Starting phenix.real_space_refine on Wed Mar 4 03:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598.map" model { file = "/net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qno_4598/03_2026/6qno_4598_neut.cif" } resolution = 4.38 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6647 2.51 5 N 1718 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10429 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1711 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain breaks: 2 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2392 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 306} Chain: "G" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "H" Number of atoms: 1660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} bond proxies already assigned to first conformer: 1692 Chain: "R" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2646 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N SER L 42 " occ=0.94 ... (4 atoms not shown) pdb=" OG SER L 42 " occ=0.94 residue: pdb=" N SER H 176 " occ=0.54 ... (7 atoms not shown) pdb=" OG BSER H 176 " occ=0.34 residue: pdb=" N GLN R 64 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN R 64 " occ=0.50 residue: pdb=" N TRP R 161 " occ=0.50 ... (12 atoms not shown) pdb=" CH2 TRP R 161 " occ=0.50 residue: pdb=" N PHE R 313 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE R 313 " occ=0.50 Time building chain proxies: 2.65, per 1000 atoms: 0.25 Number of scatterers: 10429 At special positions: 0 Unit cell: (90.47, 117.86, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1986 8.00 N 1718 7.00 C 6647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.04 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.04 Simple disulfide: pdb=" SG CYS R 2 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 15 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 611.6 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 17 sheets defined 28.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.734A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.038A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.510A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.793A pdb=" N CYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.539A pdb=" N ASN G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.535A pdb=" N GLY L 153 " --> pdb=" O GLN L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 213 Processing helix chain 'H' and resid 72 through 75 removed outlier: 4.437A pdb=" N GLY H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 213 through 218 removed outlier: 3.864A pdb=" N SER H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 65 removed outlier: 3.543A pdb=" N PHE R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Proline residue: R 53 - end of helix removed outlier: 3.598A pdb=" N HIS R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 69 removed outlier: 4.143A pdb=" N ARG R 69 " --> pdb=" O LYS R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 66 through 69' Processing helix chain 'R' and resid 73 through 101 removed outlier: 3.541A pdb=" N LEU R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 141 removed outlier: 3.508A pdb=" N GLY R 109 " --> pdb=" O PHE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.814A pdb=" N ALA R 153 " --> pdb=" O GLY R 149 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 199 through 212 removed outlier: 3.832A pdb=" N PHE R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 237 removed outlier: 3.509A pdb=" N GLN R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 278 removed outlier: 3.620A pdb=" N GLN R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 284 through 306 removed outlier: 3.923A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix Proline residue: R 303 - end of helix removed outlier: 3.579A pdb=" N TYR R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 319 removed outlier: 5.528A pdb=" N CYS R 316 " --> pdb=" O GLN R 312 