Starting phenix.real_space_refine on Sat Aug 23 11:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.map" model { file = "/net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qzx_18784/08_2025/8qzx_18784.cif" } resolution = 3.01 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 7471 2.51 5 N 1965 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 11708 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2620 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 317} Chain breaks: 2 Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2618 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 318} Chain breaks: 1 Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2629 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2580 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Chain breaks: 3 Chain: "E" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1055 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1, 'SPD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1B NAD A 401 " occ=0.73 ... (42 atoms not shown) pdb=" PN NAD A 401 " occ=0.73 residue: pdb=" C1B NAD B 401 " occ=0.88 ... (42 atoms not shown) pdb=" PN NAD B 401 " occ=0.88 residue: pdb=" C1B NAD C 401 " occ=0.75 ... (42 atoms not shown) pdb=" PN NAD C 401 " occ=0.75 residue: pdb=" C1B NAD D 402 " occ=0.79 ... (42 atoms not shown) pdb=" PN NAD D 402 " occ=0.79 Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 11708 At special positions: 0 Unit cell: (79.4864, 96.3984, 145.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 2196 8.00 N 1965 7.00 C 7471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.90 Conformation dependent library (CDL) restraints added in 555.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2660 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 53.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.868A pdb=" N ASN A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.573A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.796A pdb=" N PHE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 174 through 200 removed outlier: 4.089A pdb=" N TYR A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.008A pdb=" N ASN A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 removed outlier: 3.576A pdb=" N TRP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.530A pdb=" N ASP A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.243A pdb=" N ASP A 315 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.720A pdb=" N ALA A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.538A pdb=" N VAL A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.623A pdb=" N GLN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 51 through 69 removed outlier: 3.639A pdb=" N ASN B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.907A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.532A pdb=" N HIS B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.827A pdb=" N PHE B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 175 through 200 removed outlier: 3.972A pdb=" N CYS B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Proline residue: B 187 - end of helix Processing helix chain 'B' and resid 204 through 217 removed outlier: 3.762A pdb=" N ASN B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 removed outlier: 3.627A pdb=" N TRP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 254 removed outlier: 3.703A pdb=" N TYR B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 312 through 316 removed outlier: 4.404A pdb=" N ASP B 315 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.571A pdb=" N ALA B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.560A pdb=" N GLY C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.821A pdb=" N ASN C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 4.017A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.614A pdb=" N LEU C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.709A pdb=" N PHE C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 174 through 200 removed outlier: 4.122A pdb=" N TYR C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 204 through 215 Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.657A pdb=" N TRP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 254 removed outlier: 3.607A pdb=" N ASP C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 253 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.795A pdb=" N ASP C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.569A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 4.018A pdb=" N ASP C 315 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.608A pdb=" N ALA C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.702A pdb=" N VAL C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.671A pdb=" N