Starting phenix.real_space_refine on Sat Aug 3 20:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/08_2024/8w8b_37351.cif" } resolution = 3.0 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= -0.002 sd= 0.152 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 64 5.16 5 C 5613 2.51 5 N 1459 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8734 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1751 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1756 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 170 Unusual residues: {'CLR': 5, 'PLM': 1, 'UJL': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.60, per 1000 atoms: 0.64 Number of scatterers: 8734 At special positions: 0 Unit cell: (86.52, 115.36, 128.544, 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 64 16.00 O 1598 8.00 N 1459 7.00 C 5613 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: 3.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 40.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.585A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.569A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.182A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.177A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.567A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 65 through 68 removed outlier: 3.509A pdb=" N GLN R 68 " --> pdb=" O ARG R 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 68' Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.402A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 104 through 140 removed outlier: 4.092A pdb=" N THR R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 174 removed outlier: 3.905A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 325 through 371 Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.800A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.905A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.279A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.053A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.782A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.011A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.604A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.578A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.769A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.345A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1314 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: 2.61 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2760 1.34 - 1.46: 1943 1.46 - 1.58: 4132 1.58 - 1.69: 1 1.69 - 1.81: 90 Bond restraints: 8926 Sorted by residual: bond pdb=" C8 UJL R 507 " pdb=" S1 UJL R 507 " ideal model delta sigma weight residual 1.725 1.522 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C9 UJL R 507 " pdb=" S1 UJL R 507 " ideal model delta sigma weight residual 1.730 1.536 0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C6 UJL R 507 " pdb=" C7 UJL R 507 " ideal model delta sigma weight residual 1.428 1.600 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C7 UJL R 507 " pdb=" C8 UJL R 507 " ideal model delta sigma weight residual 1.364 1.419 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" N TYR R 35 " pdb=" CA TYR R 35 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 ... (remaining 8921 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 196 106.26 - 113.20: 4949 113.20 - 120.13: 3075 120.13 - 127.07: 3790 127.07 - 134.00: 100 Bond angle restraints: 12110 Sorted by residual: angle pdb=" C8 UJL R 507 " pdb=" S1 UJL R 507 " pdb=" C9 UJL R 507 " ideal model delta sigma weight residual 91.70 107.94 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" N ARG A 242 " pdb=" CA ARG A 242 " pdb=" C ARG A 242 " ideal model delta sigma weight residual 112.89 108.28 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 109.97 115.34 -5.37 1.47e+00 4.63e-01 1.33e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 113.21 109.45 3.76 1.15e+00 7.56e-01 1.07e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.69 114.17 -4.48 1.44e+00 4.82e-01 9.69e+00 ... (remaining 12105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4992 17.94 - 35.87: 409 35.87 - 53.80: 105 53.80 - 71.74: 22 71.74 - 89.67: 7 Dihedral angle restraints: 5535 sinusoidal: 2362 harmonic: 3173 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CG ARG G 62 " pdb=" CD ARG G 62 " pdb=" NE ARG G 62 " pdb=" CZ ARG G 62 " ideal model delta sinusoidal sigma weight residual 90.00 41.43 48.57 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 5532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1070 0.040 - 0.080: 221 0.080 - 0.120: 80 0.120 - 0.159: 14 0.159 - 0.199: 1 Chirality restraints: 1386 Sorted by residual: 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 2.33 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CB VAL R 98 " pdb=" CA VAL R 98 " pdb=" CG1 VAL R 98 " pdb=" CG2 VAL R 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" C3 UJL R 507 " pdb=" C2 UJL R 507 " pdb=" C9 UJL R 507 " pdb=" O1 UJL R 507 " both_signs ideal model delta sigma weight residual False -2.45 -2.32 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1383 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 62 " 0.172 9.50e-02 1.11e+02 7.74e-02 4.24e+00 pdb=" NE ARG G 62 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 62 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 62 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 62 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO E 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " 0.112 9.50e-02 1.11e+02 5.02e-02 1.84e+00 pdb=" NE ARG B 219 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " 0.001 2.00e-02 2.50e+03 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 109 2.63 - 3.20: 7774 3.20 - 3.77: 13188 3.77 - 4.33: 19297 4.33 - 4.90: 32905 Nonbonded interactions: 73273 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.063 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.182 3.040 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.200 3.040 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.232 3.040 ... (remaining 