Starting phenix.real_space_refine on Thu Mar 14 17:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/03_2024/7v4l_31715.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5980 2.51 5 N 1530 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E ASP 339": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9345 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "D" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Time building chain proxies: 5.27, per 1000 atoms: 0.56 Number of scatterers: 9345 At special positions: 0 Unit cell: (117.665, 120.19, 61.61, 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 55 16.00 O 1780 8.00 N 1530 7.00 C 5980 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: 3.38 Conformation dependent library (CDL) restraints added in 1.8 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 19 sheets defined 23.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.706A pdb=" N GLY A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 215 through 228 removed outlier: 4.460A pdb=" N LEU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.913A pdb=" N ALA A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.516A pdb=" N GLY B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.559A pdb=" N ASP B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.976A pdb=" N LEU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.588A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 228 removed outlier: 3.559A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.712A pdb=" N THR C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.710A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 183 " --> pdb=" O CYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.180A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 223 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.718A pdb=" N THR D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.636A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 228 removed outlier: 4.180A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 removed outlier: 3.526A pdb=" N THR E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.803A pdb=" N ALA A 76 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.071A pdb=" N SER A 205 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.860A pdb=" N GLN A 130 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 126 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 205 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.534A pdb=" N TYR B 132 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 130 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 133 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.320A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.190A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.085A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR E 95 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU E 72 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 136 323 hydrogen bonds defined for protein. 903 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: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1677 1.33 - 1.45: 2459 1.45 - 1.57: 5334 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9560 Sorted by residual: bond pdb=" C ASP C 339 " pdb=" N PRO C 340 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.36e+01 bond pdb=" C ASP E 339 " pdb=" N PRO E 340 " ideal model delta sigma weight residual 1.336 1.374 -0.039 1.08e-02 8.57e+03 1.27e+01 bond pdb=" CA ASP C 339 " pdb=" C ASP C 339 " ideal model delta sigma weight residual 1.522 1.564 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA ASP B 339 " pdb=" C ASP B 339 " ideal model delta sigma weight residual 1.521 1.558 -0.037 1.32e-02 5.74e+03 8.06e+00 bond pdb=" C ASP B 339 " pdb=" O ASP B 339 " ideal model delta sigma weight residual 1.246 1.221 0.025 9.20e-03 