ASN D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 4.109A pdb=" N ILE D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.738A pdb=" N PHE D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 175 through 200 removed outlier: 4.099A pdb=" N CYS D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 241 through 252 removed outlier: 3.686A pdb=" N TYR D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.939A pdb=" N ASP D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.926A pdb=" N TYR D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 4.251A pdb=" N ASP D 315 " --> pdb=" O HIS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 removed outlier: 3.784A pdb=" N ALA D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.541A pdb=" N PHE D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234 removed outlier: 7.047A pdb=" N VAL A 130 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 304 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 305 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 341 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 307 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 131 removed outlier: 6.553A pdb=" N ILE B 101 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 131 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 103 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 305 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 341 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR B 307 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.574A pdb=" N ASN B 166 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 233 through 234 removed outlier: 7.059A pdb=" N VAL C 130 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AA6, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.877A pdb=" N VAL D 130 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL D 129 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 101 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL D 131 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 103 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 305 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL D 341 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR D 307 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.241A pdb=" N VAL E 47 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR E 68 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.664A pdb=" N GLN E 107 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.724A pdb=" N ASP E 161 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU E 151 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 159 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER E 153 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 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: 1.33 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.19: 7 1.19 - 1.37: 3991 1.37 - 1.55: 7832 1.55 - 1.72: 51 1.72 - 1.90: 105 Bond restraints: 11986 Sorted by residual: bond pdb=" C ILE E 159 " pdb=" N VAL E 160 " ideal model delta sigma weight residual 1.335 1.015 0.320 1.22e-02 6.72e+03 6.89e+02 bond pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 1.331 1.022 0.308 1.41e-02 5.03e+03 4.78e+02 bond pdb=" C VAL E 146 " pdb=" N VAL E 147 " ideal model delta sigma weight residual 1.330 1.021 0.309 1.48e-02 4.57e+03 4.37e+02 bond pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 1.234 1.475 -0.241 1.25e-02 6.40e+03 3.72e+02 bond pdb=" C ASP E 134 " pdb=" N LEU E 135 " ideal model delta sigma weight residual 1.333 1.049 0.284 1.55e-02 4.16e+03 3.36e+02 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.09: 16201 8.09 - 16.18: 56 16.18 - 24.27: 5 24.27 - 32.36: 3 32.36 - 40.45: 1 Bond angle restraints: 16266 Sorted by residual: angle pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta sigma weight residual 121.85 162.30 -40.45 1.77e+00 3.19e-01 5.22e+02 angle pdb=" C ASN E 143 " pdb=" N ASP E 144 " pdb=" CA ASP E 144 " ideal model delta sigma weight residual 121.50 150.36 -28.86 1.43e+00 4.89e-01 4.07e+02 angle pdb=" O ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 122.39 95.96 26.43 1.48e+00 4.57e-01 3.19e+02 angle pdb=" CA TYR E 37 " pdb=" C TYR E 37 " pdb=" O TYR E 37 " ideal model delta sigma weight residual 121.66 100.37 21.29 1.22e+00 6.72e-01 3.05e+02 angle pdb=" CA ASN E 143 " pdb=" C ASN E 143 " pdb=" N ASP E 144 " ideal model delta sigma weight residual 118.44 142.98 -24.54 1.41e+00 5.03e-01 3.03e+02 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.08: 6395 19.08 - 38.16: 571 38.16 - 57.25: 141 57.25 - 76.33: 44 76.33 - 95.41: 22 Dihedral angle restraints: 7173 sinusoidal: 3002 harmonic: 4171 Sorted by residual: dihedral pdb=" CA GLY E 104 " pdb=" C GLY E 104 " pdb=" N