73268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.203 8926 Z= 0.353 Angle : 0.576 16.239 12110 Z= 0.314 Chirality : 0.040 0.199 1386 Planarity : 0.004 0.077 1492 Dihedral : 14.501 89.673 3489 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.54 % Allowed : 14.72 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1076 helix: 2.56 (0.27), residues: 375 sheet: 0.50 (0.31), residues: 275 loop : -0.32 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE B 292 TYR 0.010 0.001 TYR E 190 ARG 0.013 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.926 Fit side-chains REVERT: A 8 GLU cc_start: 0.8761 (pt0) cc_final: 0.8298 (pt0) REVERT: A 275 GLU cc_start: 0.7322 (tp30) cc_final: 0.7075 (tp30) REVERT: E 18 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7770 (tpt170) outliers start: 5 outliers final: 3 residues processed: 112 average time/residue: 1.4278 time to fit residues: 170.2211 Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain R residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 82 GLN R 72 ASN R 408 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8926 Z= 0.201 Angle : 0.537 9.226 12110 Z= 0.289 Chirality : 0.042 0.138 1386 Planarity : 0.004 0.048 1492 Dihedral : 5.511 57.700 1542 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 13.43 % Favored : 84.64 % 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: 1.51 (0.26), residues: 1076 helix: 2.66 (0.27), residues: 378 sheet: 0.66 (0.30), residues: 278 loop : -0.29 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 362 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.943 Fit side-chains REVERT: B 59 TYR cc_start: 0.9003 (m-80) cc_final: 0.8793 (m-80) REVERT: B 134 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7663 (ptp90) REVERT: B 217 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6986 (pp-130) REVERT: B 270 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 333 ASP cc_start: 0.7677 (t0) cc_final: 0.7433 (t0) REVERT: G 38 MET cc_start: 0.7610 (mtp) cc_final: 0.7296 (mtp) outliers start: 18 outliers final: 4 residues processed: 109 average time/residue: 1.2703 time to fit residues: 147.5269 Evaluate side-chains 99 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 chunk 77 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8926 Z= 0.153 Angle : 0.483 6.452 12110 Z= 0.261 Chirality : 0.041 0.129 1386 Planarity : 0.003 0.038 1492 Dihedral : 5.118 57.550 1537 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 14.93 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1076 helix: 2.75 (0.27), residues: 381 sheet: 0.52 (0.31), residues: 271 loop : -0.13 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.010 0.001 PHE R 362 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.000 Fit side-chains REVERT: A 205 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7288 (mpp80) REVERT: B 134 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7649 (ptt-90) REVERT: B 153 ASP cc_start: 0.8108 (m-30) cc_final: 0.7898 (m-30) REVERT: B 270 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8017 (pp) REVERT: G 38 MET cc_start: 0.7626 (mtp) cc_final: 0.7284 (mtp) REVERT: R 227 ARG cc_start: 0.7033 (mmt90) cc_final: 0.6808 (mmt180) outliers start: 14 outliers final: 5 residues processed: 115 average time/residue: 1.1877 time to fit residues: 145.9528 Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8926 Z= 0.182 Angle : 0.488 6.464 12110 Z= 0.263 Chirality : 0.041 0.127 1386 Planarity : 0.003 0.039 1492 Dihedral : 5.145 55.767 1537 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 15.79 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1076 helix: 2.68 (0.27), residues: 383 sheet: 0.49 (0.31), residues: 266 loop : -0.19 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.010 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.870 Fit side-chains REVERT: A 205 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7279 (mpp80) REVERT: B 134 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7669 (ptt-90) REVERT: B 153 ASP cc_start: 0.8212 (m-30) cc_final: 0.7898 (m-30) REVERT: B 270 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8111 (pp) REVERT: G 38 MET cc_start: 0.7625 (mtp) cc_final: 0.7311 (mtp) outliers start: 18 outliers final: 8 residues processed: 113 average time/residue: 1.2501 time to fit residues: 150.6314 Evaluate side-chains 102 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8926 Z= 0.220 Angle : 0.509 6.968 12110 Z= 0.272 Chirality : 0.041 0.136 1386 Planarity : 0.004 0.040 1492 Dihedral : 5.299 51.958 1537 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.58 % Allowed : 16.22 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.26), residues: 1076 helix: 2.67 (0.27), residues: 381 sheet: 0.38 (0.30), residues: 271 loop : -0.21 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.873 Fit side-chains REVERT: A 205 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7573 (mtm180) REVERT: B 134 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7629 (ptt-90) REVERT: B 153 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: B 270 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8141 (pp) REVERT: E 38 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8436 (ptt180) REVERT: E 87 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6836 (mtt180) REVERT: G 38 MET cc_start: 0.7663 (mtp) cc_final: 0.7336 (mtp) REVERT: G 58 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7851 (pm20) outliers start: 24 outliers final: 11 residues processed: 113 average time/residue: 1.3068 time to fit residues: 156.7587 Evaluate side-chains 108 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.0050 chunk 98 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8926 Z= 0.151 Angle : 0.475 6.406 12110 Z= 0.255 Chirality : 0.040 0.127 1386 Planarity : 0.003 0.039 1492 Dihedral : 5.035 46.583 1537 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.61 % Allowed : 17.83 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1076 helix: 2.73 (0.27), residues: 383 sheet: 0.41 (0.31), residues: 266 loop : -0.21 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.009 