Starting phenix.real_space_refine on Fri Aug 22 21:18:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8q_37356/08_2025/8w8q_37356_neut.cif" } resolution = 2.89 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5209 2.51 5 N 1417 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8168 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2283 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2579 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8168 At special positions: 0 Unit cell: (77.848, 124.136, 92.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1493 8.00 N 1417 7.00 C 5209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.69 Conformation dependent library (CDL) restraints added in 453.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 42.9% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 27 through 59 removed outlier: 3.591A pdb=" N LYS C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 93 removed outlier: 3.732A pdb=" N PHE C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 100 through 135 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 168 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 201 through 228 Processing helix chain 'C' and resid 394 through 425 Proline residue: C 414 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.904A pdb=" N GLN C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 445 removed outlier: 3.637A pdb=" N ILE C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Proline residue: C 451 - end of helix Processing helix chain 'C' and resid 458 through 473 Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.573A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.540A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.538A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.615A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.194A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 174 through 176 removed outlier: 3.585A pdb=" N SER C 183 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 176 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 181 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.404A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.425A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.512A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.526A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.600A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.324A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1269 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: 1.21 Time building geometry restraints manager: 0.95 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: 2098 1.33 - 1.45: 1585 1.45 - 1.57: 4592 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8342 Sorted by residual: bond pdb=" C CYS B 233 " pdb=" N PHE B 234 " ideal model delta sigma weight residual 1.331 1.231 0.099 1.41e-02 5.03e+03 4.94e+01 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.32e-02 5.74e+03 1.01e+01 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.26e+00 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N ILE B 232 " pdb=" CA ILE B 232 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.59e+00 ... (remaining 8337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10931 1.97 - 3.95: 350 3.95 - 5.92: 35 5.92 - 7.89: 3 7.89 - 9.86: 2 Bond angle restraints: 11321 Sorted by residual: angle pdb=" CA THR B 274 " pdb=" CB THR B 274 " pdb=" OG1 THR B 274 " ideal model delta sigma weight residual 109.60 99.74 9.86 1.50e+00 4.44e-01 4.32e+01 angle pdb=" C CYS B 233 " pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 121.50 129.91 -8.41 1.43e+00 4.89e-01 3.46e+01 angle pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" C ASP A 284 " ideal model delta sigma weight residual 113.30 106.71 6.59 1.34e+00 5.57e-01 2.42e+01 angle pdb=" O ASP B 247 " pdb=" C ASP B 247 " pdb=" N ALA B 248 " ideal model delta sigma weight residual 122.39 127.12 -4.73 1.29e+00 6.01e-01 1.34e+01 angle pdb=" C ASP B 298 " pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " ideal model delta sigma weight residual 109.89 115.50 -5.61 1.60e+00 3.91e-01 1.23e+01 ... (remaining 11316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4364 17.17 - 34.34: 445 34.34 - 51.51: 122 51.51 - 68.67: 27 68.67 - 85.84: 4 Dihedral angle restraints: 4962 sinusoidal: 1918 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ILE C 201 " pdb=" C ILE C 201 " pdb=" N VAL C 202 " pdb=" CA VAL C 202 " ideal model delta harmonic sigma weight residual 180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.31 27.69 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 4959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1007 0.052 - 0.103: 204 0.103 - 0.155: 57 0.155 - 0.207: 17 0.207 - 0.258: 7 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU B 146 " pdb=" N LEU B 146 " pdb=" C LEU B 146 " pdb=" CB LEU B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1289 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 29 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ALA C 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA C 29 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS C 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 40 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ILE C 40 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 40 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 41 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 413 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 414 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " 0.023 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1068 2.75 - 3.29: 7912 3.29 - 3.83: 14110 3.83 - 4.36: 16957 4.36 - 4.90: 29011 Nonbonded interactions: 69058 Sorted by model distance: nonbonded pdb=" O PHE C 200 " pdb=" OH TYR C 408 " model vdw 2.216 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.255 3.120 nonbonded pdb=" N GLU G 58 " pdb=" OE1 GLU G 58 " model vdw 2.259 3.120 nonbonded pdb=" O MET C 143 " pdb=" NH2 ARG A 38 " model vdw 2.281 3.120 nonbonded pdb=" O VAL C 88 " pdb=" OG1 THR C 91 " model vdw 2.290 3.040 ... (remaining 69053 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: 0.660 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.430 Find NCS groups from input model: 0.040 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:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.099 8345 Z= 0.355 Angle : 0.741 9.863 11327 Z= 0.491 Chirality : 0.051 0.258 1292 Planarity : 0.004 0.041 1435 Dihedral : 15.287 85.843 2981 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 21.53 % Favored : 76.77 % 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: 1.04 (0.25), residues: 1028 helix: 1.98 (0.25), residues: 407 sheet: 0.61 (0.33), residues: 219 loop : -0.60 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.015 0.001 TYR C 454 PHE 0.011 0.001 PHE A 376 TRP 0.017 0.001 TRP B 297 HIS 0.006 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 8342) covalent geometry : angle 0.74139 (11321) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.40255 ( 6) hydrogen bonds : bond 0.16202 ( 440) hydrogen bonds : angle 6.02101 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.315 Fit side-chains REVERT: C 61 GLN cc_start: 0.7222 (mt0) cc_final: 0.6987 (tp40) REVERT: C 96 PHE cc_start: 0.6225 (m-80) cc_final: 0.5766 (t80) REVERT: C 183 SER cc_start: 0.8282 (t) cc_final: 0.7815 (p) REVERT: C 464 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 221 MET cc_start: 0.8966 (ttp) cc_final: 0.8424 (ttp) REVERT: B 59 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (t80) outliers start: 15 outliers final: 5 residues processed: 138 average time/residue: 0.5966 time to fit residues: 86.7943 Evaluate side-chains 121 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 222 GLN C 223 HIS A 294 GLN A 357 HIS A 371 ASN B 9 GLN B 32 GLN B 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093140 restraints weight = 11337.945| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.11 r_work: 0.2972 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8345 Z= 0.128 Angle : 0.533 7.600 11327 Z= 0.288 Chirality : 0.041 0.160 1292 Planarity : 0.004 0.043 1435 Dihedral : 4.780 53.110 1147 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.64 % Allowed : 20.05 % Favored : 76.31 % 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: 1.26 (0.25), residues: 1028 helix: 2.25 (0.25), residues: 411 sheet: 0.59 (0.33), residues: 222 loop : -0.52 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.012 0.001 TYR C 454 PHE 0.013 0.001 PHE C 41 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8342) covalent geometry : angle 0.53355 (11321) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.31765 ( 6) hydrogen bonds : bond 0.04995 ( 440) hydrogen bonds : angle 4.68316 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.317 Fit side-chains REVERT: C 61 GLN cc_start: 0.7338 (mt0) cc_final: 0.6957 (tp40) REVERT: C 96 PHE cc_start: 0.6316 (m-80) cc_final: 0.5652 (t80) REVERT: C 424 TRP cc_start: 0.6922 (m100) cc_final: 0.6656 (m-90) REVERT: A 221 MET cc_start: 0.9085 (ttp) cc_final: 0.8576 (ttp) REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8568 (t80) REVERT: B 198 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 262 MET cc_start: 0.9182 (mtp) cc_final: 0.8893 (mmm) outliers start: 32 outliers final: 13 residues processed: 155 average time/residue: 0.4629 time to fit residues: 76.3296 Evaluate side-chains 130 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.0870 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 GLN C 223 HIS A 357 HIS B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093859 restraints weight = 11309.631| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.10 r_work: 0.2983 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8345 Z= 0.115 Angle : 0.507 7.409 11327 Z= 0.272 Chirality : 0.041 0.164 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.475 52.059 1139 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.87 % Allowed : 21.18 % Favored : 74.94 % 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: 1.34 (0.25), residues: 1028 helix: 2.37 (0.24), residues: 411 sheet: 0.51 (0.32), residues: 226 loop : -0.46 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.011 0.001 TYR N 95 PHE 0.013 0.001 PHE A 376 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8342) covalent geometry : angle 0.50735 (11321) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.24550 ( 6) hydrogen bonds : bond 0.04593 ( 440) hydrogen bonds : angle 4.47197 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.327 Fit side-chains REVERT: C 61 GLN cc_start: 0.7352 (mt0) cc_final: 0.6978 (tp40) REVERT: C 96 PHE cc_start: 0.6264 (m-80) cc_final: 0.5567 (t80) REVERT: C 440 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7358 (mp) REVERT: C 473 PHE cc_start: 0.5897 (OUTLIER) cc_final: 0.5683 (t80) REVERT: A 221 MET cc_start: 0.9086 (ttp) cc_final: 0.8554 (ttp) REVERT: B 59 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8581 (t80) REVERT: B 198 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (pp) REVERT: B 217 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8345 (pmm) REVERT: G 20 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7875 (mttp) outliers start: 34 outliers final: 14 residues processed: 146 average time/residue: 0.5093 time to fit residues: 78.9395 Evaluate side-chains 133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 9.9990 chunk 73 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 390 GLN B 9 GLN B 237 ASN B 239 ASN N 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095102 restraints weight = 11511.590| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.13 r_work: 0.3005 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8345 Z= 0.104 Angle : 0.486 7.134 11327 Z= 0.260 Chirality : 0.040 0.154 1292 Planarity : 0.003 0.042 1435 Dihedral : 4.263 51.579 1137 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.21 % Allowed : 21.30 % Favored : 74.49 % 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: 1.44 (0.25), residues: 1028 helix: 2.48 (0.24), residues: 404 sheet: 0.55 (0.33), residues: 222 loop : -0.36 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.010 0.001 TYR N 95 PHE 0.012 0.001 PHE C 41 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8342) covalent geometry : angle 0.48606 (11321) SS BOND : bond 0.00074 ( 3) SS BOND : angle 0.20187 ( 6) hydrogen bonds : bond 0.04285 ( 440) hydrogen bonds : angle 4.33839 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.347 Fit side-chains REVERT: C 61 GLN cc_start: 0.7318 (mt0) cc_final: 0.6933 (tp-100) REVERT: C 96 PHE cc_start: 0.6340 (m-80) cc_final: 0.5599 (t80) REVERT: C 424 TRP cc_start: 0.7213 (m100) cc_final: 0.6861 (m-90) REVERT: C 440 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 221 MET cc_start: 0.9043 (ttp) cc_final: 0.8579 (ttp) REVERT: B 59 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8560 (t80) REVERT: B 198 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8351 (pp) REVERT: B 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8316 (pmm) outliers start: 37 outliers final: 17 residues processed: 148 average time/residue: 0.5320 time to fit residues: 83.4170 Evaluate side-chains 135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094139 restraints weight = 11394.046| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.12 r_work: 0.2985 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8345 Z= 0.121 Angle : 0.505 7.206 11327 Z= 0.270 Chirality : 0.041 0.168 1292 Planarity : 0.004 0.044 1435 Dihedral : 4.304 53.164 1137 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.21 % Allowed : 21.30 % Favored : 74.49 % 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: 1.44 (0.25), residues: 1028 helix: 2.48 (0.24), residues: 411 sheet: 0.45 (0.33), residues: 228 loop : -0.37 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.013 0.001 TYR N 95 PHE 0.012 0.001 PHE C 41 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8342) covalent geometry : angle 0.50498 (11321) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.28774 ( 6) hydrogen bonds : bond 0.04377 ( 440) hydrogen bonds : angle 4.29707 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.245 Fit side-chains REVERT: C 61 GLN cc_start: 0.7307 (mt0) cc_final: 0.7060 (tp40) REVERT: C 96 PHE cc_start: 0.6351 (m-80) cc_final: 0.5590 (t80) REVERT: C 440 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 221 MET cc_start: 0.9038 (ttp) cc_final: 0.8619 (ttp) REVERT: B 59 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 198 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 217 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8198 (pmm) outliers start: 37 outliers final: 21 residues processed: 152 average time/residue: 0.4667 time to fit residues: 75.2514 Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 93 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS A 29 GLN A 294 GLN B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094933 restraints weight = 11332.795| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.10 r_work: 0.3002 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8345 Z= 0.110 Angle : 0.503 6.975 11327 Z= 0.268 Chirality : 0.041 0.152 1292 Planarity : 0.003 