HIS E 105 " pdb=" CA HIS E 105 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C PHE D 52 " pdb=" N PHE D 52 " pdb=" CA PHE D 52 " pdb=" CB PHE D 52 " ideal model delta harmonic sigma weight residual -122.60 -138.72 16.12 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" C ASP D 303 " pdb=" N ASP D 303 " pdb=" CA ASP D 303 " pdb=" CB ASP D 303 " ideal model delta harmonic sigma weight residual -122.60 -135.59 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1058 0.110 - 0.219: 591 0.219 - 0.329: 124 0.329 - 0.439: 9 0.439 - 0.548: 3 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA PHE D 52 " pdb=" N PHE D 52 " pdb=" C PHE D 52 " pdb=" CB PHE D 52 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.52e+00 chirality pdb=" CA GLN E 130 " pdb=" N GLN E 130 " pdb=" C GLN E 130 " pdb=" CB GLN E 130 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB VAL B 130 " pdb=" CA VAL B 130 " pdb=" CG1 VAL B 130 " pdb=" CG2 VAL B 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 1782 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 401 " -0.096 2.00e-02 2.50e+03 7.76e-02 1.20e+02 pdb=" C2N NAD C 401 " 0.170 2.00e-02 2.50e+03 pdb=" C3N NAD C 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4N NAD C 401 " -0.030 2.00e-02 2.50e+03 pdb=" C5N NAD C 401 " 0.017 2.00e-02 2.50e+03 pdb=" C6N NAD C 401 " -0.017 2.00e-02 2.50e+03 pdb=" C7N NAD C 401 " -0.087 2.00e-02 2.50e+03 pdb=" N1N NAD C 401 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 401 " 0.081 2.00e-02 2.50e+03 6.79e-02 9.23e+01 pdb=" C2N NAD A 401 " -0.018 2.00e-02 2.50e+03 pdb=" C3N NAD A 401 " 0.014 2.00e-02 2.50e+03 pdb=" C4N NAD A 401 " 0.111 2.00e-02 2.50e+03 pdb=" C5N NAD A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C6N NAD A 401 " -0.120 2.00e-02 2.50e+03 pdb=" C7N NAD A 401 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NAD A 401 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 402 " 0.107 2.00e-02 2.50e+03 6.71e-02 9.01e+01 pdb=" C2N NAD D 402 " -0.112 2.00e-02 2.50e+03 pdb=" C3N NAD D 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4N NAD D 402 " 0.083 2.00e-02 2.50e+03 pdb=" C5N NAD D 402 " -0.007 2.00e-02 2.50e+03 pdb=" C6N NAD D 402 " -0.060 2.00e-02 2.50e+03 pdb=" C7N NAD D 402 " 0.021 2.00e-02 2.50e+03 pdb=" N1N NAD D 402 " -0.034 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4405 2.90 - 3.40: 11287 3.40 - 3.90: 20052 3.90 - 4.40: 24306 4.40 - 4.90: 38363 Nonbonded interactions: 98413 Sorted by model distance: nonbonded pdb=" O ASP E 134 " pdb=" CA LEU E 135 " model vdw 2.405 2.776 nonbonded pdb=" O ALA D 226 " pdb=" N ILE D 231 " model vdw 2.408 3.120 nonbonded pdb=" N PHE E 136 " pdb=" N ASN E 137 " model vdw 2.420 2.560 nonbonded pdb=" O VAL E 146 " pdb=" CA VAL E 147 " model vdw 2.438 2.776 nonbonded pdb=" O ILE E 159 " pdb=" CA VAL E 160 " model vdw 2.453 2.776 ... (remaining 98408 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 363)) selection = (chain 'B' and (resid 26 through 34 or resid 38 through 150 or resid 154 through \ 168 or resid 171 through 363)) selection = (chain 'C' and (resid 26 through 34 or resid 38 through 73 or resid 81 through 1 \ 50 or resid 154 through 168 or resid 171 through 363)) selection = (chain 'D' and (resid 26 through 73 or resid 81 through 168 or resid 171 through \ 363)) } 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=0.73 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: 3.660 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.470 Find NCS groups from input model: 0.210 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.015 0.320 11986 Z= 1.095 Angle : 1.923 40.445 16266 Z= 1.437 Chirality : 0.128 0.548 1785 Planarity : 0.008 0.078 2070 Dihedral : 16.904 95.409 4513 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 7.06 % Allowed : 12.51 % Favored : 80.43 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.06 (0.21), residues: 1440 helix: 1.62 (0.19), residues: 664 sheet: 0.57 (0.40), residues: 156 loop : -0.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 131 TYR 0.030 0.003 TYR C 70 PHE 0.032 0.003 PHE E 136 TRP 0.031 0.003 TRP A 329 HIS 0.006 0.002 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.01457 (11986) covalent geometry : angle 1.92327 (16266) hydrogen bonds : bond 0.26141 ( 516) hydrogen bonds : angle 8.30060 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7447 (tpt) cc_final: 0.7169 (tpt) REVERT: A 150 MET cc_start: 0.6676 (mtp) cc_final: 0.5670 (mmt) REVERT: A 155 HIS cc_start: 0.4025 (OUTLIER) cc_final: 0.2898 (m90) REVERT: A 166 ASN cc_start: 0.7661 (t0) cc_final: 0.6896 (t0) REVERT: A 220 ASP cc_start: 0.5449 (t0) cc_final: 0.5193 (t0) REVERT: A 298 TYR cc_start: 0.7939 (m-80) cc_final: 0.7698 (m-10) REVERT: B 47 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6597 (mmt) REVERT: B 67 MET cc_start: 0.6728 (mtt) cc_final: 0.6436 (mtm) REVERT: B 130 VAL cc_start: 0.5044 (OUTLIER) cc_final: 0.4826 (t) REVERT: B 138 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: B 145 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7095 (mt) REVERT: B 278 THR cc_start: 0.7760 (p) cc_final: 0.7560 (p) REVERT: B 299 ARG cc_start: 0.5600 (ptp-110) cc_final: 0.5315 (tpt170) REVERT: B 329 TRP cc_start: 0.6341 (OUTLIER) cc_final: 0.5624 (m-10) REVERT: C 313 ASP cc_start: 0.6943 (p0) cc_final: 0.6569 (t0) REVERT: D 41 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6784 (t0) REVERT: D 73 GLU cc_start: 0.7044 (mp0) cc_final: 0.6391 (tm-30) REVERT: D 109 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6162 (mp) REVERT: D 163 ARG cc_start: 0.6646 (mtt180) cc_final: 0.6143 (mmt90) REVERT: D 176 LYS cc_start: 0.7309 (tttt) cc_final: 0.6633 (tptt) REVERT: D 361 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6238 (mp) outliers start: 88 outliers final: 15 residues processed: 345 average time/residue: 0.0860 time to fit residues: 43.6351 Evaluate side-chains 196 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 329 TRP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 361 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 108 ASN A 166 ASN A 296 ASN B 177 ASN B 230 ASN B 296 ASN C 46 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN D 46 GLN D 124 HIS E 84 HIS E 105 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.202069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179920 restraints weight = 14751.333| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.71 r_work: 0.4101 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4007 r_free = 0.4007 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11986 Z= 0.167 Angle : 0.655 9.449 16266 Z= 0.349 Chirality : 0.046 0.166 1785 Planarity : 0.005 0.069 2070 Dihedral : 13.218 86.933 1849 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.89 % Allowed : 15.48 % Favored : 81.64 % 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: 0.77 (0.21), residues: 1440 helix: 1.11 (0.19), residues: 694 sheet: 0.50 (0.37), residues: 188 loop : -0.11 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 167 TYR 0.020 0.002 TYR A 224 PHE 0.021 0.002 PHE A 357 TRP 0.025 0.002 TRP A 203 HIS 0.006 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00342 (11986) covalent geometry : angle 0.65492 (16266) hydrogen bonds : bond 0.05969 ( 516) hydrogen bonds : angle 5.78671 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6299 (mtp) cc_final: 0.5450 (mmt) REVERT: A 155 HIS cc_start: 0.4152 (OUTLIER) cc_final: 0.3696 (m90) REVERT: B 47 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.4797 (mpt) REVERT: B 299 ARG cc_start: 0.5603 (ptp-110) cc_final: 0.4878 (tpt170) REVERT: B 328 SER cc_start: 0.7459 (t) cc_final: 0.7189 (p) REVERT: B 344 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5424 (mp0) REVERT: C 260 ASP cc_start: 0.7610 (t0) cc_final: 0.7362 (t70) REVERT: C 313 ASP cc_start: 0.7534 (p0) cc_final: 0.6458 (t0) REVERT: D 41 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7091 (t0) REVERT: D 145 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7324 (mt) REVERT: D 176 LYS cc_start: 0.7131 (tttt) cc_final: 0.6652 (tptp) REVERT: D 186 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7325 (mtt) REVERT: D 359 LYS cc_start: 0.5537 (mptt) cc_final: 0.4324 (ptmt) outliers start: 36 outliers final: 15 residues processed: 230 average time/residue: 0.0934 time to fit residues: 30.8556 Evaluate side-chains 190 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain E residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 122 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 108 ASN B 296 ASN ** C 108 ASN ** 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 = 0.4432 r_free = 0.4432 target = 0.200007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172526 restraints weight = 15265.497| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.00 r_work: 0.4044 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11986 Z= 0.162 Angle : 0.609 7.047 16266 Z= 0.321 Chirality : 0.046 0.170 1785 Planarity : 0.005 0.060 2070 Dihedral : 11.253 75.662 1827 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.13 % Allowed : 16.60 % Favored : 80.27 % 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: 0.57 (0.22), residues: 1440 helix: 0.82 (0.19), residues: 697 sheet: 0.36 (0.37), residues: 188 loop : -0.02 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 322 TYR 0.027 0.002 TYR D 224 PHE 0.023 0.002 PHE A 357 TRP 0.020 0.002 TRP C 329 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00362 (11986) covalent geometry : angle 0.60930 (16266) hydrogen bonds : bond 0.05285 ( 516) hydrogen bonds : angle 5.45356 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4178 (OUTLIER) cc_final: 0.3709 (m90) REVERT: A 234 TYR cc_start: 0.8166 (m-80) cc_final: 0.7966 (m-80) REVERT: A 315 ASP cc_start: 0.8460 (p0) cc_final: 0.8252 (p0) REVERT: B 47 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.4757 (mpt) REVERT: B 138 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6328 (tm-30) REVERT: B 145 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7114 (mm) REVERT: B 246 MET cc_start: 0.7941 (mmt) cc_final: 0.7584 (mmp) REVERT: B 299 ARG cc_start: 0.5764 (ptp-110) cc_final: 0.4744 (tpt170) REVERT: B 328 SER cc_start: 0.7442 (t) cc_final: 0.7190 (p) REVERT: B 344 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6093 (tp30) REVERT: C 313 ASP cc_start: 0.7658 (p0) cc_final: 0.5963 (t0) REVERT: D 41 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7247 (t0) REVERT: D 145 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7379 (mt) REVERT: D 176 LYS cc_start: 0.7016 (tttt) cc_final: 0.6469 (tptp) REVERT: D 186 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7315 (mtt) REVERT: E 151 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7385 (tp) outliers start: 39 outliers final: 20 residues processed: 203 average time/residue: 0.0934 time to fit residues: 27.7644 Evaluate side-chains 191 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 291 HIS B 124 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS E 58 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.195436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.167724 restraints weight = 15397.104| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.00 r_work: 0.3993 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11986 Z= 0.202 Angle : 0.646 7.140 16266 Z= 0.339 Chirality : 0.047 0.179 1785 Planarity : 0.005 0.063 2070 Dihedral : 10.593 73.304 1827 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.69 % Allowed : 16.84 % Favored : 79.47 % 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: 0.16 (0.22), residues: 1440 helix: 0.44 (0.19), residues: 698 sheet: 0.31 (0.38), residues: 186 loop : -0.21 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 322 TYR 0.015 0.002 TYR A 224 PHE 0.017 0.002 PHE C 153 TRP 0.020 0.002 TRP C 329 HIS 0.006 0.002 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00465 (11986) covalent geometry : angle 0.64582 (16266) hydrogen bonds : bond 0.05524 ( 516) hydrogen bonds : angle 5.50753 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4276 (OUTLIER) cc_final: 0.3698 (m90) REVERT: A 352 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6895 (mp) REVERT: B 47 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.4695 (mpt) REVERT: B 145 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7127 (mm) REVERT: B 220 ASP cc_start: 0.6762 (t0) cc_final: 0.6486 (t0) REVERT: B 246 MET cc_start: 0.7966 (mmt) cc_final: 0.7625 (mmp) REVERT: B 328 SER cc_start: 0.7498 (t) cc_final: 0.7210 (p) REVERT: B 344 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6126 (tp30) REVERT: C 313 ASP cc_start: 0.7877 (p0) cc_final: 0.5875 (t0) REVERT: D 41 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7275 (t0) REVERT: D 163 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6110 (mtt-85) REVERT: D 176 LYS cc_start: 0.7203 (tttt) cc_final: 0.6569 (tptp) REVERT: D 186 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7425 (mtt) REVERT: D 291 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.6198 (t-170) REVERT: E 39 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5041 (mt) REVERT: E 75 ARG cc_start: 0.5110 (ptm160) cc_final: 0.4797 (ttp-110) REVERT: E 102 ASP cc_start: 0.4647 (m-30) cc_final: 0.3822 (t0) REVERT: E 151 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7341 (tp) outliers start: 46 outliers final: 23 residues processed: 209 average time/residue: 0.1043 time to fit residues: 32.2996 Evaluate side-chains 191 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 329 TRP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN C 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.170430 restraints weight = 15428.992| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.01 r_work: 0.4025 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11986 Z= 0.148 Angle : 0.577 7.136 16266 Z= 0.302 Chirality : 0.045 0.203 1785 Planarity : 0.005 0.057 2070 Dihedral : 9.729 72.269 1823 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.73 % Allowed : 18.68 % Favored : 78.59 % 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: 0.25 (0.22), residues: 1440 helix: 0.50 (0.19), residues: 700 sheet: 0.33 (0.39), residues: 180 loop : -0.13 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 