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.513A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.622A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.979A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 4.085A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.952A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.714A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 7.062A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.521A pdb=" N ASN L 78 " --> pdb=" O TYR L 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 70 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 60 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR L 74 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU L 58 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 139 through 143 Processing sheet with id=AB3, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AB4, first strand: chain 'H' and resid 22 through 26 removed outlier: 5.604A pdb=" N GLY H 35 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU H 98 " --> pdb=" O CYS H 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.074A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 151 removed outlier: 6.457A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU H 197 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 203 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA H 195 " --> pdb=" O THR H 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 178 through 181 Processing sheet with id=AB8, first strand: chain 'R' and resid 178 through 181 removed outlier: 4.261A pdb=" N SER R 186 " --> pdb=" O GLU R 181 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1214 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: 1.60 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3215 1.34 - 1.46: 2756 1.46 - 1.59: 4591 1.59 - 1.71: 5 1.71 - 1.83: 113 Bond restraints: 10680 Sorted by residual: bond pdb=" C6 RET R 401 " pdb=" C7 RET R 401 " ideal model delta sigma weight residual 1.459 1.657 -0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C8 RET R 401 " pdb=" C9 RET R 401 " ideal model delta sigma weight residual 1.450 1.593 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C10 RET R 401 " pdb=" C11 RET R 401 " ideal model delta sigma weight residual 1.433 1.548 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C14 RET R 401 " pdb=" C15 RET R 401 " ideal model delta sigma weight residual 1.448 1.536 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C12 RET R 401 " pdb=" C13 RET R 401 " ideal model delta sigma weight residual 1.446 1.534 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 10675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13645 2.42 - 4.84: 719 4.84 - 7.27: 106 7.27 - 9.69: 23 9.69 - 12.11: 5 Bond angle restraints: 14498 Sorted by residual: angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C GLN A 204 " pdb=" N ARG A 205 " pdb=" CA ARG A 205 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C LYS R 311 " pdb=" N GLN R 312 " pdb=" CA GLN R 312 " ideal model delta sigma weight residual 120.38 126.94 -6.56 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA GLU A 43 " pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CA TYR R 301 " pdb=" CB TYR R 301 " pdb=" CG TYR R 301 " ideal model delta sigma weight residual 113.90 121.38 -7.48 1.80e+00 3.09e-01 1.73e+01 ... (remaining 14493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 5828 15.88 - 31.76: 406 31.76 - 47.64: 73 47.64 - 63.52: 12 63.52 - 79.39: 8 Dihedral angle restraints: 6327 sinusoidal: 2470 harmonic: 3857 Sorted by residual: dihedral pdb=" CA PHE H 173 " pdb=" C PHE H 173 " pdb=" N PRO H 174 " pdb=" CA PRO H 174 " ideal model delta harmonic sigma weight residual 180.00 125.94 54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA TRP R 175 " pdb=" C TRP R 175 " pdb=" N SER R 176 " pdb=" CA SER R 176 " ideal model delta harmonic sigma weight residual 180.00 -127.18 -52.82 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO R 327 " pdb=" C PRO R 327 " pdb=" N LEU R 328 " pdb=" CA LEU R 328 " ideal model delta harmonic sigma weight residual 180.00 130.79 49.21 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1206 