0.043 1435 Dihedral : 4.251 53.045 1137 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.67 % Allowed : 21.18 % Favored : 74.15 % 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: 1.40 (0.25), residues: 1028 helix: 2.44 (0.24), residues: 411 sheet: 0.43 (0.33), residues: 228 loop : -0.39 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.010 0.001 TYR C 454 PHE 0.012 0.001 PHE C 41 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8342) covalent geometry : angle 0.50297 (11321) SS BOND : bond 0.00050 ( 3) SS BOND : angle 0.25092 ( 6) hydrogen bonds : bond 0.04244 ( 440) hydrogen bonds : angle 4.24293 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.336 Fit side-chains REVERT: C 59 LYS cc_start: 0.7726 (mppt) cc_final: 0.7516 (mppt) REVERT: C 96 PHE cc_start: 0.6349 (m-80) cc_final: 0.5582 (t80) REVERT: C 440 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7328 (mp) REVERT: C 473 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5488 (t80) REVERT: A 221 MET cc_start: 0.9014 (ttp) cc_final: 0.8638 (ttp) REVERT: B 59 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8524 (t80) REVERT: B 198 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8302 (pp) REVERT: B 217 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: G 42 GLU cc_start: 0.8224 (pp20) cc_final: 0.7953 (pp20) outliers start: 41 outliers final: 22 residues processed: 149 average time/residue: 0.5009 time to fit residues: 79.3901 Evaluate side-chains 147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS A 31 GLN A 294 GLN B 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087202 restraints weight = 11619.484| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.11 r_work: 0.2874 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8345 Z= 0.328 Angle : 0.677 8.036 11327 Z= 0.366 Chirality : 0.049 0.187 1292 Planarity : 0.005 0.059 1435 Dihedral : 5.109 59.207 1137 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.67 % Allowed : 21.41 % Favored : 73.92 % 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: 0.97 (0.25), residues: 1028 helix: 1.96 (0.24), residues: 411 sheet: 0.43 (0.33), residues: 230 loop : -0.64 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 283 TYR 0.024 0.002 TYR A 339 PHE 0.018 0.002 PHE B 199 TRP 0.011 0.002 TRP A 234 HIS 0.009 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 8342) covalent geometry : angle 0.67658 (11321) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.72716 ( 6) hydrogen bonds : bond 0.05684 ( 440) hydrogen bonds : angle 4.75640 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: C 46 PHE cc_start: 0.8211 (t80) cc_final: 0.7894 (t80) REVERT: C 96 PHE cc_start: 0.6489 (m-80) cc_final: 0.5583 (t80) REVERT: C 440 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7234 (mp) REVERT: A 216 LYS cc_start: 0.8872 (mttp) cc_final: 0.8637 (mtpp) REVERT: A 221 MET cc_start: 0.9000 (ttp) cc_final: 0.8702 (ttp) REVERT: B 59 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8643 (t80) REVERT: B 198 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8301 (pp) REVERT: B 217 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8144 (pmm) REVERT: B 314 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8608 (ptm160) outliers start: 41 outliers final: 23 residues processed: 149 average time/residue: 0.5044 time to fit residues: 79.7045 Evaluate side-chains 141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS A 31 GLN B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091690 restraints weight = 11333.326| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.10 r_work: 0.2948 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8345 Z= 0.131 Angle : 0.552 8.485 11327 Z= 0.296 Chirality : 0.041 0.171 1292 Planarity : 0.004 0.045 1435 Dihedral : 4.604 56.905 1137 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.76 % Allowed : 23.12 % 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: 1.19 (0.25), residues: 1028 helix: 2.29 (0.24), residues: 411 sheet: 0.36 (0.33), residues: 224 loop : -0.54 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.013 0.001 TYR C 168 PHE 0.023 0.001 PHE C 41 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8342) covalent geometry : angle 0.55176 (11321) SS BOND : bond 0.00091 ( 3) SS BOND : angle 0.46612 ( 6) hydrogen bonds : bond 0.04600 ( 440) hydrogen bonds : angle 4.48983 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.315 Fit side-chains REVERT: C 93 VAL cc_start: 0.7152 (t) cc_final: 0.6950 (p) REVERT: C 96 PHE cc_start: 0.6386 (m-80) cc_final: 0.5447 (t80) REVERT: C 463 LYS cc_start: 0.8928 (tppt) cc_final: 0.8601 (tppt) REVERT: C 473 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.5555 (t80) REVERT: A 221 MET cc_start: 0.8995 (ttp) cc_final: 0.8686 (ttp) REVERT: B 3 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6455 (tm-30) REVERT: B 59 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8551 (t80) REVERT: B 198 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8288 (pp) REVERT: B 217 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8146 (pmm) outliers start: 33 outliers final: 21 