299 TYR 0.024 0.002 TYR D 224 PHE 0.014 0.002 PHE A 120 TRP 0.038 0.002 TRP A 203 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00333 (11986) covalent geometry : angle 0.57718 (16266) hydrogen bonds : bond 0.04737 ( 516) hydrogen bonds : angle 5.29673 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.6594 (mmt) cc_final: 0.6243 (mmt) REVERT: A 155 HIS cc_start: 0.4273 (OUTLIER) cc_final: 0.3689 (m90) REVERT: B 47 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.4248 (mpt) REVERT: B 145 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7150 (mm) REVERT: B 220 ASP cc_start: 0.6671 (t0) cc_final: 0.6450 (t0) REVERT: B 246 MET cc_start: 0.7933 (mmt) cc_final: 0.7662 (mmp) REVERT: B 328 SER cc_start: 0.7480 (t) cc_final: 0.7228 (p) REVERT: B 344 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5796 (tp30) REVERT: C 313 ASP cc_start: 0.7807 (p0) cc_final: 0.5852 (t0) REVERT: D 41 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7271 (t0) REVERT: D 176 LYS cc_start: 0.7124 (tttt) cc_final: 0.6459 (tptp) REVERT: D 186 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7378 (mtt) REVERT: E 102 ASP cc_start: 0.4756 (m-30) cc_final: 0.3917 (t0) REVERT: E 151 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7399 (tp) outliers start: 34 outliers final: 17 residues processed: 197 average time/residue: 0.1041 time to fit residues: 30.2884 Evaluate side-chains 181 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.198420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.171136 restraints weight = 15529.949| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.00 r_work: 0.4031 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11986 Z= 0.141 Angle : 0.563 10.198 16266 Z= 0.294 Chirality : 0.044 0.201 1785 Planarity : 0.004 0.054 2070 Dihedral : 9.242 72.359 1821 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.97 % Allowed : 18.77 % Favored : 78.27 % 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: 0.30 (0.22), residues: 1440 helix: 0.57 (0.19), residues: 701 sheet: 0.31 (0.39), residues: 180 loop : -0.14 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 299 TYR 0.019 0.002 TYR D 224 PHE 0.014 0.002 PHE A 120 TRP 0.045 0.002 TRP A 203 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00316 (11986) covalent geometry : angle 0.56253 (16266) hydrogen bonds : bond 0.04500 ( 516) hydrogen bonds : angle 5.20949 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4293 (OUTLIER) cc_final: 0.3731 (m90) REVERT: B 47 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.4153 (mpt) REVERT: B 145 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7161 (mm) REVERT: B 220 ASP cc_start: 0.6655 (t0) cc_final: 0.6421 (t0) REVERT: B 246 MET cc_start: 0.7946 (mmt) cc_final: 0.7670 (mmp) REVERT: B 300 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.6674 (t0) REVERT: B 328 SER cc_start: 0.7485 (t) cc_final: 0.7237 (p) REVERT: B 344 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5679 (tp30) REVERT: C 313 ASP cc_start: 0.7836 (p0) cc_final: 0.5874 (t0) REVERT: D 41 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7270 (t0) REVERT: D 163 ARG cc_start: 0.6581 (mtt180) cc_final: 0.5965 (mtt-85) REVERT: D 176 LYS cc_start: 0.7079 (tttt) cc_final: 0.6454 (tptp) REVERT: D 186 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7263 (mtt) REVERT: E 102 ASP cc_start: 0.4846 (m-30) cc_final: 0.3918 (t0) REVERT: E 151 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7354 (tp) outliers start: 37 outliers final: 24 residues processed: 192 average time/residue: 0.1094 time to fit residues: 30.6499 Evaluate side-chains 188 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 138 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 129 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.200834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173856 restraints weight = 15388.685| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.00 r_work: 0.4062 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3960 r_free = 0.3960 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11986 Z= 0.117 Angle : 0.535 10.658 16266 Z= 0.278 Chirality : 0.043 0.189 1785 Planarity : 0.004 0.049 2070 Dihedral : 8.868 71.108 1821 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.89 % Allowed : 19.57 % Favored : 77.55 % 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: 0.50 (0.22), residues: 1440 helix: 0.75 (0.19), residues: 700 sheet: 0.41 (0.39), residues: 180 loop : -0.05 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 299 TYR 0.020 0.001 TYR D 224 PHE 0.013 0.001 PHE A 357 TRP 0.028 0.002 TRP A 203 HIS 0.003 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00257 (11986) covalent geometry : angle 0.53540 (16266) hydrogen bonds : bond 