Starting phenix.real_space_refine on Thu Feb 13 12:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3x_27872/02_2025/8e3x_27872.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3x_27872/02_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_27872/02_2025/8e3x_27872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3x_27872/02_2025/8e3x_27872.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3x_27872/02_2025/8e3x_27872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3x_27872/02_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-5592/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: 5.47, per 1000 atoms: 0.61 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.86 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: 2.51 Time building geometry restraints manager: 2.36 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: 1.700 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.260 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- 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 : 1.033 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: 1.6828 time to fit residues: 260.3378 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 : 1.078 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076309 restraints weight = 14542.019| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.56 r_work: 0.2916 rms_B_bonded: 3.05 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: 0.8584 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 : 0.985 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: 0.7225 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: R 82 ARG cc_start: 0.7530 (tpt-90) cc_final: 0.7055 (mtp85) REVERT: R 174 ILE cc_start: 0.7963 (tt) cc_final: 0.7642 (tp) REVERT: R 412 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7615 (mmtt) outliers start: 8 outliers final: 0 residues processed: 116 average time/residue: 1.4147 time to fit residues: 174.0249 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 : 0.982 ------------------------------------------------------------------------------- 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: 5.9990 chunk 84 optimal weight: 0.9980 chunk 95 optimal weight: 0.0050 chunk 79 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 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: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.116771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075668 restraints weight = 14770.145| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.57 r_work: 0.2906 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9159 Z= 0.153 Angle : 0.473 7.835 12400 Z= 0.254 Chirality : 0.039 0.188 1373 Planarity : 0.003 0.046 1585 Dihedral : 3.585 15.633 1241 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.95 % Allowed : 9.18 % 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: 1.85 (0.25), residues: 1120 helix: 2.72 (0.25), residues: 434 sheet: 1.27 (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 0.028 0.001 TYR R 157 ARG 0.009 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 119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8439 (pm20) cc_final: 0.8149 (pm20) REVERT: B 134 ARG cc_start: 0.8574 (ptp-110) cc_final: 0.8281 (ptp-110) REVERT: R 82 ARG cc_start: 0.7555 (tpt-90) cc_final: 0.7073 (mtp85) REVERT: R 174 ILE cc_start: 0.8002 (tt) cc_final: 0.7682 (tp) REVERT: R 412 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7603 (mmtt) outliers start: 9 outliers final: 0 residues processed: 114 average time/residue: 1.5999 time to fit residues: 192.6414 Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069540 restraints weight = 14513.340| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.56 r_work: 0.2753 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9159 Z= 0.324 Angle : 0.554 7.679 12400 Z= 0.302 Chirality : 0.043 0.197 1373 Planarity : 0.004 0.054 1585 Dihedral : 4.247 20.589 1241 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.36 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: 1.53 (0.25), residues: 1120 helix: 2.37 (0.25), residues: 440 sheet: 0.91 (0.32), residues: 233 loop : -0.30 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.002 PHE G 61 TYR 0.031 0.002 TYR R 157 ARG 0.010 0.001 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 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7991 (mtm-85) REVERT: A 314 GLU cc_start: 0.8464 (pm20) cc_final: 0.8117 (pm20) REVERT: B 134 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8150 (ptp-110) REVERT: R 412 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7677 (mmtt) outliers start: 14 outliers final: 3 residues processed: 117 average time/residue: 1.6938 time to fit residues: 208.5246 Evaluate side-chains 106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU 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: 0.0970 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.6356 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.114254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072509 restraints weight = 14549.611| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.56 r_work: 0.2840 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9159 Z= 0.160 Angle : 0.488 9.593 12400 Z= 0.263 Chirality : 0.039 0.137 1373 Planarity : 0.003 0.048 1585 Dihedral : 3.866 17.708 1241 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.16 % Allowed : 11.50 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.25), residues: 1120 helix: 2.62 (0.25), residues: 435 sheet: 1.00 (0.32), residues: 223 loop : -0.32 (0.28), residues: 462 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 0.011 0.001 PHE A 212 TYR 0.025 0.001 TYR R 157 ARG 0.010 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 119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8443 (pm20) cc_final: 0.8077 (pm20) REVERT: B 134 ARG cc_start: 0.8511 (ptp-110) cc_final: 0.8151 (ptp-110) REVERT: B 334 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7314 (t) REVERT: N 89 GLU cc_start: 0.8693 (pm20) cc_final: 0.8390 (pm20) REVERT: P 21 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8542 (tmmt) REVERT: R 412 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7651 (mmtt) outliers start: 11 outliers final: 2 residues processed: 112 average time/residue: 1.5274 time to fit residues: 180.9186 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 : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 334 SER 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: 3.