Starting phenix.real_space_refine on Thu Feb 15 17:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dou_27623/02_2024/8dou_27623_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2287 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 7090 2.51 5 N 1676 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10666 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.52 Number of scatterers: 10666 At special positions: 0 Unit cell: (94.08, 101.92, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 1864 8.00 N 1676 7.00 C 7090 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 11 sheets defined 45.5% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 100 through 111 removed outlier: 4.089A pdb=" N TYR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 129 removed outlier: 4.770A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.959A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 23 through 47 removed outlier: 5.195A pdb=" N TRP B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.905A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 87 removed outlier: 3.802A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 102 through 128 removed outlier: 3.825A pdb=" N VAL B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 168 through 181 removed outlier: 4.619A pdb=" N TRP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 224 through 255 Proline residue: B 235 - end of helix removed outlier: 4.586A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 26 removed outlier: 4.055A pdb=" N PHE C 26 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 101 through 111 removed outlier: 4.405A pdb=" N TYR C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 144 through 158 Processing helix chain 'C' and resid 176 through 190 removed outlier: 3.984A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 314 through 317 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 23 through 47 removed outlier: 4.985A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.809A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 83 removed outlier: 3.859A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.593A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.988A pdb=" N LYS D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 94' Processing helix chain 'D' and resid 102 through 128 removed outlier: 4.203A pdb=" N VAL D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 139 removed outlier: 4.760A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 139 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 164 removed outlier: 3.505A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 removed outlier: 4.359A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 194 through 201 removed outlier: 3.626A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.516A pdb=" N VAL D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 255 Proline residue: D 235 - end of helix removed outlier: 5.733A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.581A pdb=" N PHE A 77 " --> pdb=" O PHE A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.364A pdb=" N ILE A 194 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A 52 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 196 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY A 54 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.688A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 367 through 371 removed outlier: 3.997A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 347 through 349 removed outlier: 4.173A pdb=" N HIS A 361 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.368A pdb=" N TYR A 11 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TRP A 35 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU A 33 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.501A pdb=" N ILE C 52 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 212 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 257 through 259 removed outlier: 3.628A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 262 through 265 Processing sheet with id= J, first strand: chain 'C' and resid 344 through 349 Processing sheet with id= K, first strand: chain 'C' and resid 341 through 343 444 hydrogen bonds defined for protein. 1248 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: 2.77 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1656 1.30 - 1.43: 2980 1.43 - 1.56: 6254 1.56 - 1.69: 6 1.69 - 1.82: 52 Bond restraints: 10948 Sorted by residual: bond pdb=" C HIS B 212 " pdb=" O HIS B 212 " ideal model delta sigma weight residual 1.237 1.168 0.068 1.16e-02 7.43e+03 3.46e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" N ILE D 211 " pdb=" CA ILE D 211 " ideal model delta sigma weight residual 1.459 1.531 -0.071 1.33e-02 5.65e+03 2.88e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N LEU D 139 " pdb=" CA LEU D 139 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.50e+01 ... (remaining 10943 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.64: 348 107.64 - 114.75: 6443 114.75 - 121.87: 5919 121.87 - 128.99: 2031 128.99 - 