0.04062 ( 516) hydrogen bonds : angle 5.03593 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6484 (mmt) cc_final: 0.6255 (mmm) REVERT: A 155 HIS cc_start: 0.4194 (OUTLIER) cc_final: 0.3693 (m90) REVERT: B 47 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.3892 (mpt) REVERT: B 220 ASP cc_start: 0.6628 (t0) cc_final: 0.6401 (t0) REVERT: B 246 MET cc_start: 0.7942 (mmt) cc_final: 0.7633 (mmp) REVERT: B 300 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6776 (t0) REVERT: B 328 SER cc_start: 0.7507 (t) cc_final: 0.7278 (p) REVERT: B 344 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5648 (tp30) REVERT: C 313 ASP cc_start: 0.7803 (p0) cc_final: 0.5889 (t0) REVERT: D 41 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7220 (t0) REVERT: D 163 ARG cc_start: 0.6599 (mtt180) cc_final: 0.5982 (mtt-85) REVERT: D 176 LYS cc_start: 0.6934 (tttt) cc_final: 0.6362 (tptp) REVERT: D 186 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: E 60 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.4335 (t-90) REVERT: E 102 ASP cc_start: 0.4984 (m-30) cc_final: 0.3993 (t0) REVERT: E 151 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (tp) outliers start: 36 outliers final: 23 residues processed: 194 average time/residue: 0.1065 time to fit residues: 30.5189 Evaluate side-chains 187 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.190929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167782 restraints weight = 15237.954| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.80 r_work: 0.3930 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11986 Z= 0.133 Angle : 0.552 9.380 16266 Z= 0.288 Chirality : 0.044 0.189 1785 Planarity : 0.004 0.050 2070 Dihedral : 8.741 71.283 1819 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.29 % Allowed : 19.41 % Favored : 77.31 % 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: 0.48 (0.22), residues: 1440 helix: 0.74 (0.19), residues: 700 sheet: 0.35 (0.39), residues: 180 loop : -0.07 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 299 TYR 0.021 0.001 TYR D 224 PHE 0.014 0.001 PHE A 120 TRP 0.025 0.002 TRP A 203 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00299 (11986) covalent geometry : angle 0.55184 (16266) hydrogen bonds : bond 0.04260 ( 516) hydrogen bonds : angle 5.06813 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.6473 (mmt) cc_final: 0.6142 (mmm) REVERT: A 155 HIS cc_start: 0.4162 (OUTLIER) cc_final: 0.3641 (m90) REVERT: B 47 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.3770 (mpt) REVERT: B 138 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6216 (pt0) REVERT: B 145 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7162 (mm) REVERT: B 220 ASP cc_start: 0.6619 (t0) cc_final: 0.6318 (t0) REVERT: B 246 MET cc_start: 0.7939 (mmt) cc_final: 0.7623 (mmp) REVERT: B 300 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6662 (t0) REVERT: B 328 SER cc_start: 0.7409 (t) cc_final: 0.7173 (p) REVERT: B 344 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5724 (tp30) REVERT: C 313 ASP cc_start: 0.7854 (p0) cc_final: 0.5891 (t0) REVERT: D 41 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7128 (t0) REVERT: D 163 ARG cc_start: 0.6556 (mtt180) cc_final: 0.5932 (mtt-85) REVERT: D 176 LYS cc_start: 0.6963 (tttt) cc_final: 0.6354 (tptp) REVERT: D 186 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7150 (mtt) REVERT: E 60 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.4216 (t-90) REVERT: E 102 ASP cc_start: 0.5194 (m-30) cc_final: 0.4229 (t0) outliers start: 41 outliers final: 27 residues processed: 188 average time/residue: 0.1086 time to fit residues: 29.9055 Evaluate side-chains 187 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 230 ASN D 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.185127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161558 restraints weight = 15240.501| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.79 r_work: 0.3854 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11986 Z= 0.229 Angle : 0.658 8.884 16266 Z= 0.346 Chirality : 0.048 0.194 1785 Planarity : 0.005 0.059 2070 Dihedral : 9.203 72.855 1819 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.69 % Allowed : 19.09 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.22), residues: 1440 helix: 0.41 (0.19), residues: 699 sheet: 0.10 (0.38), residues: 185 loop : -0.37 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 299 TYR 0.022 0.002 TYR D 224 PHE 0.016 0.002 PHE C 153 TRP 0.031 0.003 TRP A 203 HIS 0.008 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00530 (11986) covalent geometry : angle 0.65815 (16266) hydrogen bonds : bond 0.05408 ( 516) hydrogen bonds : angle 5.41381 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4342 (OUTLIER) cc_final: 0.3713 (m90) REVERT: B 47 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.3904 (mpt) REVERT: B 138 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: B 145 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (mt) REVERT: B 246 MET cc_start: 0.7872 (mmt) cc_final: 0.7582 (mmp) REVERT: B 300 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6904 (t0) REVERT: B 328 SER cc_start: 0.7435 (t) cc_final: 0.7171 (p) REVERT: B 344 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5797 (tp30) REVERT: C 313 ASP cc_start: 0.7953 (p0) cc_final: 0.5856 (t0) REVERT: D 41 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7206 (t0) REVERT: D 163 ARG cc_start: 0.6692 (mtt180) cc_final: 0.6050 (mtt-85) REVERT: D 176 LYS cc_start: 0.7196 (tttt) cc_final: 0.6606 (tptp) REVERT: D 186 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7261 (mtt) REVERT: E 60 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.4282 (t-90) REVERT: E 102 ASP cc_start: 0.4783 (m-30) cc_final: 0.3807 (t0) outliers start: 46 outliers final: 27 residues processed: 189 average time/residue: 0.1146 time to fit residues: 31.1234 Evaluate side-chains 183 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 130 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164885 restraints weight = 15306.653| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.91 r_work: 0.3923 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11986 Z= 0.125 Angle : 0.562 8.651 16266 Z= 0.294 Chirality : 0.044 0.184 1785 Planarity : 0.005 0.053 2070 Dihedral : 8.853 69.853 1819 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.73 % Allowed : 20.29 % Favored : 76.98 % 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 aren not related in a simple way. whole: 0.29 (0.22), residues: 1440 helix: 0.65 (0.20), residues: 701 sheet: 0.17 (0.39), residues: 179 loop : -0.22 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 299 TYR 0.024 0.001 TYR D 224 PHE 0.013 0.001 PHE A 120 TRP 0.027 0.002 TRP A 203 HIS 0.004 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00274 (11986) covalent geometry : angle 0.56198 (16266) hydrogen bonds : bond 0.04198 ( 516) hydrogen bonds : angle 5.14135 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 155 HIS cc_start: 0.4384 (OUTLIER) cc_final: 0.3784 (m90) REVERT: B 47 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.3610 (mpt) REVERT: B 138 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6291 (pt0) REVERT: B 145 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7223 (mt) REVERT: B 220 ASP cc_start: 0.6523 (t0) cc_final: 0.6169 (t0) REVERT: B 246 MET cc_start: 0.7870 (mmt) cc_final: 0.7618 (mmp) REVERT: B 300 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6679 (t0) REVERT: B 328 SER cc_start: 0.7397 (t) cc_final: 0.7157 (p) REVERT: B 344 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5638 (tp30) REVERT: C 313 ASP cc_start: 0.7853 (p0) cc_final: 0.5809 (t0) REVERT: D 41 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7061 (t0) REVERT: D 163 ARG cc_start: 0.6531 (mtt180) cc_final: 0.5902 (mtt-85) REVERT: D 176 LYS cc_start: 0.6992 (tttt) cc_final: 0.6350 (tptp) REVERT: D 186 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7117 (mtt) REVERT: E 60 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.4094 (t-90) REVERT: E 102 ASP cc_start: 0.4944 (m-30) cc_final: 0.3930 (t0) outliers start: 34 outliers final: 21 residues processed: 180 average time/residue: 0.1079 time to fit residues: 28.5811 Evaluate side-chains 181 residues out of total 1247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 60 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.188405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162550 restraints weight = 15305.981| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.92 r_work: 0.3881 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11986 Z= 0.159 Angle : 0.602 9.374 16266 Z= 0.314 Chirality : 0.045 0.185 1785 Planarity : 0.005 0.053 2070 Dihedral : 8.871 70.863 1819 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 19.97 % Favored : 77.39 % 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 aren not related in a simple way. whole: 0.18 (0.22), residues: 1440 helix: 0.59 (0.19), residues: 700 sheet: 0.12 (0.38), residues: 185 loop : -0.32 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 299 TYR 0.023 0.002 TYR D 224 PHE 0.014 0.002 PHE A 120 TRP 0.026 0.002 TRP A 203 HIS 0.005 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00364 (11986) covalent geometry : angle 0.60177 (16266) hydrogen bonds : bond 0.04644 ( 516) hydrogen bonds : angle 5.21550 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.12 seconds wall clock time: 56 minutes 29.11 seconds (3389.11 seconds total)