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.114148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.072389 restraints weight = 14440.917| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.56 r_work: 0.2809 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2435 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= 0.175 Angle : 0.485 8.572 12400 Z= 0.262 Chirality : 0.039 0.138 1373 Planarity : 0.003 0.049 1585 Dihedral : 3.818 17.518 1241 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.74 % Allowed : 13.40 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.25), residues: 1120 helix: 2.68 (0.24), residues: 435 sheet: 0.96 (0.32), residues: 223 loop : -0.29 (0.29), residues: 462 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 G 61 TYR 0.024 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 110 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8447 (pm20) cc_final: 0.8064 (pm20) REVERT: B 134 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8166 (ptp-110) REVERT: B 334 SER cc_start: 0.8062 (m) cc_final: 0.7333 (t) REVERT: P 20 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7636 (mmpt) REVERT: P 21 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8530 (tmmt) REVERT: R 412 LYS cc_start: 0.8071 (ptpt) cc_final: 0.7616 (mmtt) outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 1.5545 time to fit residues: 176.0309 Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073896 restraints weight = 14652.582| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.57 r_work: 0.2841 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2457 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= 0.151 Angle : 0.484 11.750 12400 Z= 0.259 Chirality : 0.039 0.134 1373 Planarity : 0.003 0.051 1585 Dihedral : 3.683 17.133 1241 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.53 % Allowed : 14.03 % 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: 2.76 (0.24), residues: 435 sheet: 0.95 (0.32), residues: 224 loop : -0.28 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.023 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 108 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8447 (pm20) cc_final: 0.8059 (pm20) REVERT: B 134 ARG cc_start: 0.8532 (ptp-110) cc_final: 0.8178 (ptp-110) REVERT: B 217 MET cc_start: 0.9118 (pmm) cc_final: 0.8908 (pmm) REVERT: P 20 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7642 (mmpt) REVERT: R 412 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7647 (mmtt) outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 1.5184 time to fit residues: 170.1988 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 : 0.954 ------------------------------------------------------------------------------- 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: 0.5980 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.115440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073947 restraints weight = 14743.945| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.57 r_work: 0.2845 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9159 Z= 0.156 Angle : 0.485 10.700 12400 Z= 0.260 Chirality : 0.038 0.134 1373 Planarity : 0.004 0.057 1585 Dihedral : 3.669 16.983 1241 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 2.81 (0.25), residues: 435 sheet: 0.96 (0.33), residues: 219 loop : -0.28 (0.28), residues: 466 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 0.022 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 : 1.022 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8453 (pm20) cc_final: 0.8061 (pm20) REVERT: B 134 ARG cc_start: 0.8533 (ptp-110) cc_final: 0.8175 (ptp-110) REVERT: P 20 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7641 (mmpt) REVERT: R 412 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7658 (mmtt) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 1.5531 time to fit residues: 173.9478 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 : 0.957 ------------------------------------------------------------------------------- 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: 0.8980 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 103 optimal weight: 0.0270 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.115988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074644 restraints weight = 14643.704| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.56 r_work: 0.2859 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9159 Z= 0.153 Angle : 0.497 12.063 12400 Z= 0.263 Chirality : 0.038 0.133 1373 Planarity : 0.004 0.060 1585 Dihedral : 3.623 16.934 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.53 % Allowed : 14.35 % 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: 1.83 (0.25), residues: 1120 helix: 2.82 (0.24), residues: 435 sheet: 1.02 (0.33), residues: 222 loop : -0.26 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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: 5 poor density : 102 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8446 (pm20) cc_final: 0.8052 (pm20) REVERT: B 134 ARG cc_start: 0.8520 (ptp-110) cc_final: 0.8188 (ptp-110) REVERT: P 21 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8456 (tmmt) outliers start: 5 outliers final: 2 residues processed: 105 average time/residue: 1.5622 time to fit residues: 173.3645 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 : 0.984 ------------------------------------------------------------------------------- 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: 0.7980 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 91 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.114326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072562 restraints weight = 14630.170| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.56 r_work: 0.2818 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2613 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= 0.188 Angle : 0.512 11.847 12400 Z= 0.272 Chirality : 0.039 0.140 1373 Planarity : 0.004 0.063 1585 Dihedral : 3.796 17.685 1241 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.53 % Allowed : 14.24 % 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: 1.85 (0.25), residues: 1120 helix: 2.78 (0.24), residues: 435 sheet: 1.03 (0.32), residues: 226 loop : -0.20 (0.29), residues: 459 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 0.012 0.001 PHE G 61 TYR 0.024 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: 5 poor density : 101 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8451 (pm20) cc_final: 0.8059 (pm20) REVERT: B 134 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.8175 (ptp-110) REVERT: B 334 SER cc_start: 0.8069 (m) cc_final: 0.7318 (t) REVERT: P 20 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7607 (mmpt) REVERT: P 21 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8433 (tmmt) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 1.7701 time to fit residues: 193.5475 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 : 1.216 ------------------------------------------------------------------------------- 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 74 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.112760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070263 restraints weight = 14626.632| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.59 r_work: 0.2785 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9159 Z= 0.234 Angle : 0.540 12.330 12400 Z= 0.287 Chirality : 0.040 0.148 1373 Planarity : 0.004 0.062 1585 Dihedral : 3.993 19.159 1241 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 1.70 (0.25), residues: 1120 helix: 2.59 (0.24), residues: 442 sheet: 0.94 (0.32), residues: 233 loop : -0.26 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE G 61 TYR 0.026 0.001 TYR R 157 ARG 0.014 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10441.03 seconds wall clock time: 183 minutes 51.02 seconds (11031.02 seconds total)