1.18e+04 7.67e+00 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.31: 359 106.31 - 113.29: 5037 113.29 - 120.27: 3459 120.27 - 127.26: 3977 127.26 - 134.24: 123 Bond angle restraints: 12955 Sorted by residual: angle pdb=" N LYS E 255 " pdb=" CA LYS E 255 " pdb=" C LYS E 255 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 angle pdb=" N LYS D 255 " pdb=" CA LYS D 255 " pdb=" C LYS D 255 " ideal model delta sigma weight residual 112.23 104.18 8.05 1.26e+00 6.30e-01 4.08e+01 angle pdb=" N ASN B 349 " pdb=" CA ASN B 349 " pdb=" C ASN B 349 " ideal model delta sigma weight residual 110.55 102.31 8.24 1.35e+00 5.49e-01 3.73e+01 angle pdb=" N ALA B 348 " pdb=" CA ALA B 348 " pdb=" C ALA B 348 " ideal model delta sigma weight residual 113.28 106.87 6.41 1.22e+00 6.72e-01 2.76e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 109.37 116.17 -6.80 1.35e+00 5.49e-01 2.54e+01 ... (remaining 12950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4994 16.73 - 33.47: 544 33.47 - 50.20: 120 50.20 - 66.94: 37 66.94 - 83.67: 5 Dihedral angle restraints: 5700 sinusoidal: 2275 harmonic: 3425 Sorted by residual: dihedral pdb=" C ILE A 352 " pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual -122.00 -133.91 11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CA ARG A 38 " pdb=" C ARG A 38 " pdb=" N THR A 39 " pdb=" CA THR A 39 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual 123.40 132.55 -9.15 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1162 0.068 - 0.136: 208 0.136 - 0.204: 34 0.204 - 0.272: 4 0.272 - 0.340: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR C 351 " pdb=" N THR C 351 " pdb=" C THR C 351 " pdb=" CB THR C 351 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG B 258 " pdb=" N ARG B 258 " pdb=" C ARG B 258 " pdb=" CB ARG B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1407 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 339 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 340 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 103 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 194 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 195 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " 0.032 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 197 2.66 - 3.22: 9031 3.22 - 3.78: 14294 3.78 - 4.34: 18893 4.34 - 4.90: 31070 Nonbonded interactions: 73485 Sorted by model distance: nonbonded pdb=" NH1 ARG B 169 " pdb=" OD1 ASP B 173 " model vdw 2.102 2.520 nonbonded pdb=" NH1 ARG C 169 " pdb=" OD1 ASP C 173 " model vdw 2.104 2.520 nonbonded pdb=" OE2 GLU D 22 " pdb=" OG SER D 35 " model vdw 2.148 2.440 nonbonded pdb=" OE2 GLU B 22 " pdb=" OG SER B 35 " model vdw 2.154 2.440 nonbonded pdb=" OE2 GLU C 22 " pdb=" OG SER C 35 " model vdw 2.180 2.440 ... (remaining 73480 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.860 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: 26.810 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.920 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 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 0.049 9560 Z= 0.295 Angle : 0.817 9.185 12955 Z= 0.475 Chirality : 0.056 0.340 1410 Planarity : 0.007 0.114 1640 Dihedral : 15.200 83.670 3500 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.84 % Favored : 90.62 % Rotamer: Outliers : 3.71 % Allowed : 1.56 % Favored : 94.