Starting phenix.real_space_refine on Wed Aug 5 08:43:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwq_64563/08_2026/9uwq_64563.map" } resolution = 3.1 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= 0.008 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5679 2.51 5 N 1543 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8883 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "C" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2519 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 237 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 759 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 351 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3067 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 16, 'TRANS': 352} Time building chain proxies: 1.65, per 1000 atoms: 0.19 Number of scatterers: 8883 At special positions: 0 Unit cell: (88.33, 96.36, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1597 8.00 N 1543 7.00 C 5679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " 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: 0.67 Conformation dependent library (CDL) restraints added in 383.6 milliseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 49.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.688A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.583A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.875A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'E' and resid 34 through 48 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 58 through 81 removed outlier: 3.925A pdb=" N THR E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 63 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 142 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix removed outlier: 3.654A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 42 through 62 removed outlier: 3.817A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.176A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.575A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 210 through 215 removed outlier: 3.538A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.324A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 267 removed outlier: 4.298A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 285 removed outlier: 3.732A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.535A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU R 291 " --> pdb=" O ASN R 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 287 through 291' Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.623A pdb=" N VAL R 311 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR R 325 " --> pdb=" O ARG R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.136A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 327 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 51 removed outlier: 5.010A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.994A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.207A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.521A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.088A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 217 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.721A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.733A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.705A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1383 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: 1.25 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2883 1.34 - 1.46: 2201 1.46 - 1.58: 3931 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9105 Sorted by residual: bond pdb=" C MET A 198 " pdb=" N PHE A 199 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.34e-02 5.57e+03 3.34e+00 bond pdb=" N MET A 198 " pdb=" CA MET A 198 " ideal model delta sigma weight residual 1.454 1.475 -0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" C VAL R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.23e+00 bond pdb=" CA MET A 198 " pdb=" C MET A 198 " ideal model delta sigma weight residual 1.523 1.510 0.013 1.18e-02 7.18e+03 1.27e+00 bond pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.06e+00 ... (remaining 9100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 12100 1.35 - 2.71: 236 2.71 - 4.06: 34 4.06 - 5.41: 13 5.41 - 6.77: 2 Bond angle restraints: 12385 Sorted by residual: angle pdb=" N VAL R 203 " pdb=" CA VAL R 203 " pdb=" C VAL R 203 " ideal model delta sigma weight residual 113.71 110.02 