0.071 - 0.142: 357 0.142 - 0.212: 53 0.212 - 0.283: 4 0.283 - 0.354: 4 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 15 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE H 119 " pdb=" CA ILE H 119 " pdb=" CG1 ILE H 119 " pdb=" CG2 ILE H 119 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CG LEU H 237 " pdb=" CB LEU H 237 " pdb=" CD1 LEU H 237 " pdb=" CD2 LEU H 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1621 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 297 " 0.041 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP B 297 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 297 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 297 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 297 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 297 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 130 " 0.008 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP H 130 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 130 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP H 130 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 130 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP H 130 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 130 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 130 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 130 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 130 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 163 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ASP B 163 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 163 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 164 " -0.017 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1916 2.76 - 3.30: 10033 3.30 - 3.83: 17865 3.83 - 4.37: 19716 4.37 - 4.90: 32970 Nonbonded interactions: 82500 Sorted by model distance: nonbonded pdb=" O PHE R 273 " pdb=" OG1 THR R 277 " model vdw 2.227 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.243 3.040 nonbonded pdb=" OG SER L 90 " pdb=" O THR L 97 " model vdw 2.245 3.040 nonbonded pdb=" O VAL R 157 " pdb=" OG1 THR R 160 " model vdw 2.251 3.040 ... (remaining 82495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.010 0.198 10689 Z= 0.474 Angle : 1.252 12.112 14516 Z= 0.684 Chirality : 0.066 0.354 1624 Planarity : 0.008 0.069 1841 Dihedral : 11.761 79.395 3835 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.65 % Allowed : 3.83 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.19), residues: 1318 helix: -2.37 (0.21), residues: 341 sheet: -1.91 (0.26), residues: 322 loop : -3.18 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG H 57 TYR 0.041 0.004 TYR R 257 PHE 0.042 0.005 PHE A 215 TRP 0.066 0.006 TRP B 297 HIS 0.027 0.005 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.01016 (10680) covalent geometry : angle 1.24755 (14498) SS BOND : bond 0.00957 ( 6) SS BOND : angle 1.98476 ( 12) hydrogen bonds : bond 0.11947 ( 438) hydrogen bonds : angle 8.05162 ( 1214) Misc. bond : bond 0.00152 ( 1) link_BETA1-4 : bond 0.00613 ( 1) link_BETA1-4 : angle 3.69685 ( 3) link_NAG-ASN : bond 0.00876 ( 1) link_NAG-ASN : angle 5.43787 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8725 (m-40) cc_final: 0.7308 (t0) REVERT: A 304 GLN cc_start: 0.7462 (tt0) cc_final: 0.7236 (tm-30) REVERT: B 76 ASP cc_start: 0.8235 (p0) cc_final: 0.7855 (t0) REVERT: B 187 VAL cc_start: 0.7742 (t) cc_final: 0.7525 (t) REVERT: B 313 ASN cc_start: 0.8473 (t0) cc_final: 0.8099 (t0) REVERT: G 36 CYS cc_start: 0.8316 (m) cc_final: 0.7327 (m) REVERT: G 39 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8750 (mt-10) REVERT: G 62 ASN cc_start: 0.8563 (t0) cc_final: 0.8326 (t0) REVERT: L 34 THR cc_start: 0.8661 (m) cc_final: 0.8190 (p) REVERT: L 37 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7984 (mt-10) REVERT: H 172 TYR cc_start: 0.7838 (p90) cc_final: 0.7176 (p90) REVERT: R 39 MET cc_start: 0.7449 (mmp) cc_final: 0.7204 (mmm) REVERT: R 69 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7606 (ptp-170) REVERT: R 207 MET cc_start: 0.9121 (mmm) cc_final: 