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.25), residues: 1120 helix: -0.22 (0.32), residues: 253 sheet: -2.45 (0.25), residues: 359 loop : -1.82 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.014 0.002 PHE C 200 TYR 0.021 0.002 TYR A 132 ARG 0.009 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.5582 (m-10) cc_final: 0.4857 (m-10) REVERT: A 55 TYR cc_start: 0.6694 (p90) cc_final: 0.6013 (p90) REVERT: A 197 GLN cc_start: 0.7203 (mp10) cc_final: 0.6578 (mp10) REVERT: B 55 TYR cc_start: 0.6776 (p90) cc_final: 0.6086 (p90) REVERT: B 129 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6362 (mm-30) REVERT: C 55 TYR cc_start: 0.6574 (p90) cc_final: 0.5917 (p90) REVERT: D 55 TYR cc_start: 0.6712 (p90) cc_final: 0.5911 (p90) REVERT: E 55 TYR cc_start: 0.6758 (p90) cc_final: 0.6010 (p90) outliers start: 38 outliers final: 5 residues processed: 196 average time/residue: 0.1871 time to fit residues: 52.1665 Evaluate side-chains 151 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 256 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 ASN D 190 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9560 Z= 0.204 Angle : 0.646 7.682 12955 Z= 0.338 Chirality : 0.047 0.159 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.950 53.051 1280 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 1.27 % Allowed : 11.32 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.24), residues: 1120 helix: 0.30 (0.31), residues: 267 sheet: -2.39 (0.25), residues: 356 loop : -1.89 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 53 HIS 0.004 0.001 HIS A 249 PHE 0.022 0.001 PHE D 200 TYR 0.022 0.002 TYR D 73 ARG 0.006 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 53 TRP cc_start: 0.5459 (m-10) cc_final: 0.5032 (m-10) REVERT: A 55 TYR cc_start: 0.6587 (p90) cc_final: 0.5760 (p90) REVERT: A 197 GLN cc_start: 0.7025 (mp10) cc_final: 0.6524 (mp10) REVERT: B 55 TYR cc_start: 0.6662 (p90) cc_final: 0.5933 (p90) REVERT: B 123 GLU cc_start: 0.6322 (tt0) cc_final: 0.5558 (mt-10) REVERT: C 55 TYR cc_start: 0.6457 (p90) cc_final: 0.5649 (p90) REVERT: C 194 MET cc_start: 0.3964 (tpp) cc_final: 0.3560 (tpt) REVERT: D 55 TYR cc_start: 0.6622 (p90) cc_final: 0.5772 (p90) REVERT: D 257 MET cc_start: 0.4556 (tpt) cc_final: 0.4336 (mmm) REVERT: E 55 TYR cc_start: 0.6591 (p90) cc_final: 0.5786 (p90) REVERT: E 69 GLU cc_start: 0.6110 (tp30) cc_final: 0.5890 (tp30) outliers start: 13 outliers final: 12 residues processed: 165 average time/residue: 0.1779 time to fit residues: 43.2039 Evaluate side-chains 162 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 256 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9560 Z= 0.267 Angle : 0.658 8.148 12955 Z= 0.347 Chirality : 0.049 0.194 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.864 31.745 1271 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 2.73 % Allowed : 13.76 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1120 helix: 0.08 (0.31), residues: 264 sheet: -2.56 (0.24), residues: 366 loop : -1.98 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 53 HIS 0.005 0.001 HIS C 175 PHE 0.015 0.002 PHE A 200 TYR 0.018 0.002 TYR A 132 ARG 0.004 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.6008 (m-10) cc_final: 0.5608 (m-10) REVERT: A 55 TYR cc_start: 0.6605 (p90) cc_final: 0.5779 (p90) REVERT: B 55 TYR cc_start: 0.6811 (p90) cc_final: 0.5976 (p90) REVERT: B 123 GLU cc_start: 0.6399 (tt0) cc_final: 0.5855 (mt-10) REVERT: B 338 MET cc_start: 0.6777 (tpp) cc_final: 0.6172 (tpt) REVERT: C 55 TYR cc_start: 0.6505 (p90) cc_final: 0.5742 (p90) REVERT: D 55 TYR cc_start: 0.6757 (p90) cc_final: 0.5882 (p90) REVERT: D 197 GLN cc_start: 0.7260 (pp30) cc_final: 0.6960 (pp30) REVERT: D 257 MET cc_start: 0.4640 (tpt) cc_final: 0.4226 (mmm) REVERT: E 55 TYR cc_start: 0.6731 (p90) cc_final: 0.5838 (p90) REVERT: E 69 GLU cc_start: 0.6264 (tp30) cc_final: 0.5998 (tp30) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.1641 time to fit residues: 42.0335 Evaluate side-chains 167 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 255 LYS Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5298 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9560 Z= 0.189 Angle : 0.600 8.451 12955 Z= 0.309 Chirality : 0.046 0.183 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.407 26.300 1271 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 3.61 % Allowed : 15.