residues processed: 145 average time/residue: 0.5186 time to fit residues: 79.5408 Evaluate side-chains 139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS C 458 HIS A 31 GLN B 9 GLN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092270 restraints weight = 11419.446| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.12 r_work: 0.2955 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8345 Z= 0.130 Angle : 0.552 8.738 11327 Z= 0.295 Chirality : 0.041 0.169 1292 Planarity : 0.004 0.048 1435 Dihedral : 4.513 56.537 1137 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.76 % Allowed : 23.58 % Favored : 72.67 % 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: 1.28 (0.25), residues: 1028 helix: 2.36 (0.25), residues: 411 sheet: 0.30 (0.33), residues: 227 loop : -0.42 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.011 0.001 TYR N 95 PHE 0.023 0.001 PHE C 41 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8342) covalent geometry : angle 0.55232 (11321) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.40947 ( 6) hydrogen bonds : bond 0.04501 ( 440) hydrogen bonds : angle 4.41106 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.261 Fit side-chains REVERT: C 59 LYS cc_start: 0.7750 (mppt) cc_final: 0.7502 (mptt) REVERT: C 96 PHE cc_start: 0.6413 (m-80) cc_final: 0.5478 (t80) REVERT: C 440 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 463 LYS cc_start: 0.8852 (tppt) cc_final: 0.8528 (tppt) REVERT: C 473 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.5545 (t80) REVERT: A 221 MET cc_start: 0.8940 (ttp) cc_final: 0.8642 (ttp) REVERT: B 59 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8556 (t80) REVERT: B 198 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8286 (pp) REVERT: B 217 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8155 (pmm) outliers start: 33 outliers final: 21 residues processed: 144 average time/residue: 0.5022 time to fit residues: 76.5669 Evaluate side-chains 143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 223 HIS A 31 GLN B 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093539 restraints weight = 11403.245| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.11 r_work: 0.2972 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8345 Z= 0.123 Angle : 0.545 9.026 11327 Z= 0.292 Chirality : 0.041 0.161 1292 Planarity : 0.004 0.051 1435 Dihedral : 4.425 56.082 1137 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.96 % Allowed : 24.94 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.32 (0.25), residues: 1028 helix: 2.39 (0.24), residues: 411 sheet: 0.34 (0.33), residues: 226 loop : -0.42 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.010 0.001 TYR N 95 PHE 0.024 0.001 PHE C 41 TRP 0.015 0.001 TRP C 441 HIS 0.004 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8342) covalent geometry : angle 0.54523 (11321) SS BOND : bond 0.00069 ( 3) SS BOND : angle 0.38143 ( 6) hydrogen bonds : bond 0.04343 ( 440) hydrogen bonds : angle 4.34716 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.206 Fit side-chains REVERT: C 59 LYS cc_start: 0.7719 (mppt) cc_final: 0.7313 (mttt) REVERT: C 96 PHE cc_start: 0.6395 (m-80) cc_final: 0.5471 (t80) REVERT: C 168 TYR cc_start: 0.7989 (p90) cc_final: 0.7724 (p90) REVERT: C 424 TRP cc_start: 0.7173 (m100) cc_final: 0.6741 (m-90) REVERT: C 440 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7344 (mp) REVERT: A 216 LYS cc_start: 0.8805 (mttp) cc_final: 0.8547 (mtpp) REVERT: A 221 MET cc_start: 0.8904 (ttp) cc_final: 0.8642 (ttp) REVERT: B 59 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8565 (t80) REVERT: B 198 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8257 (pp) REVERT: B 217 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7990 (pmm) REVERT: N 5 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7705 (mm110) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.5004 time to fit residues: 71.0598 Evaluate side-chains 137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 HIS B 9 GLN B 237 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.091963 restraints weight = 11444.234| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.11 r_work: 0.2949 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8345 Z= 0.146 Angle : 0.557 7.264 11327 Z= 0.296 Chirality : 0.042 0.163 1292 Planarity : 0.004 0.051 1435 Dihedral : 4.522 56.812 1137 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.42 % Allowed : 24.26 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.25), residues: 1028 helix: 2.35 (0.24), residues: 411 sheet: 0.27 (0.33), residues: 232 loop : -0.35 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 283 TYR 0.013 0.001 TYR A 339 PHE 0.023 0.001 PHE C 41 TRP 0.015 0.001 TRP C 441 HIS 0.004 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8342) covalent geometry : angle 0.55741 (11321) SS BOND : bond 0.00102 ( 3) SS BOND : angle 0.44948 ( 6) hydrogen bonds : bond 0.04514 ( 440) hydrogen bonds : angle 4.40113 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.48 seconds wall clock time: 46 minutes 38.40 seconds (2798.40 seconds total)