0.8707 (tpp) REVERT: R 308 MET cc_start: 0.8799 (mtp) cc_final: 0.8478 (mtp) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.1159 time to fit residues: 34.3090 Evaluate side-chains 120 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 204 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 91 HIS B 176 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN L 235 ASN H 101 GLN H 191 HIS R 73 ASN R 100 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 312 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.078377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062073 restraints weight = 91530.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062760 restraints weight = 41304.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063624 restraints weight = 30144.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.063974 restraints weight = 24709.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.064161 restraints weight = 22448.790| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10689 Z= 0.170 Angle : 0.778 8.857 14516 Z= 0.412 Chirality : 0.046 0.213 1624 Planarity : 0.006 0.080 1841 Dihedral : 8.011 68.039 1488 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.35 % Allowed : 3.65 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.21), residues: 1318 helix: -0.97 (0.25), residues: 337 sheet: -1.51 (0.27), residues: 322 loop : -2.77 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.032 0.002 TYR R 301 PHE 0.018 0.002 PHE A 215 TRP 0.029 0.002 TRP B 297 HIS 0.007 0.002 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00363 (10680) covalent geometry : angle 0.77315 (14498) SS BOND : bond 0.00525 ( 6) SS BOND : angle 1.36485 ( 12) hydrogen bonds : bond 0.05199 ( 438) hydrogen bonds : angle 6.57322 ( 1214) Misc. bond : bond 0.00581 ( 1) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 3.28871 ( 3) link_NAG-ASN : bond 0.00548 ( 1) link_NAG-ASN : angle 4.38960 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8758 (m-40) cc_final: 0.7604 (t0) REVERT: A 24 ARG cc_start: 0.8467 (ppt170) cc_final: 0.8220 (ttp80) REVERT: B 58 ILE cc_start: 0.8903 (mt) cc_final: 0.8389 (pt) REVERT: B 76 ASP cc_start: 0.8284 (p0) cc_final: 0.8050 (t0) REVERT: B 91 HIS cc_start: 0.7226 (m90) cc_final: 0.6950 (m170) REVERT: B 160 SER cc_start: 0.8789 (p) cc_final: 0.8219 (p) REVERT: B 217 MET cc_start: 0.7179 (mpp) cc_final: 0.6893 (mpp) REVERT: B 313 ASN cc_start: 0.8503 (t0) cc_final: 0.8108 (t0) REVERT: G 36 CYS cc_start: 0.8295 (m) cc_final: 0.6891 (m) REVERT: G 39 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8808 (mt-10) REVERT: G 41 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8396 (mtt90) REVERT: L 34 THR cc_start: 0.8859 (m) cc_final: 0.8417 (p) REVERT: L 37 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7892 (mt-10) REVERT: L 172 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8327 (mtmm) REVERT: L 190 ASP cc_start: 0.8281 (p0) cc_final: 0.8030 (p0) REVERT: H 22 GLN cc_start: 0.7723 (mp10) cc_final: 0.7437 (mp10) REVERT: H 129 PHE cc_start: 0.8659 (t80) cc_final: 0.8318 (t80) REVERT: H 172 TYR cc_start: 0.7937 (p90) cc_final: 0.7150 (p90) REVERT: R 39 MET cc_start: 0.7434 (mmp) cc_final: 0.7233 (mmm) REVERT: R 69 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7283 (mpt-90) REVERT: R 183 MET cc_start: 0.8871 (mtm) cc_final: 0.8452 (mmm) REVERT: R 207 MET cc_start: 0.9080 (mmm) cc_final: 0.8692 (tpp) REVERT: R 305 ILE cc_start: 0.9326 (pt) cc_final: 0.9044 (tt) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1071 time to fit residues: 26.2242 Evaluate side-chains 118 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 63 optimal weight: 0.1980 chunk 22 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.080070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064809 restraints weight = 78027.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065324 restraints weight = 42360.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066076 restraints weight = 31500.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.066320 restraints weight = 25819.