Starting phenix.real_space_refine (version: dev) on Tue Apr 5 01:07:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/04_2022/6wun_21917.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.023 sd= 0.112 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "B" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Chain: "C" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "D" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Time building chain proxies: 6.07, per 1000 atoms: 0.60 Number of scatterers: 10082 At special positions: 0 Unit cell: (149.46, 121.9, 95.4, 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 16 16.00 O 1882 8.00 N 1814 7.00 C 6370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 28.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.605A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.888A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU A 182 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.820A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.565A pdb=" N ALA A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.670A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.766A pdb=" N SER B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.604A pdb=" N ARG C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 82 removed outlier: 4.889A pdb=" N TRP C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU C 182 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.819A pdb=" N ALA C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 removed outlier: 3.566A pdb=" N ALA C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.539A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.671A pdb=" N MET C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.765A pdb=" N SER D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 105 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.643A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 141 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 172 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 159 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 189 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 191 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AA4, first strand: chain 'B' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.715A pdb=" N ARG B 426 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 419 removed outlier: 3.575A pdb=" N GLN B 419 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU C 52 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 105 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.642A pdb=" N VAL D 158 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 141 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN D 172 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 159 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 189 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 191 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 197 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU D 339 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 396 through 397 removed outlier: 3.714A pdb=" N ARG D 426 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.576A pdb=" N GLN D 419 " --> pdb=" O GLY D 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 482 through 483 244 hydrogen bonds defined for protein. 672 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: 2.42 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3386 1.34 - 1.46: 1864 1.46 - 1.57: 5020 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 10298 Sorted by residual: bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.02e+00 bond pdb=" C PHE C 27 " pdb=" N PRO C 28 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C SER D 255 " pdb=" N PRO D 256 " ideal model delta sigma weight residual 1.331 1.318 0.014 7.90e-03 1.60e+04 2.94e+00 bond pdb=" C SER B 255 " pdb=" N PRO B 256 " ideal model delta sigma weight residual 1.331 1.318 0.013 7.90e-03 1.60e+04 2.90e+00 bond pdb=" CA ALA B 182 " pdb=" C ALA B 182 " ideal model delta sigma weight residual 1.518 1.462 0.056 4.01e-02 6.22e+02 1.92e+00 ... (remaining 10293 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 420 106.73 - 113.55: 5593 113.55 - 120.37: 3839 120.37 - 127.19: 3989 127.19 - 134.01: 143 Bond angle restraints: 13984 Sorted by residual: angle pdb=" N VAL D 258 " pdb=" CA VAL D 258 " pdb=" C VAL D 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N VAL B 258 " pdb=" CA VAL B 258 " pdb=" C VAL B 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N GLU C 36 " pdb=" CA GLU C 36 " pdb=" C GLU C 36 " ideal model delta sigma weight residual 111.02 115.67 -4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" N GLU A 36 " pdb=" CA GLU A 36 " pdb=" C GLU A 36 " ideal model delta sigma weight residual 111.02 115.64 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N VAL D 139 " pdb=" CA VAL D 139 " pdb=" C VAL D 139 " ideal model delta sigma weight residual 108.82 105.18 3.64 1.22e+00 6.72e-01 8.88e+00 ... (remaining 