.000 ARG N 105 *********************** 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 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8452 (pm20) cc_final: 0.8026 (pm20) REVERT: B 134 ARG cc_start: 0.8519 (ptp-110) cc_final: 0.8164 (ptp-110) REVERT: B 334 SER cc_start: 0.8012 (m) cc_final: 0.7435 (t) REVERT: P 21 LYS cc_start: 0.8746 (mmmm) cc_final: 0.8535 (tmmt) REVERT: R 412 LYS cc_start: 0.8108 (ptpt) cc_final: 0.7686 (mmtt) outliers start: 9 outliers final: 2 residues processed: 114 average time/residue: 1.6660 time to fit residues: 201.1003 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 : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 87 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072362 restraints weight = 14638.513| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.56 r_work: 0.2808 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9159 Z= 0.173 Angle : 0.489 10.041 12400 Z= 0.264 Chirality : 0.039 0.139 1373 Planarity : 0.004 0.050 1585 Dihedral : 3.832 17.665 1241 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.63 % Allowed : 14.35 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1120 helix: 2.61 (0.24), residues: 441 sheet: 0.95 (0.33), residues: 224 loop : -0.32 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.024 0.001 TYR R 157 ARG 0.012 0.000 ARG N 105 *********************** 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 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8453 (pm20) cc_final: 0.8081 (pm20) REVERT: B 134 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8170 (ptp-110) REVERT: B 334 SER cc_start: 0.7964 (m) cc_final: 0.7388 (t) REVERT: P 20 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7642 (mmpt) REVERT: P 21 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8509 (tmmt) REVERT: R 412 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7696 (mmtt) outliers start: 6 outliers final: 2 residues processed: 103 average time/residue: 1.6881 time to fit residues: 184.0686 Evaluate side-chains 99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072700 restraints weight = 14769.461| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.57 r_work: 0.2816 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9159 Z= 0.171 Angle : 0.492 11.299 12400 Z= 0.265 Chirality : 0.039 0.138 1373 Planarity : 0.004 0.056 1585 Dihedral : 3.798 17.370 1241 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.42 % Allowed : 14.14 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.25), residues: 1120 helix: 2.73 (0.25), residues: 435 sheet: 0.95 (0.32), residues: 229 loop : -0.26 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.023 0.001 TYR R 157 ARG 0.013 0.000 ARG N 105 *********************** 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 107 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8448 (pm20) cc_final: 0.8073 (pm20) REVERT: B 134 ARG cc_start: 0.8516 (ptp-110) cc_final: 0.8163 (ptp-110) REVERT: B 334 SER cc_start: 0.7872 (m) cc_final: 0.7287 (t) REVERT: P 21 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8515 (tmmt) REVERT: R 412 LYS cc_start: 0.8088 (ptpt) cc_final: 0.7686 (mmtt) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 1.4910 time to fit residues: 167.1201 Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 51 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.115108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073597 restraints weight = 14609.447| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.57 r_work: 0.2836 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9159 Z= 0.157 Angle : 0.491 11.402 12400 Z= 0.262 Chirality : 0.039 0.135 1373 Planarity : 0.004 0.058 1585 Dihedral : 3.705 17.130 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.42 % Allowed : 14.45 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1120 helix: 2.79 (0.24), residues: 435 sheet: 1.02 (0.33), residues: 222 loop : -0.29 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.022 0.001 TYR R 157 ARG 0.015 0.000 ARG N 105 *********************** 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 107 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8434 (pm20) cc_final: 0.7998 (pm20) REVERT: B 134 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.8184 (ptp-110) REVERT: B 334 SER cc_start: 0.7744 (m) cc_final: 0.7185 (t) REVERT: P 20 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7684 (mmpt) REVERT: P 21 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8485 (tmmt) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 1.4128 time to fit residues: 159.0473 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 54 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.115549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074160 restraints weight = 14645.618| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.56 r_work: 0.2848 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9159 Z= 0.157 Angle : 0.503 12.158 12400 Z= 0.267 Chirality : 0.039 0.134 1373 Planarity : 0.004 0.063 1585 Dihedral : 3.666 17.071 1241 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.21 % Allowed : 14.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1120 helix: 2.82 (0.25), residues: 435 sheet: 1.08 (0.33), residues: 220 loop : -0.30 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.009 0.001 PHE A 212 TYR 0.022 0.001 TYR R 157 ARG 0.015 0.000 ARG N 105 ********************** 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 106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8433 (pm20) cc_final: 0.8053 (pm20) REVERT: B 134 ARG cc_start: 0.8526 (ptp-110) cc_final: 0.8188 (ptp-110) REVERT: B 334 SER cc_start: 0.7634 (m) cc_final: 0.7093 (t) REVERT: P 21 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8489 (tmmt) outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 1.4253 time to fit residues: 160.2459 Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 74 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 0.0060 chunk 23 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073133 restraints weight = 14592.071| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.55 r_work: 0.2824 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9159 Z= 0.176 Angle : 0.510 12.078 12400 Z= 0.271 Chirality : 0.039 0.138 1373 Planarity : 0.004 0.063 1585 Dihedral : 3.740 17.268 1241 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.42 % Allowed : 14.35 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1120 helix: 2.77 (0.24), residues: 435 sheet: 1.01 (0.32), residues: 228 loop : -0.24 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE A 212 TYR 0.023 0.001 TYR R 157 ARG 0.015 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10987.79 seconds wall clock time: 190 minutes 22.95 seconds (11422.95 seconds total)