3.69 9.50e-01 1.11e+00 1.51e+01 angle pdb=" N VAL E 51 " pdb=" CA VAL E 51 " pdb=" C VAL E 51 " ideal model delta sigma weight residual 106.21 110.26 -4.05 1.07e+00 8.73e-01 1.43e+01 angle pdb=" N PHE R 137 " pdb=" CA PHE R 137 " pdb=" C PHE R 137 " ideal model delta sigma weight residual 113.61 108.70 4.91 1.50e+00 4.44e-01 1.07e+01 angle pdb=" C HIS A 197 " pdb=" N MET A 198 " pdb=" CA MET A 198 " ideal model delta sigma weight residual 122.87 117.86 5.01 1.61e+00 3.86e-01 9.66e+00 angle pdb=" N ILE E 118 " pdb=" CA ILE E 118 " pdb=" C ILE E 118 " ideal model delta sigma weight residual 113.39 108.87 4.52 1.47e+00 4.63e-01 9.45e+00 ... (remaining 12380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 5032 13.77 - 27.55: 247 27.55 - 41.32: 43 41.32 - 55.10: 12 55.10 - 68.87: 4 Dihedral angle restraints: 5338 sinusoidal: 1987 harmonic: 3351 Sorted by residual: dihedral pdb=" CA ALA A 220 " pdb=" C ALA A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ARG R 362 " pdb=" C ARG R 362 " pdb=" N PRO R 363 " pdb=" CA PRO R 363 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN D 21 " pdb=" C ASN D 21 " pdb=" N ASN D 22 " pdb=" CA ASN D 22 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 884 0.027 - 0.054: 308 0.054 - 0.081: 114 0.081 - 0.108: 60 0.108 - 0.135: 15 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE D 26 " pdb=" N ILE D 26 " pdb=" C ILE D 26 " pdb=" CB ILE D 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL C 296 " pdb=" N VAL C 296 " pdb=" C VAL C 296 " pdb=" CB VAL C 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1378 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 294 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 295 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO A 299 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 104 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO E 105 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 105 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 105 " -0.016 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1298 2.76 - 3.29: 8821 3.29 - 3.83: 15154 3.83 - 4.36: 17181 4.36 - 4.90: 29650 Nonbonded interactions: 72104 Sorted by model distance: nonbonded pdb=" OG1 THR R 330 " pdb=" OE1 GLU R 332 " model vdw 2.222 3.040 nonbonded pdb=" O LEU D 16 " pdb=" OG SER D 20 " model vdw 2.253 3.040 nonbonded pdb=" O PHE D 15 " pdb=" OG SER D 19 " model vdw 2.267 3.040 nonbonded pdb=" O THR C 86 " pdb=" OG1 THR C 87 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN A 351 " pdb=" NZ LYS R 326 " model vdw 2.335 3.120 ... (remaining 72099 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: 3.190 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 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 : 0.002 0.026 9107 Z= 0.110 Angle : 0.485 6.765 12389 Z= 0.296 Chirality : 0.037 0.135 1381 Planarity : 0.004 0.059 1580 Dihedral : 8.889 68.872 3164 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.55 % Allowed : 4.07 % Favored : 95.38 % 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 are not related in a simple way. whole: 1.73 (0.26), residues: 1131 helix: 2.26 (0.24), residues: 505 sheet: 0.98 (0.38), residues: 178 loop : -0.03 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 150 TYR 0.008 0.001 TYR R 149 PHE 0.006 0.001 PHE A 189 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.000 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.11 ( 9105) covalent geometry : angle 0.48532 / 0.30 (12385) SS BOND : bond 0.00032 / 0.02 ( 2) SS BOND : angle 0.41327 / 0.18 ( 4) hydrogen bonds : bond 0.13062 / 8.51 ( 477) hydrogen bonds : angle 6.16925 / 4.20 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 245 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASP cc_start: 0.7673 (p0) cc_final: 0.7363 (p0) REVERT: E 111 VAL cc_start: 0.7158 (t) cc_final: 0.6795 (m) REVERT: G 61 PHE cc_start: 0.0841 (OUTLIER) cc_final: 0.0477 (t80) REVERT: R 55 CYS cc_start: 0.8239 (t) cc_final: 0.7023 (t) REVERT: R 59 MET cc_start: 0.6214 (mtm) cc_final: 0.5720 (mtt) outliers start: 5 outliers final: 1 residues processed: 249 average time/residue: 0.0921 time to fit residues: 30.6577 Evaluate side-chains 141 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain G residue 61 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 54 HIS C 268 ASN D 10 GLN R 408 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.158340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122014 