13979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5521 17.13 - 34.26: 524 34.26 - 51.39: 79 51.39 - 68.53: 14 68.53 - 85.66: 6 Dihedral angle restraints: 6144 sinusoidal: 2398 harmonic: 3746 Sorted by residual: dihedral pdb=" CA PRO C 34 " pdb=" C PRO C 34 " pdb=" N ASN C 35 " pdb=" CA ASN C 35 " ideal model delta harmonic sigma weight residual -180.00 -148.60 -31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PRO A 34 " pdb=" C PRO A 34 " pdb=" N ASN A 35 " pdb=" CA ASN A 35 " ideal model delta harmonic sigma weight residual -180.00 -148.62 -31.38 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LEU C 101 " pdb=" C LEU C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 310 0.090 - 0.135: 90 0.135 - 0.180: 12 0.180 - 0.225: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB THR A 92 " pdb=" CA THR A 92 " pdb=" OG1 THR A 92 " pdb=" CG2 THR A 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR C 92 " pdb=" CA THR C 92 " pdb=" OG1 THR C 92 " pdb=" CG2 THR C 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL D 139 " pdb=" N VAL D 139 " pdb=" C VAL D 139 " pdb=" CB VAL D 139 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1567 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 478 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 479 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO B 479 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 189 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 190 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.025 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 644 2.71 - 3.26: 10480 3.26 - 3.81: 14724 3.81 - 4.35: 18561 4.35 - 4.90: 31280 Nonbonded interactions: 75689 Sorted by model distance: nonbonded pdb=" NE2 GLN B 419 " pdb=" OE1 GLU B 484 " model vdw 2.166 2.520 nonbonded pdb=" NE2 GLN D 419 " pdb=" OE1 GLU D 484 " model vdw 2.166 2.520 nonbonded pdb=" O VAL A 283 " pdb=" OG SER A 287 " model vdw 2.176 2.440 nonbonded pdb=" O VAL C 283 " pdb=" OG SER C 287 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 181 " pdb=" ND2 ASN B 184 " model vdw 2.187 2.520 ... (remaining 75684 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 6370 2.51 5 N 1814 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 2.860 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 28.790 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.005 0.056 10298 Z= 0.324 Angle : 0.804 6.441 13984 Z= 0.447 Chirality : 0.046 0.225 1570 Planarity : 0.005 0.057 1828 Dihedral : 13.701 85.657 3740 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -6.35 (0.17), residues: 1288 helix: -3.60 (0.19), residues: 342 sheet: -4.96 (0.21), residues: 320 loop : -4.12 (0.19), residues: 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 143 average time/residue: 0.2323 time to fit residues: 46.9789 Evaluate side-chains 96 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0883 time to fit residues: 2.7723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10298 Z= 0.215 Angle : 0.716 8.356 13984 Z= 0.356 Chirality : 0.044 0.157 1570 Planarity : 0.005 0.069 1828 Dihedral : 6.270 33.745 1444 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -5.21 (0.20), residues: 1288 helix: -1.89 (0.25), residues: 344 sheet: -4.63 (0.22), residues: 310 loop : -3.74 (0.21), residues: 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 106 average time/residue: 0.2041 time to fit residues: 32.3185 Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0907 time to fit residues: 2.5239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 40 optimal weight: 0.0070 chunk 96 optimal weight: 10.0000 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 10298 Z= 0.177 Angle : 0.659 8.828 13984 Z= 0.326 Chirality : 0.042 0.152 1570 Planarity : 0.005 0.074 1828 Dihedral : 5.955 34.658 1444 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.54 (0.21), residues: 1288 helix: -0.87 (0.29), residues: 330 sheet: -4.25 (0.24), residues: 298 loop : -3.61 (0.21), residues: 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.215 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 112 average time/residue: 0.1778 time to fit residues: 31.0295 Evaluate side-chains 96 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1083 time to fit residues: 2.4854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.0070 chunk 114 optimal weight: 0.0030 chunk 34 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10298 Z= 0.169 Angle : 0.653 10.508 13984 Z= 0.319 Chirality : 0.042 0.148 1570 Planarity : 0.005 0.063 1828 Dihedral : 5.761 34.634 1444 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.18 (0.22), residues: 1288 helix: -0.46 (0.29), residues: 332 sheet: -3.99 (0.25), residues: 294 loop : -3.49 (0.21), residues: 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.239 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.1736 time to fit residues: 29.5483 Evaluate side-chains 95 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0901 time to fit residues: 3.0033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10298 