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.066362 restraints weight = 23960.932| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10689 Z= 0.134 Angle : 0.699 7.979 14516 Z= 0.369 Chirality : 0.045 0.213 1624 Planarity : 0.005 0.051 1841 Dihedral : 7.263 70.468 1488 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.26 % Allowed : 3.13 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.22), residues: 1318 helix: -0.50 (0.27), residues: 341 sheet: -1.20 (0.29), residues: 308 loop : -2.48 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.019 0.002 TYR B 59 PHE 0.037 0.002 PHE R 85 TRP 0.020 0.002 TRP R 175 HIS 0.007 0.001 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00284 (10680) covalent geometry : angle 0.69560 (14498) SS BOND : bond 0.00496 ( 6) SS BOND : angle 1.19612 ( 12) hydrogen bonds : bond 0.04505 ( 438) hydrogen bonds : angle 6.09670 ( 1214) Misc. bond : bond 0.00291 ( 1) link_BETA1-4 : bond 0.00143 ( 1) link_BETA1-4 : angle 1.91140 ( 3) link_NAG-ASN : bond 0.00399 ( 1) link_NAG-ASN : angle 3.98852 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8821 (m-40) cc_final: 0.7391 (t0) REVERT: A 24 ARG cc_start: 0.8519 (ppt170) cc_final: 0.8251 (ttp80) REVERT: A 53 MET cc_start: 0.5011 (ttp) cc_final: 0.4709 (ttp) REVERT: B 58 ILE cc_start: 0.8764 (mt) cc_final: 0.8280 (pt) REVERT: B 111 TYR cc_start: 0.7793 (m-10) cc_final: 0.7445 (m-10) REVERT: B 313 ASN cc_start: 0.8468 (t0) cc_final: 0.8165 (t0) REVERT: B 325 MET cc_start: 0.7789 (tmm) cc_final: 0.6987 (tmm) REVERT: G 36 CYS cc_start: 0.8066 (m) cc_final: 0.7325 (m) REVERT: G 41 ARG cc_start: 0.8913 (mtt90) cc_final: 0.8218 (mtt90) REVERT: L 34 THR cc_start: 0.8830 (m) cc_final: 0.8363 (p) REVERT: L 37 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7704 (mt-10) REVERT: H 172 TYR cc_start: 0.7758 (p90) cc_final: 0.7114 (p90) REVERT: H 198 GLN cc_start: 0.8798 (tp40) cc_final: 0.8407 (tp40) REVERT: R 39 MET cc_start: 0.7467 (mmp) cc_final: 0.7165 (mmm) REVERT: R 69 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7333 (mtt90) REVERT: R 183 MET cc_start: 0.8740 (mtm) cc_final: 0.8379 (mmm) REVERT: R 189 ILE cc_start: 0.8569 (pt) cc_final: 0.8253 (mp) REVERT: R 253 MET cc_start: 0.9229 (mmm) cc_final: 0.8924 (mmt) REVERT: R 305 ILE cc_start: 0.9303 (pt) cc_final: 0.9101 (tt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0971 time to fit residues: 24.4359 Evaluate side-chains 124 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 100 optimal weight: 0.0060 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.079705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063225 restraints weight = 107207.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064910 restraints weight = 51404.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065455 restraints weight = 37730.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.065485 restraints weight = 29519.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065898 restraints weight = 27398.981| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10689 Z= 0.146 Angle : 0.693 8.754 14516 Z= 0.363 Chirality : 0.046 0.209 1624 Planarity : 0.005 0.062 1841 Dihedral : 7.035 71.212 1488 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.35 % Allowed : 2.70 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1318 helix: -0.15 (0.27), residues: 333 sheet: -1.19 (0.28), residues: 321 loop : -2.38 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.014 0.002 TYR R 178 PHE 0.026 0.002 PHE A 215 TRP 0.021 0.002 TRP B 297 HIS 0.007 0.001 HIS R 211 Details of bonding type rmsd covalent geometry : bond 0.00317 (10680) covalent geometry : angle 0.68931 (14498) SS BOND : bond 0.00574 ( 6) SS BOND : angle 1.23290 ( 12) hydrogen bonds : bond 0.04261 ( 438) hydrogen bonds : angle 5.90298 ( 1214) Misc. bond : bond 0.00314 ( 1) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 1.85641 ( 3) link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 3.87554 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8799 (m-40) cc_final: 