restraints weight = 15889.628| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.28 r_work: 0.3703 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9107 Z= 0.158 Angle : 0.561 8.175 12389 Z= 0.297 Chirality : 0.043 0.154 1381 Planarity : 0.004 0.055 1580 Dihedral : 4.252 46.726 1249 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.87 % Allowed : 11.33 % Favored : 86.80 % 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 are not related in a simple way. whole: 1.70 (0.25), residues: 1131 helix: 2.43 (0.23), residues: 507 sheet: 0.58 (0.36), residues: 188 loop : -0.15 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 45 TYR 0.019 0.002 TYR R 191 PHE 0.017 0.002 PHE R 235 TRP 0.017 0.001 TRP C 169 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9105) covalent geometry : angle 0.56119 / 0.30 (12385) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 0.76327 / 0.44 ( 4) hydrogen bonds : bond 0.03782 / 2.52 ( 477) hydrogen bonds : angle 4.45011 / 3.15 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7668 (m-30) cc_final: 0.7250 (m-30) REVERT: A 198 MET cc_start: 0.8465 (ttp) cc_final: 0.8135 (ttp) REVERT: A 276 GLU cc_start: 0.7097 (mp0) cc_final: 0.6844 (mt-10) REVERT: C 298 ASP cc_start: 0.6297 (t0) cc_final: 0.6083 (t70) REVERT: E 111 VAL cc_start: 0.7683 (t) cc_final: 0.7232 (m) REVERT: G 61 PHE cc_start: 0.1282 (OUTLIER) cc_final: -0.0017 (t80) REVERT: R 59 MET cc_start: 0.6630 (mtm) cc_final: 0.6125 (mtt) REVERT: R 217 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7288 (t) REVERT: R 393 PHE cc_start: 0.7410 (m-80) cc_final: 0.7040 (m-80) outliers start: 17 outliers final: 5 residues processed: 163 average time/residue: 0.0830 time to fit residues: 19.1409 Evaluate side-chains 133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 332 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 50 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 HIS C 88 ASN C 268 ASN R 227 GLN R 277 HIS R 377 HIS R 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116912 restraints weight = 15800.073| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.78 r_work: 0.3558 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9107 Z= 0.188 Angle : 0.571 9.195 12389 Z= 0.300 Chirality : 0.043 0.141 1381 Planarity : 0.004 0.055 1580 Dihedral : 4.334 49.257 1247 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.53 % Allowed : 13.42 % Favored : 84.05 % 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 are not related in a simple way. whole: 1.41 (0.25), residues: 1131 helix: 2.20 (0.23), residues: 511 sheet: 0.19 (0.36), residues: 197 loop : -0.21 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 45 TYR 0.016 0.002 TYR R 191 PHE 0.017 0.002 PHE R 313 TRP 0.019 0.002 TRP C 169 HIS 0.008 0.002 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 9105) covalent geometry : angle 0.57058 / 0.30 (12385) SS BOND : bond 0.00209 / 0.11 ( 2) SS BOND : angle 0.52148 / 0.29 ( 4) hydrogen bonds : bond 0.04022 / 2.70 ( 477) hydrogen bonds : angle 4.35574 / 3.11 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8527 (ttp) cc_final: 0.8276 (ttp) REVERT: E 111 VAL cc_start: 0.7839 (t) cc_final: 0.7413 (m) REVERT: G 61 PHE cc_start: 0.1826 (OUTLIER) cc_final: 0.0546 (t80) REVERT: R 49 MET cc_start: 0.8665 (tpp) cc_final: 0.7943 (mmt) REVERT: R 59 MET cc_start: 0.6409 (mtm) cc_final: 0.5976 (mtt) REVERT: R 187 MET cc_start: 0.8081 (tpt) cc_final: 0.7771 (tpt) REVERT: R 217 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7448 (t) REVERT: R 393 PHE cc_start: 0.7923 (m-80) cc_final: 0.7630 (m-10) outliers start: 23 outliers final: 10 residues processed: 147 average time/residue: 0.0781 time to fit residues: 16.4284 Evaluate side-chains 131 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.152134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.116584 restraints weight = 15884.536| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.74 r_work: 0.3550 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9107 Z= 0.178 Angle : 0.551 8.780 12389 Z= 0.289 Chirality : 0.042 0.139 1381 Planarity : 0.004 0.054 1580 Dihedral : 4.343 52.981 1247 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.42 % Allowed : 14.19 % Favored : 83.39 % 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 are not related in a simple way. whole: 1.35 (0.25), residues: 1131 helix: 2.14 (0.23), residues: 511 sheet: 0.14 (0.36), residues: 198 loop : -0.22 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 