Starting phenix.real_space_refine (version: dev) on Mon Apr 4 23:44:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/04_2022/6v4p_21044.pdb" } resolution = 2.8 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= -0.000 sd= 0.012 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 Residue "A ARG 77": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9717 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2927 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 15, 'TRANS': 356, 'PCIS': 3} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 10, 'TRANS': 208, 'PCIS': 2} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 203, 'PCIS': 4} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' CA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.84, per 1000 atoms: 0.60 Number of scatterers: 9717 At special positions: 0 Unit cell: (99, 150, 76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 41 16.00 Mg 1 11.99 O 1902 8.00 N 1636 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 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: 4.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 12.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.763A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.665A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.311A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.765A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.505A pdb=" N SER C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.936A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 4.083A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 8.111A pdb=" N GLY A 63 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 10 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN A 7 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG A 449 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.338A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.583A pdb=" N GLN A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.748A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.521A pdb=" N GLY A 398 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.503A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.161A pdb=" N PHE B 153 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR B 195 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 151 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 197 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 149 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR B 311 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 250 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.351A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 174 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.480A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.928A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 147 through 150 347 hydrogen bonds defined for protein. 888 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: 3.23 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1634 1.32 - 1.44: 2738 1.44 - 1.57: 5507 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 9938 Sorted by residual: bond pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" CA ASN D 32 " pdb=" C ASN D 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.12e+01 bond pdb=" C ILE D 29 " pdb=" O ILE D 29 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C SER D 30 " pdb=" O SER D 30 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.11e+00 bond pdb=" C ASN D 32 " pdb=" O ASN D 32 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 313 106.37 - 113.27: 5373 113.27 - 120.17: 3321 120.17 - 127.08: 4388 127.08 - 133.98: 119 Bond angle restraints: 13514 Sorted by residual: angle pdb=" C LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta sigma weight residual 109.61 117.10 -7.49 1.58e+00 4.01e-01 2.25e+01 angle pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " pdb=" CG LEU B 375 " ideal model delta sigma weight residual 116.30 102.78 13.52 3.50e+00 8.16e-02 1.49e+01 angle pdb=" C CYS B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 121.31 126.33 -5.02 1.49e+00 4.50e-01 1.13e+01 angle pdb=" N SER D 30 " pdb=" CA SER D 30 " pdb=" C SER D 30 " ideal model delta sigma weight residual 110.80 117.64 -6.84 2.13e+00 2.20e-01 1.03e+01 angle pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.34e+00 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5514 16.69 - 33.39: 297 33.39 - 50.08: 77 50.08 - 66.77: 25 66.77 - 83.47: 9 Dihedral angle restraints: 5922 sinusoidal: 2300 harmonic: 3622 Sorted by residual: dihedral pdb=" CA LEU B 375 " pdb=" C LEU B 375 " pdb=" N ASN B 376 " pdb=" CA ASN B 376 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA THR D 39 " pdb=" C THR D 39 " pdb=" N SER D 40 " pdb=" CA SER D 40 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C LEU B 375 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta harmonic sigma weight residual -122.60 -133.94 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1328 0.073 - 0.146: 162 0.146 - 0.218: 2 0.218 - 