Z= 0.202 Angle : 0.680 9.983 13984 Z= 0.329 Chirality : 0.042 0.183 1570 Planarity : 0.004 0.059 1828 Dihedral : 5.753 34.404 1444 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.01 (0.22), residues: 1288 helix: -0.20 (0.30), residues: 332 sheet: -3.95 (0.25), residues: 298 loop : -3.41 (0.22), residues: 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.237 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1782 time to fit residues: 28.0233 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0910 time to fit residues: 3.4685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 10298 Z= 0.316 Angle : 0.734 9.228 13984 Z= 0.358 Chirality : 0.044 0.189 1570 Planarity : 0.005 0.037 1828 Dihedral : 6.083 33.928 1444 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.76 % Favored : 84.08 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.06 (0.23), residues: 1288 helix: -0.16 (0.30), residues: 330 sheet: -4.15 (0.23), residues: 358 loop : -3.19 (0.23), residues: 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.178 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.2047 time to fit residues: 29.5265 Evaluate side-chains 91 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0954 time to fit residues: 2.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 79 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 10298 Z= 0.172 Angle : 0.671 9.528 13984 Z= 0.326 Chirality : 0.041 0.149 1570 Planarity : 0.005 0.073 1828 Dihedral : 5.676 33.841 1444 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.83 (0.23), residues: 1288 helix: 0.09 (0.30), residues: 330 sheet: -3.85 (0.24), residues: 326 loop : -3.29 (0.23), residues: 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.082 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.1684 time to fit residues: 25.1713 Evaluate side-chains 86 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10298 Z= 0.167 Angle : 0.666 9.797 13984 Z= 0.322 Chirality : 0.041 0.151 1570 Planarity : 0.004 0.048 1828 Dihedral : 5.527 33.628 1444 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.67 (0.23), residues: 1288 helix: 0.19 (0.30), residues: 330 sheet: -3.78 (0.24), residues: 336 loop : -3.13 (0.23), residues: 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.264 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.1849 time to fit residues: 25.9943 Evaluate side-chains 83 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0949 time to fit residues: 1.8781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 10298 Z= 0.268 Angle : 0.710 10.047 13984 Z= 0.347 Chirality : 0.043 0.172 1570 Planarity : 0.005 0.089 1828 Dihedral : 5.769 33.334 1444 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.72 (0.23), residues: 1288 helix: 0.14 (0.30), residues: 332 sheet: -3.81 (0.24), residues: 336 loop : -3.17 (0.23), residues: 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.079 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.1903 time to fit residues: 25.5705 Evaluate side-chains 85 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0944 time to fit residues: 2.1963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 93 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 93 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 10298 Z= 0.428 Angle : 0.809 10.585 13984 Z= 0.399 Chirality : 0.046 0.206 1570 Planarity : 0.005 0.074 1828 Dihedral : 6.378 33.075 1444 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.70 % Favored : 82.14 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.98 (0.23), residues: 1288 helix: -0.06 (0.30), residues: 332 sheet: -4.19 (0.22), residues: 366 loop : -3.07 (0.24), residues: 590 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.296 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.1790 time to fit residues: 25.5747 Evaluate side-chains 88 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0876 time to fit residues: 1.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 0.0170 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** 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 = 0.3800 r_free = 0.3800 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124440 restraints weight = 15820.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124343 restraints weight = 31230.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125284 restraints weight = 24000.799| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 10298 Z= 0.349 Angle : 0.773 10.509 13984 Z= 0.379 Chirality : 0.045 0.172 1570 Planarity : 0.005 0.065 1828 Dihedral : 6.313 33.039 1444 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.24 % Favored : 82.61 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.99 (0.23), residues: 1288 helix: -0.01 (0.30), residues: 332 sheet: -4.18 (0.22), residues: 366 loop : -3.13 (0.23), residues: 590 =============================================================================== Job complete usr+sys time: 1707.84 seconds wall clock time: 31 minutes 55.17 seconds (1915.17 seconds total)