45 TYR 0.018 0.002 TYR R 191 PHE 0.018 0.001 PHE C 151 TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 9105) covalent geometry : angle 0.55077 / 0.29 (12385) SS BOND : bond 0.00199 / 0.10 ( 2) SS BOND : angle 0.36352 / 0.19 ( 4) hydrogen bonds : bond 0.03833 / 2.57 ( 477) hydrogen bonds : angle 4.25335 / 3.06 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7141 (t0) REVERT: A 47 SER cc_start: 0.7457 (m) cc_final: 0.7098 (p) REVERT: A 195 ASN cc_start: 0.7920 (p0) cc_final: 0.7632 (p0) REVERT: A 198 MET cc_start: 0.8722 (ttp) cc_final: 0.8519 (ttp) REVERT: C 62 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8794 (t70) REVERT: E 111 VAL cc_start: 0.7910 (t) cc_final: 0.7531 (m) REVERT: R 59 MET cc_start: 0.6437 (mtm) cc_final: 0.5947 (mtt) REVERT: R 187 MET cc_start: 0.8331 (tpt) cc_final: 0.7861 (tpt) REVERT: R 217 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7608 (t) REVERT: R 332 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: R 393 PHE cc_start: 0.8382 (m-80) cc_final: 0.8120 (m-80) outliers start: 22 outliers final: 10 residues processed: 150 average time/residue: 0.0745 time to fit residues: 16.1723 Evaluate side-chains 139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN R 179 GLN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.114183 restraints weight = 15832.351| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.73 r_work: 0.3520 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9107 Z= 0.189 Angle : 0.557 8.819 12389 Z= 0.293 Chirality : 0.043 0.196 1381 Planarity : 0.004 0.053 1580 Dihedral : 4.453 55.570 1247 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.63 % Allowed : 13.97 % Favored : 82.40 % 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 are not related in a simple way. whole: 1.29 (0.25), residues: 1131 helix: 2.11 (0.23), residues: 511 sheet: -0.10 (0.36), residues: 203 loop : -0.16 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.018 0.002 TYR R 372 PHE 0.018 0.001 PHE C 151 TRP 0.017 0.001 TRP C 82 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 9105) covalent geometry : angle 0.55719 / 0.29 (12385) SS BOND : bond 0.00168 / 0.09 ( 2) SS BOND : angle 0.34752 / 0.18 ( 4) hydrogen bonds : bond 0.03922 / 2.65 ( 477) hydrogen bonds : angle 4.24701 / 3.06 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7125 (t0) REVERT: A 47 SER cc_start: 0.7683 (m) cc_final: 0.7289 (p) REVERT: A 186 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: A 195 ASN cc_start: 0.7846 (p0) cc_final: 0.7607 (p0) REVERT: A 197 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7829 (t-90) REVERT: C 62 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8780 (t70) REVERT: E 111 VAL cc_start: 0.7960 (t) cc_final: 0.7570 (m) REVERT: R 49 MET cc_start: 0.8654 (tpt) cc_final: 0.8274 (mtt) REVERT: R 59 MET cc_start: 0.6425 (mtm) cc_final: 0.5953 (mtt) REVERT: R 217 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7548 (t) REVERT: R 332 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6733 (mp0) outliers start: 33 outliers final: 20 residues processed: 147 average time/residue: 0.0622 time to fit residues: 13.3995 Evaluate side-chains 148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 338 ASN D 3 ASN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.149732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114883 restraints weight = 15756.521| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.85 r_work: 0.3524 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9107 Z= 0.148 Angle : 0.522 8.175 12389 Z= 0.276 Chirality : 0.041 0.140 1381 Planarity : 0.004 0.053 1580 Dihedral : 3.992 20.489 1245 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.64 % Allowed : 15.18 % Favored : 82.18 % 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 are not related in a simple way. whole: 1.33 (0.25), residues: 1131 helix: 2.20 (0.23), residues: 511 sheet: -0.10 (0.36), residues: 204 loop : -0.19 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.023 0.001 TYR R 372 PHE 0.016 0.001 PHE C 151 TRP 0.022 0.001 TRP C 169 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9105) covalent geometry : angle 0.52253 / 0.28 (12385) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 0.36789 / 0.19 ( 4) hydrogen bonds : bond 0.03571 / 2.41 ( 477) hydrogen bonds : angle 4.10367 / 2.95 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7270 (t0) REVERT: A 47 SER cc_start: 0.7773 (m) cc_final: 