0.291: 2 0.291 - 0.364: 2 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA LEU B 375 " pdb=" N LEU B 375 " pdb=" C LEU B 375 " pdb=" CB LEU B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 375 " pdb=" CB LEU B 375 " pdb=" CD1 LEU B 375 " pdb=" CD2 LEU B 375 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER D 30 " pdb=" N SER D 30 " pdb=" C SER D 30 " pdb=" CB SER D 30 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1493 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 375 " 0.019 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU B 375 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 375 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 376 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 29 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE D 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE D 29 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 153 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 154 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 209 2.65 - 3.21: 8814 3.21 - 3.77: 15823 3.77 - 4.34: 23593 4.34 - 4.90: 38440 Nonbonded interactions: 86879 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B 701 " model vdw 2.084 2.170 nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP B 259 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS B 417 " pdb=" O PHE B 421 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR B 178 " pdb=" OD2 ASP C 57 " model vdw 2.233 2.440 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.241 2.440 ... (remaining 86874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 41 5.16 5 C 6131 2.51 5 N 1636 2.21 5 O 1902 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 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: 0.940 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: 5.610 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 30.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 0.046 9938 Z= 0.310 Angle : 0.600 13.516 13514 Z= 0.335 Chirality : 0.047 0.364 1496 Planarity : 0.004 0.042 1758 Dihedral : 12.282 83.466 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 13.43 % 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: -2.71 (0.21), residues: 1254 helix: -2.93 (0.33), residues: 116 sheet: -1.38 (0.22), residues: 448 loop : -1.87 (0.21), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.115 Fit side-chains outliers start: 34 outliers final: 10 residues processed: 209 average time/residue: 1.0833 time to fit residues: 244.7927 Evaluate side-chains 146 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0911 time to fit residues: 1.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 85 GLN A 134 GLN B 267 GLN B 280 HIS D 32 ASN D 92 ASN D 124 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 155 GLN D 166 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 9938 Z= 0.314 Angle : 0.592 8.545 13514 Z= 0.312 Chirality : 0.047 0.219 1496 Planarity : 0.005 0.071 1758 Dihedral : 5.069 35.934 1367 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.77 (0.22), residues: 1254 helix: -1.88 (0.40), residues: 121 sheet: -0.90 (0.23), residues: 448 loop : -1.16 (0.23), residues: 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 144 time to evaluate : 1.213 Fit side-chains outliers start: 43 outliers final: 20 residues processed: 170 average time/residue: 1.1586 time to fit residues: 212.5644 Evaluate side-chains 149 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.3602 time to fit residues: 4.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN B 428 GLN C 202 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 9938 Z= 0.307 Angle : 0.572 7.990 13514 Z= 0.300 Chirality : 0.046 0.160 1496 Planarity : 0.004 0.057 1758 Dihedral : 4.953 34.631 1367 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.34 (0.23), residues: 1254 helix: -1.31 (0.43), residues: 121 sheet: -0.69 (0.24), residues: 438 loop : -0.86 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.186 Fit side-chains outliers start: 47 outliers final: 21 residues processed: 163 average time/residue: 1.0823 time to fit residues: 190.9042 Evaluate side-chains 149 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.4691 time to fit residues: 5.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 9938 Z= 0.330 Angle : 0.576 9.435 13514 Z= 0.302 Chirality : 0.046 0.142 1496 Planarity : 0.004 0.052 1758 Dihedral : 4.951 34.091 1367 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.14 (0.23), residues: 1254 helix: -1.05 (0.44), residues: 121 sheet: -0.60 (0.24), residues: 445 loop : -0.71 (0.24), residues: 688 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 1.567 Fit side-chains outliers start: 42 outliers final: 21 residues processed: 159 average time/residue: 1.0917 time to fit residues: 188.2115 Evaluate side-chains 146 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.0996 time to fit residues: 2.6789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 9938 Z= 0.335 Angle : 0.584 11.082 13514 Z= 0.305 Chirality : 0.046 0.153 1496 Planarity : 0.005 0.116 1758 Dihedral : 4.954 33.150 1367 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.02 (0.23), residues: 1254 helix: -0.93 (0.44), residues: 121 sheet: -0.49 (0.23), residues: 454 loop : -0.67 (0.24), residues: 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 1.207 Fit side-chains outliers start: 47 outliers final: 24 residues processed: 161 average time/residue: 1.1389 time to fit residues: 198.1746 Evaluate side-chains 148 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.3289 time to fit residues: 4.4229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 9938 Z= 0.362 Angle : 0.595 12.127 13514 Z= 0.313 Chirality : 0.046 0.146 1496 Planarity : 0.005 0.059 1758 Dihedral : 4.959 32.851 1367 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.96 (0.23), residues: 1254 helix: -0.90 (0.44), residues: 121 sheet: -0.44 (0.24), residues: 450 loop : -0.63 (0.24), residues: 683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.230 Fit side-chains outliers start: 40 outliers final: 26 residues processed: 155 average time/residue: 1.1458 time to fit residues: 193.2163 Evaluate side-chains 148 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.7497 time to fit residues: 5.7142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 9938 Z= 0.261 Angle : 0.556 11.833 13514 Z= 0.290 Chirality : 0.045 0.141 1496 Planarity : 0.005 0.128 1758 Dihedral : 4.783 31.904 1367 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.81 (0.23), residues: 1254 helix: -0.64 (0.46), residues: 121 sheet: -0.35 (0.24), residues: 453 loop : -0.55 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.219 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 154 average time/residue: 1.0641 time to fit residues: 178.1848 Evaluate side-chains 140 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.5212 time to fit residues: 4.0498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.135 9938 Z= 0.321 Angle : 0.583 13.164 13514 Z= 0.308 Chirality : 0.046 0.267 1496 Planarity : 0.005 0.087 1758 Dihedral : 4.810 31.581 1367 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.80 (0.23), residues: 1254 helix: -0.56 (0.46), residues: 121 sheet: -0.30 (0.24), residues: 462 loop : -0.59 (0.24), residues: 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.156 Fit side-chains outliers start: 38 outliers final: 26 residues processed: 149 average time/residue: 1.0311 time to fit residues: 167.1342 Evaluate side-chains 145 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 3 average time/residue: 0.6880 time to fit residues: 4.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 101 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 9938 Z= 0.405 Angle : 0.627 15.346 13514 Z= 0.326 Chirality : 0.048 0.284 1496 Planarity : 0.006 0.146 1758 Dihedral : 5.004 31.660 1367 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.82 (0.23), residues: 1254 helix: -0.63 (0.46), residues: 120 sheet: -0.41 (0.24), residues: 450 loop : -0.52 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 1.375 Fit side-chains outliers start: 34 outliers final: 25 residues processed: 146 average time/residue: 1.0454 time to fit residues: 166.2468 Evaluate side-chains 141 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.5927 time to fit residues: 3.6095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.135 9938 Z= 0.309 Angle : 0.579 14.170 13514 Z= 0.307 Chirality : 0.046 0.216 1496 Planarity : 0.005 0.100 1758 Dihedral : 4.875 30.837 1367 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.74 (0.23), residues: 1254 helix: -0.45 (0.47), residues: 120 sheet: -0.36 (0.24), residues: 455 loop : -0.49 (0.24), residues: 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.209 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 143 average time/residue: 1.0293 time to fit residues: 160.2732 Evaluate side-chains 138 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 1.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.147305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102432 restraints weight = 9771.307| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.20 r_work: 0.2946 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2887 rms_B_bonded: 2.04 restraints_weight: 0.1250 r_work: 0.2851 rms_B_bonded: 2.27 restraints_weight: 0.0625 r_work: 0.2805 rms_B_bonded: 2.64 restraints_weight: 0.0312 r_work: 0.2747 rms_B_bonded: 3.21 restraints_weight: 0.0156 r_work: 0.2671 rms_B_bonded: 4.05 restraints_weight: 0.0078 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 9938 Z= 0.290 Angle : 0.580 13.923 13514 Z= 0.301 Chirality : 0.046 0.217 1496 Planarity : 0.006 0.147 1758 Dihedral : 4.846 30.147 1367 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.68 (0.24), residues: 1254 helix: -0.39 (0.47), residues: 120 sheet: -0.34 (0.24), residues: 455 loop : -0.43 (0.24), residues: 679 =============================================================================== Job complete usr+sys time: 3424.32 seconds wall clock time: 61 minutes 49.67 seconds (3709.67 seconds total)