136.10: 77 Bond angle restraints: 14818 Sorted by residual: angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" C THR B 128 " ideal model delta sigma weight residual 111.07 117.99 -6.92 1.07e+00 8.73e-01 4.18e+01 angle pdb=" O PHE B 126 " pdb=" C PHE B 126 " pdb=" N ILE B 127 " ideal model delta sigma weight residual 122.12 116.24 5.88 1.06e+00 8.90e-01 3.08e+01 angle pdb=" C TYR B 114 " pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " ideal model delta sigma weight residual 110.96 119.46 -8.50 1.54e+00 4.22e-01 3.05e+01 angle pdb=" CA TYR B 114 " pdb=" C TYR B 114 " pdb=" O TYR B 114 " ideal model delta sigma weight residual 121.00 115.24 5.76 1.05e+00 9.07e-01 3.01e+01 angle pdb=" C PHE B 126 " pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.22e+00 6.72e-01 2.88e+01 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.15: 6079 27.15 - 54.30: 298 54.30 - 81.44: 13 81.44 - 108.59: 1 108.59 - 135.74: 5 Dihedral angle restraints: 6396 sinusoidal: 2616 harmonic: 3780 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 75.74 -135.74 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.82 -128.82 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.56 -125.56 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1411 0.058 - 0.116: 220 0.116 - 0.174: 19 0.174 - 0.233: 2 0.233 - 0.291: 2 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB ILE D 211 " pdb=" CA ILE D 211 " pdb=" CG1 ILE D 211 " pdb=" CG2 ILE D 211 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA THR B 128 " pdb=" N THR B 128 " pdb=" C THR B 128 " pdb=" CB THR B 128 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1651 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 139 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU D 139 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 139 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.026 2.00e-02 2.50e+03 1.61e-02 5.21e+00 pdb=" CG TYR B 114 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 92 " -0.013 2.00e-02 2.50e+03 1.61e-02 4.51e+00 pdb=" CG PHE B 92 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 92 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 92 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 92 " 0.000 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1831 2.77 - 3.30: 9843 3.30 - 3.83: 16953 3.83 - 4.37: 18371 4.37 - 4.90: 33403 Nonbonded interactions: 80401 Sorted by model distance: nonbonded pdb=" OG SER A 114 " pdb=" OE1 GLU A 117 " model vdw 2.233 2.440 nonbonded pdb=" O PHE A 134 " pdb=" OH TYR A 142 " model vdw 2.249 2.440 nonbonded pdb=" OD1 ASP C 294 " pdb=" OH TYR C 315 " model vdw 2.264 2.440 nonbonded pdb=" O PHE C 134 " pdb=" OH TYR C 142 " model vdw 2.267 2.440 nonbonded pdb=" O ILE C 154 " pdb=" OG1 THR C 158 " model vdw 2.270 2.440 ... (remaining 80396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.15 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 4.140 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 29.790 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 10948 Z= 0.214 Angle : 0.632 9.135 14818 Z= 0.343 Chirality : 0.042 0.291 1654 Planarity : 0.003 0.038 1816 Dihedral : 14.699 135.740 3980 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.34 % Allowed : 0.43 % Favored : 99.22 % 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: 0.61 (0.24), residues: 1292 helix: 1.82 (0.23), residues: 595 sheet: 1.26 (0.43), residues: 170 loop : -1.64 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 181 HIS 0.005 0.000 HIS B 212 PHE 0.037 0.001 PHE B 92 TYR 0.036 0.001 TYR B 114 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.269 Fit side-chains REVERT: A 343 TYR cc_start: 0.7548 (m-80) cc_final: 0.6931 (m-80) REVERT: B 129 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7077 (mt) outliers start: 4 outliers final: 0 residues processed: 170 average time/residue: 0.1981 time to fit residues: 49.5692 Evaluate side-chains 133 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 55 ASN B 218 ASN C 361 HIS ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10948 Z= 0.171 Angle : 0.559 9.872 14818 Z= 0.270 Chirality : 0.041 0.134 1654 Planarity : 0.003 0.034 1816 Dihedral : 7.980 145.983 1424 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.69 % Allowed : 10.60 % Favored : 88.71 % 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: 0.56 (0.24), residues: 1292 helix: 1.75 (0.23), residues: 583 sheet: 1.20 (0.43), residues: 182 loop : -1.60 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 181 HIS 0.004 0.001 HIS B 212 PHE 0.014 0.001 PHE C 369 TYR 0.022 0.001 TYR B 243 ARG 0.003 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 1.103 Fit side-chains REVERT: A 318 GLU cc_start: 0.6760 (mp0) cc_final: 0.6548 (mp0) REVERT: D 131 PHE cc_start: 0.7233 (t80) cc_final: 0.6932 (t80) outliers start: 8 outliers final: 5 residues processed: 149 average time/residue: 0.2028 time to fit residues: 44.5848 Evaluate side-chains 129 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 3 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 2 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10948 