0.7412 (p) REVERT: A 197 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7851 (t-90) REVERT: E 111 VAL cc_start: 0.7998 (t) cc_final: 0.7613 (m) REVERT: R 59 MET cc_start: 0.6438 (mtm) cc_final: 0.5952 (mtt) outliers start: 24 outliers final: 16 residues processed: 137 average time/residue: 0.0672 time to fit residues: 13.4451 Evaluate side-chains 140 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN A 190 GLN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.149874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114549 restraints weight = 15852.868| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.75 r_work: 0.3536 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9107 Z= 0.140 Angle : 0.537 8.822 12389 Z= 0.280 Chirality : 0.042 0.304 1381 Planarity : 0.004 0.053 1580 Dihedral : 3.974 20.753 1245 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 15.84 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1131 helix: 2.24 (0.23), residues: 511 sheet: -0.05 (0.37), residues: 197 loop : -0.21 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.022 0.001 TYR R 372 PHE 0.015 0.001 PHE C 151 TRP 0.022 0.001 TRP C 169 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9105) covalent geometry : angle 0.53659 / 0.28 (12385) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.38141 / 0.20 ( 4) hydrogen bonds : bond 0.03520 / 2.38 ( 477) hydrogen bonds : angle 4.07437 / 2.93 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7264 (t0) REVERT: A 47 SER cc_start: 0.7852 (m) cc_final: 0.7492 (p) REVERT: A 186 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: A 197 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (t-90) REVERT: E 111 VAL cc_start: 0.7997 (t) cc_final: 0.7599 (m) REVERT: E 138 VAL cc_start: 0.8737 (t) cc_final: 0.8469 (m) REVERT: R 49 MET cc_start: 0.8600 (tpt) cc_final: 0.8153 (mtt) REVERT: R 59 MET cc_start: 0.6374 (mtm) cc_final: 0.5897 (mtt) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 0.0573 time to fit residues: 12.0554 Evaluate side-chains 139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 62 HIS C 230 ASN R 186 ASN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.146102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111022 restraints weight = 15931.134| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.86 r_work: 0.3437 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9107 Z= 0.278 Angle : 0.656 11.272 12389 Z= 0.344 Chirality : 0.047 0.311 1381 Planarity : 0.005 0.053 1580 Dihedral : 4.411 23.878 1245 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.08 % Allowed : 15.84 % Favored : 81.08 % 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 are not related in a simple way. whole: 0.91 (0.25), residues: 1131 helix: 1.83 (0.23), residues: 514 sheet: -0.49 (0.36), residues: 202 loop : -0.30 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 251 TYR 0.027 0.002 TYR R 372 PHE 0.022 0.002 PHE A 185 TRP 0.024 0.002 TRP C 169 HIS 0.008 0.002 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.28 ( 9105) covalent geometry : angle 0.65654 / 0.34 (12385) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 0.36026 / 0.20 ( 4) hydrogen bonds : bond 0.04325 / 2.91 ( 477) hydrogen bonds : angle 4.45142 / 3.22 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7323 (t0) REVERT: A 186 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: A 195 ASN cc_start: 0.7999 (p0) cc_final: 0.7659 (p0) REVERT: A 197 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7948 (t-90) REVERT: E 111 VAL cc_start: 0.8145 (t) cc_final: 0.7774 (m) REVERT: E 138 VAL cc_start: 0.8758 (t) cc_final: 0.8507 (m) REVERT: R 49 MET cc_start: 0.8655 (tpt) cc_final: 0.7921 (mmt) REVERT: R 59 MET cc_start: 0.6433 (mtm) cc_final: 0.5956 (mtt) REVERT: R 187 MET cc_start: 0.8165 (tpt) cc_final: 0.7657 (tpt) outliers start: 28 outliers final: 19 residues processed: 139 average time/residue: 0.0694 time to fit residues: 14.1744 Evaluate side-chains 135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN R 186 ASN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.148988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113472 restraints weight = 15665.935| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.82 r_work: 0.3513 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9107 Z= 0.133 Angle : 0.556 11.552 12389 Z= 0.289 Chirality : 0.043 0.343 1381 Planarity : 0.004 0.052 1580 Dihedral : 4.099 21.069 1245 