Starting phenix.real_space_refine on Fri Jul 19 20:21:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/07_2024/8w8b_37351.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/07_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_37351/07_2024/8w8b_37351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/07_2024/8w8b_37351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/07_2024/8w8b_37351.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8b_37351/07_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.45, per 1000 atoms: 0.62 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 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: 0.98 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: 2.58 Time building geometry restraints manager: 3.54 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 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.182 2.440 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.200 2.440 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.232 2.440 ... (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 ========== 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: 1.250 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- 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 : 0.946 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: 1.3153 time to fit residues: 156.7030 Evaluate side-chains 101 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8926 Z= 0.225 Angle : 0.539 9.747 12110 Z= 0.287 Chirality : 0.042 0.135 1386 Planarity : 0.004 0.049 1492 Dihedral : 5.622 56.897 1542 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.58 % Allowed : 13.10 % Favored : 84.32 % 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: 1.43 (0.26), residues: 1076 helix: 2.62 (0.27), residues: 378 sheet: 0.56 (0.30), residues: 277 loop : -0.31 (0.30), residues: 421 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 0.016 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 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.969 Fit side-chains REVERT: A 10 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8148 (mttt) REVERT: B 217 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6993 (pp-130) REVERT: B 262 MET cc_start: 0.8320 (ttm) cc_final: 0.8109 (mtp) REVERT: B 270 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7979 (pp) REVERT: B 333 ASP cc_start: 0.7742 (t0) cc_final: 0.7482 (t0) REVERT: G 38 MET cc_start: 0.7647 (mtp) cc_final: 0.7333 (mtp) outliers start: 24 outliers final: 6 residues processed: 111 average time/residue: 1.2434 time to fit residues: 147.3625 Evaluate side-chains 97 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS 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 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 108 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: 5.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8926 Z= 0.234 Angle : 0.521 9.352 12110 Z= 0.278 Chirality : 0.042 0.136 1386 Planarity : 0.004 0.050 1492 Dihedral : 5.479 55.248 1537 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 14.72 % Favored : 82.71 % 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: 1.38 (0.26), residues: 1076 helix: 2.61 (0.27), residues: 379 sheet: 0.51 (0.30), residues: 277 loop : -0.36 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE E 29 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 *********************** 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 121 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.922 Fit side-chains REVERT: A 10 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (mttt) REVERT: A 205 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7355 (mpp80) REVERT: B 146 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (tp) REVERT: B 270 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (pp) REVERT: B 333 ASP cc_start: 0.7643 (t0) cc_final: 0.7392 (t0) REVERT: E 87 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6920 (mtt180) REVERT: G 38 MET cc_start: 0.7645 (mtp) cc_final: 0.7319 (mtp) REVERT: R 227 ARG cc_start: 0.7061 (mmt90) cc_final: 0.6726 (mmt180) outliers start: 24 outliers final: 7 residues processed: 114 average time/residue: 1.3164 time to fit residues: 159.3625 Evaluate side-chains 99 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS 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 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 108 THR 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: 0.8980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 340 ASN ** 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: 0.8348 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8926 Z= 0.306 Angle : 0.558 10.588 12110 Z= 0.294 Chirality : 0.043 0.137 1386 Planarity : 0.004 0.048 1492 Dihedral : 5.864 54.174 1537 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.01 % Allowed : 15.90 % Favored : 81.10 % 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: 1.22 (0.26), residues: 1076 helix: 2.48 (0.27), residues: 379 sheet: 0.41 (0.30), residues: 278 loop : -0.45 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.002 PHE A 196 TYR 0.015 0.002 TYR E 190 ARG 0.006 0.000 ARG B 134 *********************** 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 125 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: B 161 SER cc_start: 0.9028 (p) cc_final: 0.8533 (t) REVERT: B 270 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8167 (pp) REVERT: B 333 ASP cc_start: 0.7659 (t0) cc_final: 0.7405 (t0) REVERT: E 87 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7045 (mtt180) REVERT: E 194 ASN cc_start: 0.9023 (m110) cc_final: 0.8794 (m110) outliers start: 28 outliers final: 13 residues processed: 118 average time/residue: 1.2193 time to fit residues: 153.9147 Evaluate side-chains 107 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU 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 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 335 MET 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: 0.8980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8926 Z= 0.175 Angle : 0.493 8.805 12110 Z= 0.261 Chirality : 0.040 0.129 1386 Planarity : 0.003 0.040 1492 Dihedral : 5.522 51.351 1537 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.47 % Allowed : 16.54 % Favored : 80.99 % 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: 1.38 (0.26), residues: 1076 helix: 2.65 (0.27), residues: 381 sheet: 0.40 (0.30), residues: 278 loop : -0.33 (0.31), residues: 417 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 0.011 0.001 PHE E 29 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG B 134 *********************** 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 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.951 Fit side-chains REVERT: B 270 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 87 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (mtt180) REVERT: G 38 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7349 (mtp) outliers start: 23 outliers final: 10 residues processed: 109 average time/residue: 1.2356 time to fit residues: 143.8528 Evaluate side-chains 100 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 335 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 0.0170 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8926 Z= 0.150 Angle : 0.478 8.325 12110 Z= 0.253 Chirality : 0.040 0.126 1386 Planarity : 0.003 0.040 1492 Dihedral : 5.232 49.343 1537 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 18.26 % 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: 