Z= 0.361 Angle : 0.659 7.738 14818 Z= 0.333 Chirality : 0.045 0.136 1654 Planarity : 0.004 0.032 1816 Dihedral : 7.991 163.473 1422 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.24 % Allowed : 14.74 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1292 helix: 1.36 (0.22), residues: 581 sheet: 0.33 (0.43), residues: 194 loop : -1.87 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 181 HIS 0.005 0.001 HIS A 361 PHE 0.022 0.002 PHE C 369 TYR 0.026 0.002 TYR B 243 ARG 0.005 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.179 Fit side-chains REVERT: A 201 MET cc_start: 0.8845 (tmm) cc_final: 0.8591 (tmm) REVERT: A 318 GLU cc_start: 0.7057 (mp0) cc_final: 0.6808 (mp0) REVERT: B 12 GLN cc_start: 0.8270 (mp10) cc_final: 0.8021 (mp10) REVERT: B 179 PHE cc_start: 0.8906 (t80) cc_final: 0.8704 (t80) REVERT: B 220 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7803 (mm) REVERT: C 182 ARG cc_start: 0.7271 (ptp90) cc_final: 0.7031 (ptt-90) outliers start: 26 outliers final: 15 residues processed: 154 average time/residue: 0.2308 time to fit residues: 50.4036 Evaluate side-chains 133 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 357 GLN B 2 ASN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 218 ASN C 187 HIS D 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10948 Z= 0.206 Angle : 0.573 7.865 14818 Z= 0.284 Chirality : 0.041 0.129 1654 Planarity : 0.003 0.029 1816 Dihedral : 7.815 172.674 1422 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.07 % Allowed : 17.76 % Favored : 80.17 % 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: 0.02 (0.24), residues: 1292 helix: 1.45 (0.22), residues: 581 sheet: 0.22 (0.43), residues: 196 loop : -1.82 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 181 HIS 0.013 0.001 HIS C 187 PHE 0.015 0.001 PHE B 74 TYR 0.022 0.001 TYR B 243 ARG 0.002 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.301 Fit side-chains REVERT: A 201 MET cc_start: 0.8738 (tmm) cc_final: 0.8454 (tmm) REVERT: B 16 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8166 (p0) REVERT: B 220 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7760 (mm) REVERT: C 249 GLN cc_start: 0.6663 (tm-30) cc_final: 0.6384 (tm-30) outliers start: 24 outliers final: 11 residues processed: 149 average time/residue: 0.2180 time to fit residues: 46.5833 Evaluate side-chains 134 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10948 Z= 0.278 Angle : 0.616 10.371 14818 Z= 0.306 Chirality : 0.043 0.139 1654 Planarity : 0.003 0.028 1816 Dihedral : 7.892 178.714 1422 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.28 % Allowed : 17.67 % Favored : 79.05 % 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: -0.14 (0.24), residues: 1292 helix: 1.32 (0.22), residues: 588 sheet: 0.23 (0.44), residues: 186 loop : -1.95 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 181 HIS 0.013 0.001 HIS C 187 PHE 0.023 0.002 PHE C 30 TYR 0.025 0.001 TYR B 243 ARG 0.006 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 201 MET cc_start: 0.8823 (tmm) cc_final: 0.8547 (tmm) REVERT: C 249 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6515 (tm-30) outliers start: 38 outliers final: 29 residues processed: 158 average time/residue: 0.2191 time to fit residues: 49.8932 Evaluate side-chains 156 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 0.0070 chunk 30 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.0020 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 357 GLN B 218 ASN C 187 HIS D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10948 Z= 0.146 Angle : 0.556 9.476 14818 Z= 0.272 Chirality : 0.040 0.142 1654 Planarity : 0.003 0.033 1816 Dihedral : 7.576 171.190 1422 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.59 % Allowed : 18.97 % Favored : 78.45 % 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: 0.07 (0.24), residues: 1292 helix: 1.55 (0.23), residues: 583 sheet: 0.18 (0.43), residues: 193 loop : -1.84 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 362 HIS 0.014 0.001 HIS C 187 PHE 0.013 0.001 PHE D 74 TYR 0.023 0.001 TYR B 243 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8074 (p0) REVERT: B 220 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7706 (mm) REVERT: C 23 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: D 80 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7783 (mtm-85) outliers start: 30 outliers final: 17 residues processed: 160 average time/residue: 0.2284 time to fit residues: 53.1337 Evaluate side-chains 147 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 187 HIS C 361 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10948 Z= 0.264 Angle : 0.608 9.991 14818 Z= 0.301 Chirality : 0.042 0.136 1654 Planarity : 0.003 0.028 1816 Dihedral : 7.604 165.290 1422 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.10 % Allowed : 19.48 % Favored : 77.41 % 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: -0.13 (0.24), residues: 1292 helix: 1.42 (0.22), residues: 583 sheet: -0.03 (0.43), residues: 196 loop : -1.95 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 