Starting phenix.real_space_refine on Sun May 11 21:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.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/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.map" model { file = "/net/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id8_35359/05_2025/8id8_35359.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= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5518 2.51 5 N 1468 2.21 5 O 1588 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2554 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2170 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "S" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.59 Number of scatterers: 8635 At special positions: 0 Unit cell: (105.456, 125.736, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 1 9.00 O 1588 8.00 N 1468 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.05 Conformation dependent library (CDL) restraints added in 973.8 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 35.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.463A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.740A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.640A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.617A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.213A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.710A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.885A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 176 removed outlier: 3.768A pdb=" N ALA R 156 " --> pdb=" O ARG R 152 " (cutoff:3.500A) Proline residue: R 172 - end of helix removed outlier: 3.723A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.820A pdb=" N SER R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 242 removed outlier: 3.661A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 277 removed outlier: 3.587A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 294 removed outlier: 3.617A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 321 removed outlier: 3.502A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 8 through 23 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.618A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.684A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.313A 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: 3.613A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.521A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AB4, first strand: chain 'S' and resid 195 through 196 removed outlier: 5.829A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 227 through 228 419 hydrogen bonds defined for protein. 1170 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: 2.45 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2126 1.33 - 1.45: 1761 1.45 - 1.57: 4829 1.57 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 8806 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.595 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " ideal model delta sigma weight residual 1.501 1.606 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1 YN9 R 401 " pdb=" C2 YN9 R 401 " ideal model delta sigma weight residual 1.400 1.486 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C9 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 1.353 1.432 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C5 YN9 R 401 " pdb=" C6 YN9 R 401 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11708 1.90 - 3.81: 218 3.81 - 5.71: 23 5.71 - 7.61: 5 7.61 - 9.52: 4 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N TYR S 229 " pdb=" CA TYR S 229 " pdb=" C TYR S 229 " ideal model delta sigma weight residual 109.40 116.29 -6.89 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU R 173 " pdb=" CA LEU R 173 " pdb=" C LEU R 173 " ideal model delta sigma weight residual 111.82 116.17 -4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N ASP R 30 " pdb=" CA ASP R 30 " pdb=" C ASP R 30 " ideal model delta sigma weight residual 109.24 115.20 -5.96 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 107.97 117.49 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N GLU Y 58 " pdb=" CA GLU Y 58 " pdb=" C GLU Y 58 " ideal model delta sigma weight residual 111.36 114.57 -3.21 1.09e+00 8.42e-01 8.69e+00 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 4811 20.31 - 40.62: 337 40.62 - 60.93: 41 60.93 - 81.24: 6 81.24 - 101.55: 1 Dihedral angle restraints: 5196 sinusoidal: 1904 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 54.40 38.60 