Starting phenix.real_space_refine on Fri Oct 10 15:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686.map" model { file = "/net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wog_37686/10_2025/8wog_37686_trim.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.110 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 52 5.16 5 C 4721 2.51 5 N 1242 2.21 5 O 1367 1.98 5 H 2 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7384 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2538 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1834 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7384 At special positions: 0 Unit cell: (70.55, 102, 138.55, 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 52 16.00 O 1367 8.00 N 1242 7.00 C 4721 6.00 H 2 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS A 268 " distance=2.04 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " 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: 0.64 Conformation dependent library (CDL) restraints added in 323.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.574A pdb=" N ALA A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 46 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.214A pdb=" N LEU A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 126 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.933A pdb=" N LYS A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.591A pdb=" N LEU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 228 through 259 removed outlier: 3.617A pdb=" N VAL A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.744A pdb=" N ASN A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 286 Proline residue: A 282 - end of helix removed outlier: 3.846A pdb=" N PHE A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.751A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.571A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.678A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.563A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 9 through 22 Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 removed outlier: 3.636A pdb=" N ASP E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 48' Processing helix chain 'E' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.623A pdb=" N THR A 166 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 190 removed outlier: 6.248A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 201 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU C 38 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.792A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 62 removed outlier: 3.599A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP D 83 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS D 89 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 7.058A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.769A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS D 166 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.969A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.520A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.795A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1071 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: 1.20 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 2 1.04 - 1.23: 60 1.23 - 1.43: 3119 1.43 - 1.62: 4278 1.62 - 1.82: 74 Bond restraints: 7533 Sorted by residual: bond pdb=" CA ILE A 278 " pdb=" C ILE A 278 " ideal model delta sigma weight residual 1.522 1.435 0.086 1.38e-02 5.25e+03 3.92e+01 bond pdb=" CA SER A 275 " pdb=" CB SER A 275 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.03e+01 bond pdb=" CA VAL A 279 " pdb=" C VAL A 279 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.46e-02 4.69e+03 1.99e+01 bond pdb=" CA TYR A 277 " pdb=" CB TYR A 277 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.55e-02 4.16e+03 1.99e+01 bond pdb=" C TYR A 277 " pdb=" O TYR A 277 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.92e+01 ... (remaining 7528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10068 1.88 - 3.75: 117 3.75 - 5.63: 9 5.63 - 7.50: 6 7.50 - 9.38: 1 Bond angle restraints: 10201 Sorted by residual: angle pdb=" C VAL A 279 " pdb=" CA VAL A 279 " pdb=" CB VAL A 279 " ideal model delta sigma weight residual 112.26 102.88 9.38 1.62e+00 3.81e-01 3.35e+01 angle pdb=" C SER A 275 " pdb=" N PHE A 276 " pdb=" CA PHE A 276 " ideal model delta sigma weight residual 120.29 113.88 6.41 1.42e+00 4.96e-01 2.04e+01 angle pdb=" C VAL A 272 " pdb=" CA VAL A 272 " pdb=" CB VAL A 272 " ideal model delta sigma weight residual 111.97 106.22 5.75 1.28e+00 6.10e-01 2.02e+01 angle pdb=" C ILE A 278 " pdb=" CA ILE A 278 " pdb=" CB ILE A 278 " ideal model delta sigma weight residual 112.16 105.88 6.28 1.55e+00 4.16e-01 1.64e+01 