181 HIS 0.013 0.001 HIS C 187 PHE 0.022 0.002 PHE C 128 TYR 0.025 0.001 TYR B 243 ARG 0.004 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.232 Fit side-chains REVERT: B 220 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 249 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6458 (tm-30) REVERT: C 294 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: C 392 ARG cc_start: 0.6668 (ptm-80) cc_final: 0.6452 (ptm-80) outliers start: 36 outliers final: 27 residues processed: 159 average time/residue: 0.2073 time to fit residues: 48.1566 Evaluate side-chains 156 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 187 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10948 Z= 0.244 Angle : 0.605 9.629 14818 Z= 0.300 Chirality : 0.042 0.143 1654 Planarity : 0.003 0.031 1816 Dihedral : 7.496 159.309 1422 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.45 % Allowed : 19.22 % Favored : 77.33 % 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: -0.18 (0.24), residues: 1292 helix: 1.43 (0.22), residues: 580 sheet: -0.07 (0.43), residues: 196 loop : -2.01 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 8 HIS 0.014 0.001 HIS C 187 PHE 0.020 0.001 PHE C 128 TYR 0.024 0.001 TYR B 243 ARG 0.003 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: B 220 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7801 (mm) REVERT: C 23 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 249 GLN cc_start: 0.6750 (tm-30) cc_final: 0.6466 (tm-30) outliers start: 40 outliers final: 29 residues processed: 163 average time/residue: 0.2158 time to fit residues: 52.0862 Evaluate side-chains 160 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10948 Z= 0.191 Angle : 0.585 9.719 14818 Z= 0.289 Chirality : 0.041 0.142 1654 Planarity : 0.003 0.029 1816 Dihedral : 7.266 155.254 1422 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.02 % Allowed : 19.91 % Favored : 77.07 % 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: -0.08 (0.24), residues: 1292 helix: 1.52 (0.23), residues: 580 sheet: 0.04 (0.42), residues: 198 loop : -2.03 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.015 0.001 HIS C 187 PHE 0.020 0.001 PHE C 128 TYR 0.024 0.001 TYR B 243 ARG 0.003 0.000 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.168 Fit side-chains REVERT: B 220 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7802 (mm) REVERT: C 23 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6927 (mm-30) REVERT: C 361 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7205 (t-90) outliers start: 35 outliers final: 28 residues processed: 153 average time/residue: 0.2037 time to fit residues: 46.1254 Evaluate side-chains 153 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS B 218 ASN C 187 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10948 Z= 0.322 Angle : 0.651 9.891 14818 Z= 0.324 Chirality : 0.043 0.146 1654 Planarity : 0.003 0.028 1816 Dihedral : 7.418 156.412 1422 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.36 % Allowed : 19.66 % Favored : 76.98 % 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: -0.36 (0.24), residues: 1292 helix: 1.25 (0.22), residues: 586 sheet: -0.20 (0.43), residues: 196 loop : -2.10 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 181 HIS 0.015 0.001 HIS C 187 PHE 0.019 0.002 PHE C 128 TYR 0.026 0.002 TYR B 243 ARG 0.003 0.000 ARG D 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: B 220 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7819 (mm) REVERT: C 23 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6938 (mm-30) REVERT: C 249 GLN cc_start: 0.6731 (tm-30) cc_final: 0.6341 (tm-30) REVERT: C 361 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7239 (t-90) outliers start: 39 outliers final: 31 residues processed: 163 average time/residue: 0.2083 time to fit residues: 49.8452 Evaluate side-chains 162 residues out of total 1160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 218 ASN C 187 HIS D 55 ASN D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.187524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156564 restraints weight = 14680.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155913 restraints weight = 16017.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157561 restraints weight = 14389.450| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3856 r_free = 0.3856 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10948 Z= 0.191 Angle : 0.598 9.720 14818 Z= 0.295 Chirality : 0.041 0.145 1654 Planarity : 0.003 0.032 1816 Dihedral : 7.185 156.892 1422 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.02 % Allowed : 20.34 % Favored : 76.64 % 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: -0.21 (0.24), residues: 1292 helix: 1.42 (0.22), residues: 580 sheet: -0.09 (0.42), residues: 198 loop : -2.06 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.016 0.001 HIS C 187 PHE 0.019 0.001 PHE C 128 TYR 0.024 0.001 TYR B 243 ARG 0.005 0.000 ARG C 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.42 seconds wall clock time: 37 minutes 11.34 seconds (2231.34 seconds total)