0.001 PHE A 189 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.979 Fit side-chains REVERT: B 134 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7704 (ptt-90) REVERT: B 153 ASP cc_start: 0.8128 (m-30) cc_final: 0.7724 (m-30) REVERT: B 270 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8180 (pp) REVERT: G 38 MET cc_start: 0.7606 (mtp) cc_final: 0.7241 (mtp) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 1.2079 time to fit residues: 143.4968 Evaluate side-chains 105 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8926 Z= 0.194 Angle : 0.500 6.719 12110 Z= 0.267 Chirality : 0.041 0.139 1386 Planarity : 0.003 0.039 1492 Dihedral : 5.135 44.910 1537 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 16.65 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.26), residues: 1076 helix: 2.71 (0.27), residues: 383 sheet: 0.38 (0.30), residues: 266 loop : -0.25 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.011 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.933 Fit side-chains REVERT: B 134 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7640 (ptt-90) REVERT: B 153 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: B 197 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7954 (ttp-110) REVERT: B 270 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8201 (pp) REVERT: E 38 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8416 (ptt180) REVERT: E 87 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6843 (mtt180) REVERT: G 38 MET cc_start: 0.7658 (mtp) cc_final: 0.7318 (mtp) outliers start: 26 outliers final: 8 residues processed: 114 average time/residue: 1.2261 time to fit residues: 149.5969 Evaluate side-chains 109 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 0.0010 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8926 Z= 0.190 Angle : 0.501 6.954 12110 Z= 0.267 Chirality : 0.041 0.133 1386 Planarity : 0.003 0.039 1492 Dihedral : 5.142 46.431 1537 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.26 % Allowed : 17.29 % Favored : 80.45 % 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: 1.44 (0.26), residues: 1076 helix: 2.71 (0.27), residues: 383 sheet: 0.41 (0.30), residues: 263 loop : -0.27 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.010 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.928 Fit side-chains REVERT: B 134 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7643 (ptt-90) REVERT: B 153 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: B 197 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7907 (ttp-110) REVERT: B 270 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (pp) REVERT: E 38 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (ptt180) REVERT: E 87 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6886 (mtt180) REVERT: G 38 MET cc_start: 0.7658 (mtp) cc_final: 0.7310 (mtp) outliers start: 21 outliers final: 8 residues processed: 114 average time/residue: 1.3011 time to fit residues: 158.4863 Evaluate side-chains 109 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8926 Z= 0.162 Angle : 0.488 6.440 12110 Z= 0.260 Chirality : 0.040 0.138 1386 Planarity : 0.003 0.039 1492 Dihedral : 4.993 44.773 1537 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.61 % Allowed : 18.47 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.26), residues: 1076 helix: 2.77 (0.27), residues: 383 sheet: 0.39 (0.30), residues: 264 loop : -0.26 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 196 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.952 Fit side-chains REVERT: B 134 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7650 (ptt-90) REVERT: B 153 ASP cc_start: 0.8153 (m-30) cc_final: 0.7746 (m-30) REVERT: B 197 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7933 (ttp-110) REVERT: B 270 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 87 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6903 (mtt180) REVERT: G 38 MET cc_start: 0.7650 (mtp) cc_final: 0.7300 (mtp) outliers start: 15 outliers final: 7 residues processed: 114 average time/residue: 1.1226 time to fit residues: 137.9208 Evaluate side-chains 107 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.0170 chunk 105 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8926 Z= 0.228 Angle : 0.529 7.366 12110 Z= 0.279 Chirality : 0.041 0.140 1386 Planarity : 0.004 0.039 1492 Dihedral : 5.254 48.734 1537 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.61 % Allowed : 18.47 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1076 helix: 2.69 (0.27), residues: 382 sheet: 0.31 (0.29), residues: 280 loop : -0.30 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.055 Fit side-chains REVERT: A 263 SER cc_start: 0.8804 (p) cc_final: 0.8551 (m) REVERT: B 134 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7736 (ptp90) REVERT: B 153 ASP cc_start: 0.8222 (m-30) cc_final: 0.7898 (m-30) REVERT: B 197 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7969 (ttp-110) REVERT: B 270 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 87 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6794 (mtt180) REVERT: E 194 ASN cc_start: 0.8929 (m110) cc_final: 0.8715 (m110) REVERT: G 38 MET cc_start: 0.7675 (mtp) cc_final: 0.7321 (mtp) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 1.0760 time to fit residues: 128.8842 Evaluate side-chains 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115539 restraints weight = 9477.806| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.78 r_work: 0.3147 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8926 Z= 0.186 Angle : 0.512 7.225 12110 Z= 0.271 Chirality : 0.041 0.139 1386 Planarity : 0.003 0.039 1492 Dihedral : 5.154 47.552 1537 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.18 % Allowed : 19.12 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1076 helix: 2.70 (0.27), residues: 383 sheet: 0.40 (0.30), residues: 274 loop : -0.35 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.010 0.001 PHE A 196 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.14 seconds wall clock time: 58 minutes 0.69 seconds (3480.69 seconds total)