0.7363 (t0) REVERT: A 24 ARG cc_start: 0.8510 (ppt170) cc_final: 0.8186 (ttp80) REVERT: A 188 HIS cc_start: 0.8299 (m-70) cc_final: 0.8091 (m-70) REVERT: B 58 ILE cc_start: 0.8828 (mt) cc_final: 0.8424 (pt) REVERT: B 75 GLN cc_start: 0.8876 (mm110) cc_final: 0.8591 (mm-40) REVERT: B 111 TYR cc_start: 0.7919 (m-10) cc_final: 0.7579 (m-10) REVERT: B 313 ASN cc_start: 0.8503 (t0) cc_final: 0.8182 (t0) REVERT: B 325 MET cc_start: 0.7875 (tmm) cc_final: 0.7276 (ppp) REVERT: G 36 CYS cc_start: 0.8063 (m) cc_final: 0.7326 (m) REVERT: L 34 THR cc_start: 0.8882 (m) cc_final: 0.8307 (p) REVERT: L 37 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7665 (mt-10) REVERT: H 129 PHE cc_start: 0.8886 (t80) cc_final: 0.8650 (t80) REVERT: H 172 TYR cc_start: 0.7731 (p90) cc_final: 0.7000 (p90) REVERT: H 198 GLN cc_start: 0.8836 (tp40) cc_final: 0.8435 (tp40) REVERT: R 39 MET cc_start: 0.7407 (mmp) cc_final: 0.7091 (mmm) REVERT: R 69 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7347 (mtt90) REVERT: R 86 MET cc_start: 0.8130 (mmm) cc_final: 0.7889 (mmp) REVERT: R 183 MET cc_start: 0.8802 (mtm) cc_final: 0.8473 (mmm) REVERT: R 189 ILE cc_start: 0.8610 (pt) cc_final: 0.8295 (mp) REVERT: R 207 MET cc_start: 0.8654 (tpp) cc_final: 0.7829 (tpp) REVERT: R 253 MET cc_start: 0.9281 (mmm) cc_final: 0.8911 (mmt) REVERT: R 305 ILE cc_start: 0.9312 (pt) cc_final: 0.9073 (tt) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1119 time to fit residues: 25.5381 Evaluate side-chains 116 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN L 115 GLN L 116 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 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 = 0.3763 r_free = 0.3763 target = 0.077784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062006 restraints weight = 105076.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062943 restraints weight = 51410.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063722 restraints weight = 39952.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.063896 restraints weight = 30665.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064290 restraints weight = 28274.262| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 10689 Z= 0.233 Angle : 0.750 9.101 14516 Z= 0.395 Chirality : 0.046 0.214 1624 Planarity : 0.005 0.056 1841 Dihedral : 7.074 70.731 1488 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.35 % Allowed : 2.96 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.22), residues: 1318 helix: -0.36 (0.26), residues: 339 sheet: -1.25 (0.27), residues: 322 loop : -2.40 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 32 TYR 0.015 0.002 TYR B 105 PHE 0.016 0.002 PHE R 294 TRP 0.019 0.002 TRP R 126 HIS 0.010 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00510 (10680) covalent geometry : angle 0.74595 (14498) SS BOND : bond 0.00694 ( 6) SS BOND : angle 1.68930 ( 12) hydrogen bonds : bond 0.04725 ( 438) hydrogen bonds : angle 5.99036 ( 1214) Misc. bond : bond 0.00308 ( 1) link_BETA1-4 : bond 0.00171 ( 1) link_BETA1-4 : angle 2.52502 ( 3) link_NAG-ASN : bond 0.00427 ( 1) link_NAG-ASN : angle 3.99281 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8881 (m-40) cc_final: 0.7494 (t0) REVERT: A 24 ARG cc_start: 0.8753 (ppt170) cc_final: 0.8431 (ttp80) REVERT: A 38 LEU cc_start: 0.7445 (mp) cc_final: 0.7134 (mp) REVERT: A 53 MET cc_start: 0.5018 (ttp) cc_final: 0.4642 (mtp) REVERT: A 188 HIS cc_start: 0.8249 (m-70) cc_final: 0.8020 (m-70) REVERT: A 345 LYS cc_start: 0.8311 (ptmm) cc_final: 0.8077 (pttp) REVERT: B 58 ILE cc_start: 0.9000 (mt) cc_final: 0.8621 (pt) REVERT: B 111 TYR cc_start: 0.8146 (m-10) cc_final: 0.7625 (m-10) REVERT: B 313 ASN cc_start: 0.8666 (t0) cc_final: 0.8353 (t0) REVERT: G 35 LYS cc_start: 0.8171 (tptt) cc_final: 0.7830 (ptmt) REVERT: H 172 TYR cc_start: 0.7850 (p90) cc_final: 0.7114 (p90) REVERT: R 39 MET cc_start: 0.7411 (mmp) cc_final: 0.7088 (mmm) REVERT: R 69 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7430 (mtt90) REVERT: R 183 MET cc_start: 0.8848 (mtm) cc_final: 0.8526 (mmm) REVERT: R 207 MET