1 1.00e+01 1.00e-02 2.10e+01 dihedral pdb=" CA GLN S 143 " pdb=" C GLN S 143 " pdb=" N ALA S 144 " pdb=" CA ALA S 144 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 959 0.040 - 0.080: 323 0.080 - 0.119: 103 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA THR Y 52 " pdb=" N THR Y 52 " pdb=" C THR Y 52 " pdb=" CB THR Y 52 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1400 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 282 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 107 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 54 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL Y 54 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL Y 54 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO Y 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.80: 2119 2.80 - 3.50: 11287 3.50 - 4.20: 19674 4.20 - 4.90: 36008 Nonbonded interactions: 69091 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" CE1 PHE A 274 " model vdw 1.393 3.340 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 238 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" CD1 PHE A 274 " model vdw 2.063 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR R 165 " pdb=" OD1 ASN R 215 " model vdw 2.155 3.040 ... (remaining 69086 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: 0.540 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.670 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: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.114 8808 Z= 0.227 Angle : 0.639 9.517 11962 Z= 0.358 Chirality : 0.044 0.199 1403 Planarity : 0.004 0.067 1500 Dihedral : 13.406 101.546 3058 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.33 % Allowed : 0.78 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1115 helix: 1.13 (0.29), residues: 353 sheet: -0.82 (0.29), residues: 284 loop : -0.94 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE B 234 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.14252 ( 419) hydrogen bonds : angle 6.19095 ( 1170) SS BOND : bond 0.00652 ( 2) SS BOND : angle 2.21534 ( 4) covalent geometry : bond 0.00455 ( 8806) covalent geometry : angle 0.63791 (11958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8191 (mttm) cc_final: 0.7982 (mttp) REVERT: A 208 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7764 (ttm110) REVERT: A 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7431 (m-30) REVERT: B 325 MET cc_start: 0.7529 (mmt) cc_final: 0.7132 (mmm) REVERT: R 47 LEU cc_start: 0.7519 (mt) cc_final: 0.7213 (mt) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 1.1950 time to fit residues: 196.5552 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 204 GLN B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141691 restraints weight = 9069.803| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.06 r_work: 0.3369 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8808 Z= 0.149 Angle : 0.575 7.931 11962 Z= 0.303 Chirality : 0.043 0.150 1403 Planarity : 0.005 0.061 1500 Dihedral : 5.333 56.420 1231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 9.97 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1115 helix: 1.46 (0.29), residues: 358 sheet: -0.74 (0.30), residues: 279 loop : -0.93 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.001 PHE R 177 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 24 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 419) hydrogen bonds : angle 4.75659 ( 1170) SS BOND : bond 0.00666 ( 2) SS BOND : angle 2.28028 ( 4) covalent geometry : bond 0.00348 ( 8806) covalent geometry : angle 0.57325 (11958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.879 Fit side-chains REVERT: A 309 ASP cc_start: 0.7448 (m-30) cc_final: 0.7145 (m-30) REVERT: B 31 SER cc_start: 0.7968 (t) cc_final: 0.7672 (m) REVERT: R 47 LEU cc_start: 0.7037 (mt) cc_final: 0.6751 (mt) REVERT: S 193 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7800 (ttp) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 1.1262 time to fit residues: 163.9643 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.171543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130925 restraints weight = 9462.909| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.63 r_work: 0.3260 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8808 Z= 0.166 Angle : 0.570 7.190 11962 Z= 0.303 Chirality : 0.043 0.140 1403 Planarity : 0.004 0.065 1500 Dihedral : 5.290 50.747 1229 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 13.07 