angle pdb=" CA TYR A 277 " pdb=" C TYR A 277 " pdb=" N ILE A 278 " ideal model delta sigma weight residual 117.07 121.45 -4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 10196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3886 17.98 - 35.95: 458 35.95 - 53.93: 113 53.93 - 71.90: 30 71.90 - 89.88: 3 Dihedral angle restraints: 4490 sinusoidal: 1768 harmonic: 2722 Sorted by residual: dihedral pdb=" CA ASP D 38 " pdb=" CB ASP D 38 " pdb=" CG ASP D 38 " pdb=" OD1 ASP D 38 " ideal model delta sinusoidal sigma weight residual -30.00 -89.12 59.12 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU D 172 " pdb=" CG GLU D 172 " pdb=" CD GLU D 172 " pdb=" OE1 GLU D 172 " ideal model delta sinusoidal sigma weight residual 0.00 89.88 -89.88 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 167 " pdb=" CB ASP A 167 " pdb=" CG ASP A 167 " pdb=" OD1 ASP A 167 " ideal model delta sinusoidal sigma weight residual -30.00 -85.44 55.44 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 4487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 935 0.047 - 0.095: 175 0.095 - 0.142: 53 0.142 - 0.190: 2 0.190 - 0.237: 1 Chirality restraints: 1166 Sorted by residual: chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1163 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 198 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 199 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 273 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C ILE A 273 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 273 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 274 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 21 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG C 21 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG C 21 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 22 " -0.008 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.40: 22 2.40 - 2.95: 3449 2.95 - 3.50: 8345 3.50 - 4.05: 12786 4.05 - 4.60: 19851 Nonbonded interactions: 44453 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 1.844 2.800 nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 1.963 2.800 nonbonded pdb=" O ARG D 68 " pdb=" OG SER D 84 " model vdw 2.040 2.800 nonbonded pdb=" OG SER D 74 " pdb=" OD2 ASP D 76 " model vdw 2.115 2.800 nonbonded pdb=" NH2 ARG A 217 " pdb=" OD1 ASP C 341 " model vdw 2.141 2.950 ... (remaining 44448 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: 2.880 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: 0.080 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 : 0.004 0.086 7533 Z= 0.234 Angle : 0.498 9.379 10204 Z= 0.308 Chirality : 0.041 0.237 1166 Planarity : 0.003 0.043 1288 Dihedral : 16.624 89.877 2720 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.96 % Allowed : 23.55 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.29), residues: 916 helix: 1.72 (0.27), residues: 390 sheet: 0.16 (0.39), residues: 173 loop : -1.17 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 205 TYR 0.015 0.001 TYR A 277 PHE 0.009 0.001 PHE C 189 TRP 0.017 0.001 TRP D 82 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7531) covalent geometry : angle 0.49763 (10200) SS BOND : bond 0.00443 ( 2) SS BOND : angle 0.99260 ( 4) hydrogen bonds : bond 0.15317 ( 372) hydrogen bonds : angle 5.74055 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6618 (mmp-170) REVERT: A 209 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7806 (mttm) outliers start: 24 outliers final: 17 residues processed: 122 average time/residue: 0.6145 time to fit residues: 78.8698 Evaluate side-chains 116 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 333 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 313 ASN C 241 ASN C 255 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 340 ASN E 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106452 restraints weight = 8229.438| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.69 r_work: 0.3057 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7533 Z= 0.124 Angle : 0.429 4.988 10204 Z= 0.238 Chirality : 0.040 0.134 1166 Planarity : 0.003 0.039 1288 Dihedral : 5.943 58.789 1040 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.67 % Allowed : 19.61 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 916 helix: 2.45 (0.27), residues: 396 sheet: 0.26 (0.40), residues: 169 loop : -1.29 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 205 TYR 0.014 0.001 TYR A 107 PHE 0.010 0.001 PHE C 189 TRP 0.019 0.001 TRP D 82 HIS 0.004 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7531) covalent geometry : angle 0.42905 (10200) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.84994 ( 4) hydrogen bonds : bond 0.04780 ( 372) hydrogen bonds : angle 4.28949 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6591 (mmp-170) REVERT: A 90 TYR cc_start: 0.6236 (m-80) cc_final: 0.6015 (m-80) REVERT: A 189 MET cc_start: 0.7998 (tpt) cc_final: 0.7778 (mmm) REVERT: A 263 TRP cc_start: 0.6607 (OUTLIER) cc_final: 0.6316 (t-100) REVERT: D 188 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8217 (mmm) REVERT: D 258 ASP cc_start: 0.8340 (t0) cc_final: 0.8080 (t0) outliers start: 46 outliers final: 23 residues processed: 128 average time/residue: 0.5743 time to fit residues: 77.5426 Evaluate side-chains 120 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102871 restraints weight = 8231.162| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.74 r_work: 0.3005 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7533 Z= 0.226 Angle : 0.527 7.218 10204 Z= 0.285 Chirality : 0.043 0.141 1166 Planarity : 0.004 0.041 1288 Dihedral : 5.839 59.976 1025 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 6.91 % Allowed : 18.99 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 916 helix: 2.42 (0.27), residues: 395 sheet: -0.01 (0.40), residues: 165 loop : -1.44 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.018 0.001 TYR A 107 PHE 0.016 0.002 PHE A 115 TRP 0.019 0.002 TRP D 82 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 7531) covalent geometry : angle 0.52714 (10200) SS BOND : bond 0.00435 ( 2) SS BOND : angle 1.01734 ( 4) hydrogen bonds : bond 0.05986 ( 372) hydrogen bonds : angle 4.44307 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 95 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7952 (t80) REVERT: A 81 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6552 (mmp-170) REVERT: A 90 TYR cc_start: 0.6925 (m-80) cc_final: 0.6616 (m-80) REVERT: A 263 TRP cc_start: 0.6465 (OUTLIER) cc_final: 0.6156 (t-100) REVERT: C 33 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: C 242 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6759 (mtt180) REVERT: D 82 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.9042 (m100) REVERT: D 188 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8467 (mmm) REVERT: D 189 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8878 (p) REVERT: D 198 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8830 (mp) REVERT: D 214 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7122 (mpp-170) outliers start: 56 outliers final: 28 residues processed: 131 average time/residue: 0.5595 time to fit residues: 77.2495 Evaluate side-chains 128 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 82 TRP Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108408 restraints weight = 8235.189| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.70 r_work: 0.3057 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7533 Z= 0.098 Angle : 0.403 5.169 10204 Z= 0.224 Chirality : 0.039 0.131 1166 Planarity : 0.003 0.036 1288 Dihedral : 5.369 58.412 1024 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.93 % Allowed : 20.84 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.29), residues: 916 helix: 2.69 (0.27), residues: 397 sheet: 0.14 (0.40), residues: 166 loop : -1.35 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.012 0.001 TYR A 107 PHE 0.009 0.001 PHE C 189 TRP 0.018 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7531) covalent geometry : angle 0.40290 (10200) SS BOND : bond 0.00321 ( 2) SS BOND : angle 0.73988 ( 4) hydrogen bonds : bond 0.04466 ( 372) hydrogen bonds : angle 4.12341 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 81 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6563 (mmp-170) REVERT: C 32 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7819 (mtt-85) REVERT: D 188 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: D 189 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8789 (p) REVERT: D 198 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8770 (mp) outliers start: 40 outliers final: 21 residues processed: 120 average time/residue: 0.5470 time to fit residues: 69.2467 Evaluate side-chains 118 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 87 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107708 restraints weight = 8209.396| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.74 r_work: 0.3049 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7533 Z= 0.115 Angle : 0.411 4.720 10204 Z= 0.226 Chirality : 0.039 0.133 1166 Planarity : 0.003 0.034 1288 Dihedral : 5.007 58.809 1018 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.80 % Allowed : 20.59 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 916 helix: 2.81 (0.27), residues: 394 sheet: 0.01 (0.39), residues: 167 loop : -1.30 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.013 0.001 TYR A 107 PHE 0.009 0.001 PHE D 292 TRP 0.012 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7531) covalent geometry : angle 0.41077 (10200) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.62145 ( 4) hydrogen bonds : bond 0.04435 ( 372) hydrogen bonds : angle 4.07182 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 81 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6594 (mmp-170) REVERT: A 265 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.5535 (mp10) REVERT: C 32 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7807 (mtt-85) REVERT: C 33 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: D 188 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: D 189 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8811 (p) REVERT: D 214 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7004 (mpp-170) outliers start: 47 outliers final: 29 residues processed: 123 average time/residue: 0.5981 time to fit residues: 77.6359 Evaluate side-chains 129 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 0.0270 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 340 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109454 restraints weight = 8217.773| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.69 r_work: 0.3068 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7533 Z= 0.095 Angle : 0.387 4.513 10204 Z= 0.214 Chirality : 0.039 0.130 1166 Planarity : 0.002 0.032 1288 Dihedral : 4.868 58.738 1018 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.18 % Allowed : 21.58 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 916 helix: 2.97 (0.27), residues: 396 sheet: 0.08 (0.39), residues: 177 loop : -1.19 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 205 TYR 0.012 0.001 TYR A 107 PHE 0.009 0.001 PHE C 189 TRP 0.016 0.001 TRP D 82 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7531) covalent geometry : angle 0.38704 (10200) SS BOND : bond 0.00290 ( 2) SS BOND : angle 0.56339 ( 4) hydrogen bonds : bond 0.04028 ( 372) hydrogen bonds : angle 3.95137 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6511 (mmp-170) REVERT: A 265 GLN cc_start: 0.5841 (OUTLIER) cc_final: 0.5417 (mp10) REVERT: C 20 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: C 33 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: D 189 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8805 (p) outliers start: 42 outliers final: 27 residues processed: 121 average time/residue: 0.5826 time to fit residues: 74.4208 Evaluate side-chains 123 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107861 restraints weight = 8276.776| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.72 r_work: 0.3043 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7533 Z= 0.123 Angle : 0.416 4.919 10204 Z= 0.227 Chirality : 0.039 0.138 1166 Planarity : 0.003 0.032 1288 Dihedral : 4.945 59.055 1018 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.55 % Allowed : 21.33 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.29), residues: 916 helix: 2.93 (0.27), residues: 394 sheet: 0.03 (0.40), residues: 172 loop : -1.20 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.014 0.001 TYR A 107 PHE 0.010 0.001 PHE D 292 TRP 0.010 0.001 TRP A 263 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7531) covalent geometry : angle 0.41605 (10200) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.62963 ( 4) hydrogen bonds : bond 0.04391 ( 372) hydrogen bonds : angle 4.00667 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7508 (t80) REVERT: A 81 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6517 (mmp-170) REVERT: A 265 GLN cc_start: 0.5889 (OUTLIER) cc_final: 0.5427 (mp10) REVERT: C 33 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: D 189 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 254 ASP cc_start: 0.8362 (t0) cc_final: 0.7930 (t0) outliers start: 45 outliers final: 31 residues processed: 124 average time/residue: 0.5987 time to fit residues: 78.3124 Evaluate side-chains 129 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110322 restraints weight = 8195.474| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.74 r_work: 0.3082 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7533 Z= 0.082 Angle : 0.376 4.992 10204 Z= 0.207 Chirality : 0.038 0.129 1166 Planarity : 0.002 0.031 1288 Dihedral : 4.765 58.781 1018 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.07 % Allowed : 22.81 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.29), residues: 916 helix: 3.09 (0.27), residues: 396 sheet: 0.01 (0.39), residues: 182 loop : -1.06 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 205 TYR 0.010 0.001 TYR A 107 PHE 0.008 0.001 PHE C 189 TRP 0.014 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 7531) covalent geometry : angle 0.37636 (10200) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.54718 ( 4) hydrogen bonds : bond 0.03731 ( 372) hydrogen bonds : angle 3.85581 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6586 (mmp-170) REVERT: A 265 GLN cc_start: 0.5795 (OUTLIER) cc_final: 0.5447 (mp10) REVERT: D 38 ASP cc_start: 0.8256 (m-30) cc_final: 0.7929 (t0) REVERT: D 189 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8804 (p) REVERT: D 214 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6988 (mpp-170) outliers start: 33 outliers final: 22 residues processed: 116 average time/residue: 0.6012 time to fit residues: 73.4664 Evaluate side-chains 119 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN D 340 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110878 restraints weight = 8112.285| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.69 r_work: 0.3114 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7533 Z= 0.082 Angle : 0.376 4.384 10204 Z= 0.207 Chirality : 0.038 0.129 1166 Planarity : 0.002 0.031 1288 Dihedral : 4.692 58.682 1018 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.82 % Allowed : 23.18 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.29), residues: 916 helix: 3.17 (0.27), residues: 394 sheet: 0.12 (0.39), residues: 175 loop : -1.10 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 205 TYR 0.011 0.001 TYR A 107 PHE 0.008 0.001 PHE C 189 TRP 0.013 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00175 ( 7531) covalent geometry : angle 0.37584 (10200) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.55659 ( 4) hydrogen bonds : bond 0.03680 ( 372) hydrogen bonds : angle 3.79642 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.297 Fit side-chains REVERT: A 81 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6579 (mmp-170) REVERT: A 265 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5479 (mp10) REVERT: C 20 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: D 38 ASP cc_start: 0.8219 (m-30) cc_final: 0.7920 (t0) REVERT: D 189 SER cc_start: 0.9040 (OUTLIER) cc_final: 0.8811 (p) REVERT: D 214 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.6994 (mpp-170) outliers start: 31 outliers final: 21 residues processed: 118 average time/residue: 0.5821 time to fit residues: 72.5012 Evaluate side-chains 119 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110768 restraints weight = 8213.391| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.91 r_work: 0.3061 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7533 Z= 0.081 Angle : 0.377 5.641 10204 Z= 0.206 Chirality : 0.038 0.129 1166 Planarity : 0.002 0.031 1288 Dihedral : 4.259 53.327 1015 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.33 % Allowed : 24.04 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.29), residues: 916 helix: 3.20 (0.27), residues: 396 sheet: 0.14 (0.39), residues: 175 loop : -1.07 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 205 TYR 0.011 0.001 TYR A 107 PHE 0.008 0.001 PHE C 189 TRP 0.014 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 7531) covalent geometry : angle 0.37649 (10200) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.57580 ( 4) hydrogen bonds : bond 0.03573 ( 372) hydrogen bonds : angle 3.76722 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.304 Fit side-chains REVERT: A 81 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6554 (mmp-170) REVERT: A 265 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5412 (mp10) REVERT: D 38 ASP cc_start: 0.8246 (m-30) cc_final: 0.7944 (t0) REVERT: D 189 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8842 (p) REVERT: D 214 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6958 (mpp-170) outliers start: 27 outliers final: 20 residues processed: 108 average time/residue: 0.6247 time to fit residues: 71.0718 Evaluate side-chains 117 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103701 restraints weight = 8165.706| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.68 r_work: 0.3054 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7533 Z= 0.158 Angle : 0.440 5.695 10204 Z= 0.237 Chirality : 0.040 0.134 1166 Planarity : 0.003 0.031 1288 Dihedral : 4.140 53.636 1013 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.33 % Allowed : 24.17 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.29), residues: 916 helix: 2.99 (0.27), residues: 394 sheet: 0.01 (0.40), residues: 172 loop : -1.12 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 205 TYR 0.016 0.001 TYR A 107 PHE 0.012 0.001 PHE D 292 TRP 0.011 0.001 TRP D 82 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7531) covalent geometry : angle 0.43953 (10200) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.68952 ( 4) hydrogen bonds : bond 0.04392 ( 372) hydrogen bonds : angle 3.92175 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2674.53 seconds wall clock time: 46 minutes 28.17 seconds (2788.17 seconds total)