cc_start: 0.8704 (tpp) cc_final: 0.7713 (tpp) REVERT: R 211 HIS cc_start: 0.8378 (m90) cc_final: 0.8013 (m90) REVERT: R 253 MET cc_start: 0.9373 (mmm) cc_final: 0.8948 (mmt) REVERT: R 305 ILE cc_start: 0.9314 (pt) cc_final: 0.9018 (tt) REVERT: R 309 MET cc_start: 0.8590 (mmm) cc_final: 0.8242 (mmm) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.1036 time to fit residues: 22.2861 Evaluate side-chains 113 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 HIS R 302 ASN ** R 326 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 = 0.3810 r_free = 0.3810 target = 0.079831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.063757 restraints weight = 105536.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065027 restraints weight = 50876.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065920 restraints weight = 36598.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.066023 restraints weight = 28100.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.066431 restraints weight = 26090.131| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10689 Z= 0.142 Angle : 0.677 9.965 14516 Z= 0.355 Chirality : 0.045 0.256 1624 Planarity : 0.005 0.055 1841 Dihedral : 6.768 71.783 1488 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.26 % Allowed : 1.39 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.22), residues: 1318 helix: -0.09 (0.27), residues: 338 sheet: -1.26 (0.27), residues: 333 loop : -2.28 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 147 TYR 0.014 0.001 TYR R 178 PHE 0.021 0.002 PHE L 123 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00309 (10680) covalent geometry : angle 0.67187 (14498) SS BOND : bond 0.00742 ( 6) SS BOND : angle 2.01093 ( 12) hydrogen bonds : bond 0.04124 ( 438) hydrogen bonds : angle 5.76787 ( 1214) Misc. bond : bond 0.00268 ( 1) link_BETA1-4 : bond 0.00103 ( 1) link_BETA1-4 : angle 1.85314 ( 3) link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 3.72397 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8810 (m-40) cc_final: 0.7391 (t0) REVERT: A 24 ARG cc_start: 0.8711 (ppt170) cc_final: 0.8316 (ttp80) REVERT: A 188 HIS cc_start: 0.8582 (m-70) cc_final: 0.7980 (m-70) REVERT: A 242 ARG cc_start: 0.5507 (mtt-85) cc_final: 0.4449 (mmp-170) REVERT: A 345 LYS cc_start: 0.8253 (ptmm) cc_final: 0.8000 (pttp) REVERT: B 75 GLN cc_start: 0.9204 (mm110) cc_final: 0.8648 (mm-40) REVERT: B 111 TYR cc_start: 0.7962 (m-10) cc_final: 0.7467 (m-10) REVERT: B 313 ASN cc_start: 0.8497 (t0) cc_final: 0.8042 (t0) REVERT: G 35 LYS cc_start: 0.8162 (tptt) cc_final: 0.7764 (ptmt) REVERT: L 37 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8307 (pt0) REVERT: L 114 MET cc_start: 0.7448 (ttm) cc_final: 0.7202 (ttt) REVERT: H 172 TYR cc_start: 0.7763 (p90) cc_final: 0.7022 (p90) REVERT: H 196 LEU cc_start: 0.8650 (tp) cc_final: 0.8425 (tt) REVERT: R 39 MET cc_start: 0.7366 (mmp) cc_final: 0.6998 (mmm) REVERT: R 69 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7326 (mtt90) REVERT: R 155 MET cc_start: 0.9348 (ppp) cc_final: 0.9138 (ppp) REVERT: R 183 MET cc_start: 0.8797 (mtm) cc_final: 0.8470 (mmm) REVERT: R 207 MET cc_start: 0.8907 (tpp) cc_final: 0.8107 (tpp) REVERT: R 253 MET cc_start: 0.9362 (mmm) cc_final: 0.8899 (mmt) REVERT: R 305 ILE cc_start: 0.9336 (pt) cc_final: 0.9048 (tt) REVERT: R 308 MET cc_start: 0.9200 (mtp) cc_final: 0.8582 (tmm) REVERT: R 309 MET cc_start: 0.8620 (mmm) cc_final: 0.8344 (mmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0990 time to fit residues: 22.2239 Evaluate side-chains 113 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.077538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063027 restraints weight = 59076.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.063081 restraints weight = 39823.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063768 restraints weight = 31107.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.063818 restraints weight = 26303.