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 1120 helix: 0.27 (0.31), residues: 265 sheet: -2.38 (0.25), residues: 348 loop : -1.91 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 53 HIS 0.003 0.001 HIS D 175 PHE 0.018 0.001 PHE D 200 TYR 0.014 0.001 TYR E 73 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.5841 (m-10) cc_final: 0.5330 (m-10) REVERT: A 55 TYR cc_start: 0.6552 (p90) cc_final: 0.5713 (p90) REVERT: B 55 TYR cc_start: 0.6665 (p90) cc_final: 0.5879 (p90) REVERT: B 69 GLU cc_start: 0.6100 (tp30) cc_final: 0.5795 (tp30) REVERT: B 123 GLU cc_start: 0.6259 (tt0) cc_final: 0.5914 (mt-10) REVERT: B 180 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (mm) REVERT: B 194 MET cc_start: 0.3801 (tpp) cc_final: 0.3510 (tpp) REVERT: B 338 MET cc_start: 0.6761 (tpp) cc_final: 0.6226 (tpt) REVERT: C 55 TYR cc_start: 0.6400 (p90) cc_final: 0.5605 (p90) REVERT: D 55 TYR cc_start: 0.6657 (p90) cc_final: 0.5768 (p90) REVERT: D 257 MET cc_start: 0.4738 (tpt) cc_final: 0.4381 (mmm) REVERT: E 55 TYR cc_start: 0.6653 (p90) cc_final: 0.5749 (p90) REVERT: E 69 GLU cc_start: 0.6219 (tp30) cc_final: 0.5937 (tp30) outliers start: 37 outliers final: 22 residues processed: 181 average time/residue: 0.1644 time to fit residues: 43.6734 Evaluate side-chains 175 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9560 Z= 0.235 Angle : 0.645 11.708 12955 Z= 0.331 Chirality : 0.048 0.183 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.523 18.435 1270 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.04 % Favored : 91.88 % Rotamer: Outliers : 3.22 % Allowed : 16.98 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 1120 helix: 0.12 (0.31), residues: 264 sheet: -2.46 (0.25), residues: 359 loop : -1.92 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 53 HIS 0.005 0.001 HIS D 175 PHE 0.015 0.002 PHE D 200 TYR 0.015 0.002 TYR A 132 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6591 (p90) cc_final: 0.5774 (p90) REVERT: A 180 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6694 (mp) REVERT: A 197 GLN cc_start: 0.7315 (mp10) cc_final: 0.6860 (mp10) REVERT: B 55 TYR cc_start: 0.6716 (p90) cc_final: 0.5972 (p90) REVERT: B 123 GLU cc_start: 0.6483 (tt0) cc_final: 0.6163 (mt-10) REVERT: B 173 ASP cc_start: 0.4724 (m-30) cc_final: 0.4151 (m-30) REVERT: B 338 MET cc_start: 0.6821 (tpp) cc_final: 0.6287 (tpt) REVERT: C 55 TYR cc_start: 0.6372 (p90) cc_final: 0.5584 (p90) REVERT: D 55 TYR cc_start: 0.6707 (p90) cc_final: 0.5836 (p90) REVERT: D 192 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5852 (mm-30) REVERT: D 197 GLN cc_start: 0.7259 (pp30) cc_final: 0.7004 (pp30) REVERT: D 257 MET cc_start: 0.4707 (tpt) cc_final: 0.4420 (mmm) REVERT: E 55 TYR cc_start: 0.6733 (p90) cc_final: 0.5790 (p90) REVERT: E 69 GLU cc_start: 0.6260 (tp30) cc_final: 0.5939 (tp30) REVERT: E 197 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6402 (pm20) outliers start: 33 outliers final: 19 residues processed: 173 average time/residue: 0.1749 time to fit residues: 44.2839 Evaluate side-chains 171 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 230 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9560 Z= 0.348 Angle : 0.748 11.111 12955 Z= 0.386 Chirality : 0.051 0.193 1410 Planarity : 0.007 0.060 1640 Dihedral : 5.048 20.251 1270 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.64 % Favored : 90.27 % Rotamer: Outliers : 3.80 % Allowed : 16.78 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 1120 helix: -0.39 (0.31), residues: 264 sheet: -2.57 (0.25), residues: 348 loop : -2.18 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 53 HIS 0.007 0.002 HIS D 175 PHE 0.016 0.002 PHE C 200 TYR 0.025 0.003 TYR A 132 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6648 (p90) cc_final: 0.5833 (p90) REVERT: A 180 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 