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.09 % Allowed : 17.60 % Favored : 80.31 % 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 are not related in a simple way. whole: 1.23 (0.26), residues: 1131 helix: 2.11 (0.23), residues: 514 sheet: -0.20 (0.38), residues: 197 loop : -0.23 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.024 0.001 TYR R 372 PHE 0.014 0.001 PHE A 189 TRP 0.020 0.001 TRP C 82 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9105) covalent geometry : angle 0.55561 / 0.29 (12385) SS BOND : bond 0.00094 / 0.05 ( 2) SS BOND : angle 0.34842 / 0.18 ( 4) hydrogen bonds : bond 0.03576 / 2.43 ( 477) hydrogen bonds : angle 4.13353 / 2.97 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7296 (t0) REVERT: A 47 SER cc_start: 0.7833 (m) cc_final: 0.7482 (p) REVERT: A 186 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: A 197 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7876 (t-90) REVERT: E 111 VAL cc_start: 0.8067 (t) cc_final: 0.7679 (m) REVERT: E 138 VAL cc_start: 0.8765 (t) cc_final: 0.8520 (m) REVERT: R 59 MET cc_start: 0.6360 (mtm) cc_final: 0.5880 (mtt) outliers start: 19 outliers final: 12 residues processed: 139 average time/residue: 0.0604 time to fit residues: 12.4837 Evaluate side-chains 134 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN C 259 GLN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.148143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113400 restraints weight = 15762.034| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.91 r_work: 0.3467 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9107 Z= 0.164 Angle : 0.574 10.757 12389 Z= 0.298 Chirality : 0.043 0.338 1381 Planarity : 0.004 0.053 1580 Dihedral : 4.108 22.257 1245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.87 % Allowed : 18.15 % Favored : 79.98 % 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 are not related in a simple way. whole: 1.19 (0.25), residues: 1131 helix: 2.07 (0.23), residues: 514 sheet: -0.16 (0.38), residues: 194 loop : -0.30 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 45 TYR 0.025 0.001 TYR R 372 PHE 0.015 0.001 PHE C 151 TRP 0.017 0.001 TRP C 82 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 9105) covalent geometry : angle 0.57416 / 0.30 (12385) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.39104 / 0.20 ( 4) hydrogen bonds : bond 0.03660 / 2.47 ( 477) hydrogen bonds : angle 4.15526 / 2.98 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7324 (t0) REVERT: A 47 SER cc_start: 0.7949 (m) cc_final: 0.7609 (p) REVERT: A 186 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: A 195 ASN cc_start: 0.7834 (p0) cc_final: 0.7538 (p0) REVERT: A 197 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7924 (t-90) REVERT: A 357 GLN cc_start: 0.7273 (mt0) cc_final: 0.7036 (mt0) REVERT: E 111 VAL cc_start: 0.8074 (t) cc_final: 0.7691 (m) REVERT: E 138 VAL cc_start: 0.8793 (t) cc_final: 0.8557 (m) REVERT: R 49 MET cc_start: 0.8627 (tpt) cc_final: 0.7979 (mmt) REVERT: R 59 MET cc_start: 0.6402 (mtm) cc_final: 0.5917 (mtt) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.0634 time to fit residues: 12.4656 Evaluate side-chains 136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.0020 chunk 11 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.149593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114810 restraints weight = 15607.638| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.72 r_work: 0.3533 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9107 Z= 0.123 Angle : 0.541 11.846 12389 Z= 0.282 Chirality : 0.042 0.343 1381 Planarity : 0.004 0.053 1580 Dihedral : 3.955 20.848 1245 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.65 % Allowed : 18.26 % Favored : 80.09 % 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 are not related in a simple way. whole: 1.32 (0.26), residues: 1131 helix: 2.19 (0.23), residues: 514 sheet: -0.06 (0.38), residues: 198 loop : -0.26 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.025 0.001 TYR R 372 PHE 0.014 0.001 PHE C 151 TRP 0.018 0.001 TRP C 82 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9105) covalent geometry : angle 0.54098 / 0.28 (12385) SS BOND : bond 0.00044 / 0.02 ( 2) SS BOND : angle 0.38512 / 0.20 ( 4) hydrogen bonds : bond 0.03350 / 2.26 ( 477) hydrogen bonds : angle 4.04622 / 2.90 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.47 seconds wall clock time: 38 minutes 37.66 seconds (2317.66 seconds total)