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1115 helix: 1.56 (0.28), residues: 355 sheet: -0.68 (0.29), residues: 280 loop : -0.92 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.002 PHE B 199 TYR 0.015 0.002 TYR B 105 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 419) hydrogen bonds : angle 4.61866 ( 1170) SS BOND : bond 0.00560 ( 2) SS BOND : angle 2.02857 ( 4) covalent geometry : bond 0.00394 ( 8806) covalent geometry : angle 0.56885 (11958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7451 (m-30) cc_final: 0.7160 (m-30) REVERT: B 31 SER cc_start: 0.7925 (t) cc_final: 0.7648 (m) REVERT: B 325 MET cc_start: 0.8346 (mmt) cc_final: 0.7851 (mmm) REVERT: R 68 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5693 (ttp-170) REVERT: R 214 LEU cc_start: 0.8465 (tp) cc_final: 0.8168 (tp) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 1.1091 time to fit residues: 166.3178 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133255 restraints weight = 9379.630| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.59 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8808 Z= 0.146 Angle : 0.544 6.929 11962 Z= 0.290 Chirality : 0.042 0.150 1403 Planarity : 0.004 0.064 1500 Dihedral : 5.189 47.091 1229 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.88 % Allowed : 14.51 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1115 helix: 1.67 (0.28), residues: 355 sheet: -0.55 (0.30), residues: 278 loop : -0.88 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 419) hydrogen bonds : angle 4.51531 ( 1170) SS BOND : bond 0.00508 ( 2) SS BOND : angle 1.61075 ( 4) covalent geometry : bond 0.00344 ( 8806) covalent geometry : angle 0.54319 (11958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7385 (m-30) cc_final: 0.7092 (m-30) REVERT: B 23 LYS cc_start: 0.7168 (tppt) cc_final: 0.6937 (mmpt) REVERT: B 31 SER cc_start: 0.7865 (t) cc_final: 0.7542 (m) REVERT: B 217 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7828 (ptm) REVERT: B 226 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 325 MET cc_start: 0.8335 (mmt) cc_final: 0.7846 (mmm) REVERT: R 214 LEU cc_start: 0.8425 (tp) cc_final: 0.8075 (tp) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 1.1120 time to fit residues: 164.7609 Evaluate side-chains 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 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 32 GLN B 88 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138902 restraints weight = 9220.837| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.37 r_work: 0.3274 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8808 Z= 0.142 Angle : 0.555 10.506 11962 Z= 0.290 Chirality : 0.042 0.152 1403 Planarity : 0.004 0.063 1500 Dihedral : 5.142 49.512 1229 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.65 % Allowed : 14.51 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1115 helix: 1.65 (0.28), residues: 361 sheet: -0.55 (0.30), residues: 280 loop : -0.83 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.010 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 419) hydrogen bonds : angle 4.45192 ( 1170) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.44233 ( 4) covalent geometry : bond 0.00331 ( 8806) covalent geometry : angle 0.55431 (11958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 295 THR cc_start: 0.7861 (t) cc_final: 0.7573 (t) REVERT: A 309 ASP cc_start: 0.7431 (m-30) cc_final: 0.7137 (m-30) REVERT: A 345 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7355 (mtmt) REVERT: B 31 SER cc_start: 0.7794 (t) cc_final: 0.7447 (m) REVERT: B 217 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7807 (ptm) REVERT: B 226 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: B 325 MET cc_start: 0.8317 (mmt) cc_final: 0.7850 (mmm) REVERT: R 68 ARG cc_start: 0.6263 (ttp-170) cc_final: 0.5979 (tmt-80) REVERT: R 214 LEU cc_start: 0.8497 (tp) cc_final: 0.8132 (tp) REVERT: S 214 THR cc_start: 0.8751 (t) cc_final: 0.8521 (m) outliers start: 33 outliers final: 17 residues processed: 151 average time/residue: 1.0438 time to fit residues: 169.5581 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.183037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143311 restraints weight = 9014.980| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.08 r_work: 0.3327 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8808 Z= 0.113 Angle : 0.518 8.435 11962 Z= 0.274 Chirality : 0.042 0.187 1403 Planarity : 0.004 0.058 1500 Dihedral : 4.961 49.812 