55 TYR cc_start: 0.6888 (p90) cc_final: 0.6108 (p90) REVERT: B 123 GLU cc_start: 0.6549 (tt0) cc_final: 0.6163 (mt-10) REVERT: B 338 MET cc_start: 0.6788 (tpp) cc_final: 0.6204 (tpt) REVERT: C 55 TYR cc_start: 0.6486 (p90) cc_final: 0.5756 (p90) REVERT: D 22 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6099 (tt0) REVERT: D 55 TYR cc_start: 0.6787 (p90) cc_final: 0.5898 (p90) REVERT: D 222 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5279 (mp0) REVERT: E 55 TYR cc_start: 0.6880 (p90) cc_final: 0.5919 (p90) REVERT: E 69 GLU cc_start: 0.6395 (tp30) cc_final: 0.6047 (tp30) REVERT: E 199 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7201 (tm-30) outliers start: 39 outliers final: 29 residues processed: 175 average time/residue: 0.1635 time to fit residues: 43.1740 Evaluate side-chains 175 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 67 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9560 Z= 0.223 Angle : 0.657 11.164 12955 Z= 0.336 Chirality : 0.047 0.196 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.589 18.980 1270 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 3.61 % Allowed : 18.15 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.64 (0.24), residues: 1120 helix: -0.09 (0.31), residues: 263 sheet: -2.45 (0.25), residues: 348 loop : -2.04 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.015 0.002 PHE B 200 TYR 0.015 0.002 TYR A 132 ARG 0.003 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6564 (p90) cc_final: 0.5784 (p90) REVERT: A 197 GLN cc_start: 0.7305 (mp10) cc_final: 0.6823 (mp10) REVERT: B 55 TYR cc_start: 0.6799 (p90) cc_final: 0.6062 (p90) REVERT: B 123 GLU cc_start: 0.6399 (tt0) cc_final: 0.6051 (mt-10) REVERT: B 338 MET cc_start: 0.6873 (tpp) cc_final: 0.6322 (tpt) REVERT: C 55 TYR cc_start: 0.6455 (p90) cc_final: 0.5714 (p90) REVERT: D 55 TYR cc_start: 0.6709 (p90) cc_final: 0.5866 (p90) REVERT: D 192 GLU cc_start: 0.6271 (mm-30) cc_final: 0.5879 (mm-30) REVERT: E 55 TYR cc_start: 0.6764 (p90) cc_final: 0.5840 (p90) REVERT: E 69 GLU cc_start: 0.6332 (tp30) cc_final: 0.5999 (tp30) REVERT: E 197 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: E 199 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7058 (tm-30) outliers start: 37 outliers final: 27 residues processed: 169 average time/residue: 0.1660 time to fit residues: 42.0144 Evaluate side-chains 172 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 70 optimal weight: 0.0970 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9560 Z= 0.207 Angle : 0.642 10.856 12955 Z= 0.329 Chirality : 0.047 0.202 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.381 18.003 1270 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 3.32 % Allowed : 18.73 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.24), residues: 1120 helix: 0.03 (0.30), residues: 264 sheet: -2.41 (0.25), residues: 348 loop : -1.95 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 53 HIS 0.003 0.001 HIS D 175 PHE 0.015 0.001 PHE D 200 TYR 0.014 0.001 TYR E 176 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6579 (p90) cc_final: 0.5822 (p90) REVERT: A 197 GLN cc_start: 0.7176 (mp10) cc_final: 0.6738 (mp10) REVERT: B 55 TYR cc_start: 0.6752 (p90) cc_final: 0.6028 (p90) REVERT: B 123 GLU cc_start: 0.6380 (tt0) cc_final: 0.6069 (mt-10) REVERT: B 199 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7008 (pp20) REVERT: B 338 MET cc_start: 0.6829 (tpp) cc_final: 0.6261 (tpt) REVERT: C 55 TYR cc_start: 0.6462 (p90) cc_final: 0.5706 (p90) REVERT: C 201 GLN cc_start: 0.6722 (mm-40) cc_final: 0.6500 (mm-40) REVERT: D 55 TYR cc_start: 0.6677 (p90) cc_final: 0.5830 (p90) REVERT: E 55 TYR cc_start: 0.6723 (p90) cc_final: 0.5782 (p90) REVERT: E 69 GLU cc_start: 0.6313 (tp30) cc_final: 0.5987 (tp30) outliers start: 34 outliers final: 25 residues processed: 170 average time/residue: 0.1705 