1.47 (0.26), residues: 1076 helix: 2.73 (0.27), residues: 382 sheet: 0.38 (0.30), residues: 279 loop : -0.23 (0.31), residues: 415 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 0.010 0.001 PHE E 29 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 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.139 Fit side-chains REVERT: B 79 LEU cc_start: 0.8890 (pt) cc_final: 0.8661 (pt) REVERT: B 134 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7508 (ptt-90) REVERT: B 197 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7890 (ttp-110) REVERT: B 270 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8231 (pp) REVERT: B 321 THR cc_start: 0.8704 (p) cc_final: 0.8361 (p) REVERT: G 38 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7351 (mtp) REVERT: G 58 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7441 (pm20) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 1.1308 time to fit residues: 135.8313 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE 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 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 38 MET 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: 0.9980 chunk 58 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.002 0.027 8926 Z= 0.133 Angle : 0.465 7.696 12110 Z= 0.246 Chirality : 0.040 0.124 1386 Planarity : 0.003 0.037 1492 Dihedral : 4.975 50.567 1537 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.72 % Allowed : 19.33 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1076 helix: 2.80 (0.27), residues: 382 sheet: 0.47 (0.30), residues: 275 loop : -0.21 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE E 29 TYR 0.013 0.001 TYR E 190 ARG 0.007 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 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.951 Fit side-chains REVERT: B 134 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7566 (ptt-90) REVERT: B 153 ASP cc_start: 0.8255 (m-30) cc_final: 0.7986 (m-30) REVERT: B 197 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7868 (ttp-110) REVERT: B 270 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 204 SER cc_start: 0.8726 (p) cc_final: 0.8454 (t) REVERT: G 38 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7348 (mtp) REVERT: G 58 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7251 (pm20) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 1.1436 time to fit residues: 135.0356 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN 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 318 LEU 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 38 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 108 THR 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: 0.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8926 Z= 0.158 Angle : 0.479 6.391 12110 Z= 0.254 Chirality : 0.040 0.124 1386 Planarity : 0.003 0.037 1492 Dihedral : 5.024 52.140 1537 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 19.55 % Favored : 78.41 % 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: 1.56 (0.26), residues: 1076 helix: 2.78 (0.27), residues: 382 sheet: 0.43 (0.29), residues: 281 loop : -0.16 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE E 29 TYR 0.013 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 115 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.976 Fit side-chains REVERT: B 134 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7608 (ptt-90) REVERT: B 153 ASP cc_start: 0.8193 (m-30) cc_final: 0.7946 (m-30) REVERT: B 197 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (ttp-110) REVERT: B 270 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 204 SER cc_start: 0.8721 (p) cc_final: 0.8469 (t) REVERT: G 38 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7389 (mtp) REVERT: G 58 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7245 (pm20) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 1.1660 time to fit residues: 135.1023 Evaluate side-chains 105 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN 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 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1964 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= 0.163 Angle : 0.488 6.772 12110 Z= 0.258 Chirality : 0.040 0.124 1386 Planarity : 0.003 0.037 1492 Dihedral : 5.064 53.014 1537 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.36 % Allowed : 19.23 % Favored : 78.41 % 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: 1.59 (0.26), residues: 1076 helix: 2.78 (0.27), residues: 383 sheet: 0.51 (0.30), residues: 278 loop : -0.17 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE E 29 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 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.969 Fit side-chains REVERT: B 134 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7642 (ptt-90) REVERT: B 153 ASP cc_start: 0.8239 (m-30) cc_final: 0.8000 (m-30) REVERT: B 197 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7903 (ttp-110) REVERT: B 270 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 204 SER cc_start: 0.8721 (p) cc_final: 0.8459 (t) REVERT: G 38 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7388 (mtp) outliers start: 22 outliers final: 9 residues processed: 108 average time/residue: 1.1557 time to fit residues: 134.1470 Evaluate side-chains 108 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8926 Z= 0.144 Angle : 0.485 6.891 12110 Z= 0.256 Chirality : 0.040 0.123 1386 Planarity : 0.003 0.037 1492 Dihedral : 4.977 53.821 1537 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.40 % Allowed : 20.19 % Favored : 78.41 % 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: 1.62 (0.26), residues: 1076 helix: 2.81 (0.27), residues: 383 sheet: 0.45 (0.30), residues: 284 loop : -0.11 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS B 142 PHE 0.009 0.001 PHE E 29 TYR 0.012 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 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.034 Fit side-chains REVERT: B 134 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7693 (ptt-90) REVERT: B 153 ASP cc_start: 0.8179 (m-30) cc_final: 0.7939 (m-30) REVERT: B 161 SER cc_start: 0.8897 (p) cc_final: 0.8374 (t) REVERT: B 197 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7896 (ttp-110) REVERT: B 270 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8281 (pp) REVERT: E 43 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7913 (mmmt) REVERT: E 204 SER cc_start: 0.8698 (p) cc_final: 0.8450 (t) REVERT: G 38 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7401 (mtp) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 1.1892 time to fit residues: 136.2363 Evaluate side-chains 106 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 109 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114754 restraints weight = 9511.575| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.77 r_work: 0.3107 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8926 Z= 0.258 Angle : 0.554 8.531 12110 Z= 0.289 Chirality : 0.042 0.185 1386 Planarity : 0.004 0.041 1492 Dihedral : 5.481 55.652 1537 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.61 % Allowed : 20.19 % Favored : 78.20 % 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: 1.42 (0.26), residues: 1076 helix: 2.65 (0.27), residues: 380 sheet: 0.49 (0.30), residues: 278 loop : -0.31 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.002 PHE B 234 TYR 0.015 0.002 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: 3227.73 seconds wall clock time: 57 minutes 16.64 seconds (3436.64 seconds total)