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.88 % Allowed : 15.84 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1115 helix: 1.87 (0.28), residues: 360 sheet: -0.41 (0.30), residues: 277 loop : -0.82 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG Y 27 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 419) hydrogen bonds : angle 4.34621 ( 1170) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.13143 ( 4) covalent geometry : bond 0.00248 ( 8806) covalent geometry : angle 0.51721 (11958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 295 THR cc_start: 0.7787 (t) cc_final: 0.7504 (t) REVERT: A 309 ASP cc_start: 0.7396 (m-30) cc_final: 0.7095 (m-30) REVERT: B 23 LYS cc_start: 0.7200 (tppt) cc_final: 0.6935 (mmpt) REVERT: B 31 SER cc_start: 0.7690 (t) cc_final: 0.7385 (m) REVERT: B 226 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: B 325 MET cc_start: 0.8354 (mmt) cc_final: 0.7839 (mmm) REVERT: R 68 ARG cc_start: 0.6104 (ttp-170) cc_final: 0.5900 (tmt-80) REVERT: R 214 LEU cc_start: 0.8490 (tp) cc_final: 0.8101 (tp) REVERT: S 214 THR cc_start: 0.8737 (t) cc_final: 0.8520 (m) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 1.0508 time to fit residues: 165.9570 Evaluate side-chains 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128908 restraints weight = 9376.312| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.41 r_work: 0.3235 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8808 Z= 0.244 Angle : 0.643 9.167 11962 Z= 0.342 Chirality : 0.046 0.178 1403 Planarity : 0.005 0.069 1500 Dihedral : 5.473 57.545 1229 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.10 % Allowed : 16.83 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1115 helix: 1.52 (0.28), residues: 360 sheet: -0.52 (0.29), residues: 294 loop : -0.96 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 36 HIS 0.006 0.002 HIS A 213 PHE 0.015 0.002 PHE B 199 TYR 0.013 0.002 TYR R 165 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 419) hydrogen bonds : angle 4.55811 ( 1170) SS BOND : bond 0.00683 ( 2) SS BOND : angle 1.89173 ( 4) covalent geometry : bond 0.00594 ( 8806) covalent geometry : angle 0.64179 (11958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7558 (m-30) cc_final: 0.7275 (m-30) REVERT: B 42 ARG cc_start: 0.6330 (ttt180) cc_final: 0.6012 (ttt180) REVERT: B 226 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: R 68 ARG cc_start: 0.6637 (ttp-170) cc_final: 0.6331 (tmt-80) REVERT: R 214 LEU cc_start: 0.8516 (tp) cc_final: 0.8180 (tp) REVERT: S 22 CYS cc_start: 0.8016 (t) cc_final: 0.7632 (p) REVERT: S 87 ARG cc_start: 0.6993 (mtp-110) cc_final: 0.6736 (mtm110) outliers start: 28 outliers final: 16 residues processed: 137 average time/residue: 1.0462 time to fit residues: 154.0121 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142533 restraints weight = 9226.238| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.18 r_work: 0.3353 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 0.033 8808 Z= 0.114 Angle : 0.540 8.752 11962 Z= 0.284 Chirality : 0.042 0.209 1403 Planarity : 0.004 0.060 1500 Dihedral : 5.074 55.380 1229 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.99 % Allowed : 17.50 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1115 helix: 1.79 (0.28), residues: 361 sheet: -0.37 (0.30), residues: 282 loop : -0.82 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 419) hydrogen bonds : angle 4.35753 ( 1170) SS BOND : bond 0.00398 ( 2) SS BOND : angle 1.09284 ( 4) covalent geometry : bond 0.00250 ( 8806) covalent geometry : angle 0.54000 (11958) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7486 (m-30) cc_final: 0.7189 (m-30) REVERT: B 23 LYS cc_start: 0.7251 (tppt) cc_final: 0.6976 (mmpt) REVERT: B 42 ARG cc_start: 0.6279 (ttt180) cc_final: 0.5952 (ttt180) REVERT: B 129 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6966 (ttp80) REVERT: B 226 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 325 MET cc_start: 0.8410 (mmt) cc_final: 0.7903 (mmm) REVERT: R 68 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6303 (tmt-80) REVERT: R 214 LEU cc_start: 0.8494 (tp) cc_final: 0.8105 (tp) REVERT: S 214 THR cc_start: 0.8759 (t) cc_final: 0.8529 (m) REVERT: Y 21 MET cc_start: 0.6980 (tmt) cc_final: 0.6235 (ttp) outliers start: 27 outliers final: 15 residues processed: 136 average time/residue: 1.0743 time to fit residues: 157.1557 Evaluate side-chains 134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.181052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141310 