time to fit residues: 43.3194 Evaluate side-chains 175 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 9560 Z= 0.497 Angle : 0.880 10.602 12955 Z= 0.461 Chirality : 0.057 0.243 1410 Planarity : 0.008 0.068 1640 Dihedral : 5.821 24.631 1270 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.05 % Favored : 87.68 % Rotamer: Outliers : 3.41 % Allowed : 19.32 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.24), residues: 1120 helix: -0.97 (0.30), residues: 265 sheet: -2.75 (0.25), residues: 357 loop : -2.41 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 53 HIS 0.009 0.003 HIS D 175 PHE 0.020 0.003 PHE A 82 TYR 0.031 0.004 TYR A 132 ARG 0.008 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6700 (p90) cc_final: 0.5956 (p90) REVERT: A 180 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6905 (mp) REVERT: B 55 TYR cc_start: 0.7016 (p90) cc_final: 0.6242 (p90) REVERT: B 123 GLU cc_start: 0.6564 (tt0) cc_final: 0.6205 (mt-10) REVERT: B 338 MET cc_start: 0.6885 (tpp) cc_final: 0.6228 (tpt) REVERT: C 55 TYR cc_start: 0.6627 (p90) cc_final: 0.5901 (p90) REVERT: D 55 TYR cc_start: 0.6863 (p90) cc_final: 0.5998 (p90) REVERT: E 55 TYR cc_start: 0.6980 (p90) cc_final: 0.6025 (p90) REVERT: E 69 GLU cc_start: 0.6516 (tp30) cc_final: 0.6149 (tp30) REVERT: E 197 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6741 (pm20) outliers start: 35 outliers final: 28 residues processed: 167 average time/residue: 0.1725 time to fit residues: 42.6497 Evaluate side-chains 165 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.0770 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9560 Z= 0.226 Angle : 0.683 10.251 12955 Z= 0.354 Chirality : 0.048 0.194 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.775 17.634 1270 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 2.73 % Allowed : 20.00 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), residues: 1120 helix: -0.37 (0.31), residues: 260 sheet: -2.47 (0.25), residues: 343 loop : -2.24 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 53 HIS 0.003 0.001 HIS D 175 PHE 0.014 0.001 PHE A 200 TYR 0.015 0.002 TYR C 73 ARG 0.007 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.6582 (p90) cc_final: 0.5819 (p90) REVERT: B 55 TYR cc_start: 0.6869 (p90) cc_final: 0.6102 (p90) REVERT: B 123 GLU cc_start: 0.6501 (tt0) cc_final: 0.6137 (mt-10) REVERT: B 338 MET cc_start: 0.6870 (tpp) cc_final: 0.6255 (tpt) REVERT: C 55 TYR cc_start: 0.6467 (p90) cc_final: 0.5749 (p90) REVERT: D 55 TYR cc_start: 0.6701 (p90) cc_final: 0.5828 (p90) REVERT: E 55 TYR cc_start: 0.6793 (p90) cc_final: 0.5885 (p90) REVERT: E 69 GLU cc_start: 0.6385 (tp30) cc_final: 0.6055 (tp30) REVERT: E 197 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: E 338 MET cc_start: 0.2103 (mmm) cc_final: 0.1805 (tpt) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.2054 time to fit residues: 50.8022 Evaluate side-chains 167 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.215509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.156439 restraints weight = 9275.224| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.95 r_work: 0.4155 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9560 Z= 0.210 Angle : 0.661 10.832 12955 Z= 0.340 Chirality : 0.047 0.197 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.536 16.744 1270 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.32 % Favored : 92.59 % Rotamer: Outliers : 2.44 % Allowed : 20.68 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1120 helix: -0.12 (0.31), residues: 259 sheet: -2.49 (0.24), residues: 375 loop : -1.97 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 53 HIS 0.003 0.001 HIS C 175 PHE 0.014 0.001 PHE D 200 TYR 0.015 0.001 TYR E 176 ARG 0.008 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.00 seconds wall clock time: 50 minutes 54.63 seconds (3054.63 seconds total)