restraints weight = 9150.229| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.17 r_work: 0.3339 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8808 Z= 0.133 Angle : 0.551 8.410 11962 Z= 0.292 Chirality : 0.042 0.188 1403 Planarity : 0.004 0.060 1500 Dihedral : 5.050 54.805 1229 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 18.05 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1115 helix: 1.89 (0.28), residues: 361 sheet: -0.40 (0.30), residues: 284 loop : -0.74 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 419) hydrogen bonds : angle 4.30985 ( 1170) SS BOND : bond 0.00470 ( 2) SS BOND : angle 1.21014 ( 4) covalent geometry : bond 0.00308 ( 8806) covalent geometry : angle 0.55082 (11958) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7491 (m-30) cc_final: 0.7197 (m-30) REVERT: B 23 LYS cc_start: 0.7275 (tppt) cc_final: 0.6980 (mmpt) REVERT: B 42 ARG cc_start: 0.6239 (ttt180) cc_final: 0.5877 (ttt180) REVERT: B 129 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6984 (ttp80) REVERT: B 226 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 325 MET cc_start: 0.8388 (mmt) cc_final: 0.7920 (mmm) REVERT: R 68 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6441 (tmt-80) REVERT: R 214 LEU cc_start: 0.8454 (tp) cc_final: 0.8057 (tp) REVERT: S 214 THR cc_start: 0.8763 (t) cc_final: 0.8519 (m) REVERT: Y 21 MET cc_start: 0.7033 (tmt) cc_final: 0.6388 (ttp) outliers start: 25 outliers final: 16 residues processed: 135 average time/residue: 1.0960 time to fit residues: 158.9897 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.182752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.143295 restraints weight = 9116.475| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.16 r_work: 0.3269 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8808 Z= 0.117 Angle : 0.539 8.458 11962 Z= 0.285 Chirality : 0.042 0.179 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.952 53.522 1229 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 19.27 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1115 helix: 2.06 (0.28), residues: 360 sheet: -0.35 (0.30), residues: 277 loop : -0.70 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 419) hydrogen bonds : angle 4.24872 ( 1170) SS BOND : bond 0.00417 ( 2) SS BOND : angle 1.03307 ( 4) covalent geometry : bond 0.00264 ( 8806) covalent geometry : angle 0.53894 (11958) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7380 (m-30) cc_final: 0.7078 (m-30) REVERT: B 23 LYS cc_start: 0.7078 (tppt) cc_final: 0.6818 (mmpt) REVERT: B 42 ARG cc_start: 0.6417 (ttt180) cc_final: 0.6064 (ttt180) REVERT: B 129 ARG cc_start: 0.7291 (mtp85) cc_final: 0.6874 (ttp80) REVERT: B 130 GLU cc_start: 0.7861 (mp0) cc_final: 0.7397 (mp0) REVERT: B 217 MET cc_start: 0.7740 (tmm) cc_final: 0.6963 (ppp) REVERT: B 226 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 325 MET cc_start: 0.8373 (mmt) cc_final: 0.7872 (mmm) REVERT: R 68 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6284 (tmt-80) REVERT: R 214 LEU cc_start: 0.8389 (tp) cc_final: 0.7981 (tp) REVERT: S 214 THR cc_start: 0.8719 (t) cc_final: 0.8476 (m) REVERT: Y 21 MET cc_start: 0.7012 (tmt) cc_final: 0.6228 (ttp) outliers start: 18 outliers final: 15 residues processed: 126 average time/residue: 1.1690 time to fit residues: 157.5200 Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 232 GLN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.184608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145103 restraints weight = 9082.510| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.16 r_work: 0.3387 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8808 Z= 0.106 Angle : 0.521 8.191 11962 Z= 0.275 Chirality : 0.041 0.180 1403 Planarity : 0.004 0.053 1500 Dihedral : 4.799 52.257 1229 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.99 % Allowed : 19.82 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1115 helix: 2.25 (0.28), residues: 359 sheet: -0.33 (0.30), residues: 283 loop : -0.63 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR B 124 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 419) hydrogen bonds : angle 4.16701 ( 1170) SS BOND : bond 0.00365 ( 2) SS BOND : angle 0.88438 ( 4) covalent geometry : bond 0.00230 ( 8806) covalent geometry : angle 0.52080 (11958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6835.67 seconds wall clock time: 118 minutes 13.07 seconds (7093.07 seconds total)