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.063910 restraints weight = 24022.888| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 10689 Z= 0.234 Angle : 0.766 9.580 14516 Z= 0.401 Chirality : 0.047 0.334 1624 Planarity : 0.005 0.047 1841 Dihedral : 6.998 70.841 1488 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.22), residues: 1318 helix: -0.33 (0.26), residues: 337 sheet: -1.29 (0.27), residues: 341 loop : -2.34 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.017 0.002 TYR R 301 PHE 0.019 0.002 PHE A 189 TRP 0.026 0.002 TRP B 297 HIS 0.009 0.002 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00512 (10680) covalent geometry : angle 0.76182 (14498) SS BOND : bond 0.00612 ( 6) SS BOND : angle 1.92331 ( 12) hydrogen bonds : bond 0.04767 ( 438) hydrogen bonds : angle 5.93490 ( 1214) Misc. bond : bond 0.00691 ( 1) link_BETA1-4 : bond 0.00537 ( 1) link_BETA1-4 : angle 2.23819 ( 3) link_NAG-ASN : bond 0.00309 ( 1) link_NAG-ASN : angle 3.84014 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8841 (m-40) cc_final: 0.7395 (t0) REVERT: A 24 ARG cc_start: 0.8763 (ppt170) cc_final: 0.8389 (ttp80) REVERT: A 345 LYS cc_start: 0.8277 (ptmm) cc_final: 0.8021 (pttp) REVERT: B 111 TYR cc_start: 0.7984 (m-10) cc_final: 0.7497 (m-10) REVERT: B 313 ASN cc_start: 0.8627 (t0) cc_final: 0.8340 (t0) REVERT: L 114 MET cc_start: 0.7388 (ttm) cc_final: 0.7033 (ttp) REVERT: L 123 PHE cc_start: 0.7127 (m-10) cc_final: 0.6831 (m-80) REVERT: H 172 TYR cc_start: 0.7744 (p90) cc_final: 0.7080 (p90) REVERT: R 39 MET cc_start: 0.7433 (mmp) cc_final: 0.7076 (mmm) REVERT: R 69 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7447 (mtt90) REVERT: R 155 MET cc_start: 0.9327 (ppp) cc_final: 0.9108 (ppp) REVERT: R 207 MET cc_start: 0.8549 (tpp) cc_final: 0.7736 (tpp) REVERT: R 253 MET cc_start: 0.9272 (mmm) cc_final: 0.8783 (mmt) REVERT: R 305 ILE cc_start: 0.9398 (pt) cc_final: 0.9062 (tt) REVERT: R 308 MET cc_start: 0.9137 (mtp) cc_final: 0.8738 (ttm) REVERT: R 309 MET cc_start: 0.8638 (mmm) cc_final: 0.8357 (mmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1005 time to fit residues: 19.8509 Evaluate side-chains 107 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 56 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.078722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.061195 restraints weight = 119104.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.064289 restraints weight = 54168.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064085 restraints weight = 34613.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.064246 restraints weight = 29389.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064528 restraints weight = 25677.108| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10689 Z= 0.153 Angle : 0.716 12.839 14516 Z= 0.369 Chirality : 0.046 0.375 1624 Planarity : 0.005 0.066 1841 Dihedral : 6.740 72.177 1488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.26 % Allowed : 1.57 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.22), residues: 1318 helix: -0.06 (0.27), residues: 336 sheet: -1.10 (0.28), residues: 324 loop : -2.25 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 41 TYR 0.015 0.002 TYR H 121 PHE 0.034 0.002 PHE R 159 TRP 0.021 0.002 TRP R 175 HIS 0.007 0.001 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00334 (10680) covalent geometry : angle 0.71266 (14498) SS BOND : bond 0.00474 ( 6) SS BOND : angle 1.60172 ( 12) hydrogen bonds : bond 0.04353 ( 438) hydrogen bonds : angle 5.76705 ( 1214) Misc. bond : bond 0.01002 ( 1) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.88137 ( 3) link_NAG-ASN : bond 0.00354 ( 1) link_NAG-ASN : angle 3.64452 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8769 (m-40) cc_final: 0.7370 (t0) REVERT: A 24 ARG cc_start: 0.8755 (ppt170) cc_final: 0.8315 (ttp80) REVERT: A 188 HIS cc_start: 0.8460 (m-70) cc_final: 0.8022 (m-70) REVERT: A 345 LYS cc_start: 0.8233 (ptmm) cc_final: 0.7922 (pttp) REVERT: B 75 GLN cc_start: 0.9246 (mm110) cc_final: 0.9011 (mm-40) REVERT: B 111 TYR cc_start: 0.8081 (m-10) cc_final: 0.7368 (m-10) REVERT: B 217 MET cc_start: 0.7326 (mpp) cc_final: 0.7044 (mpp) REVERT: B 253 PHE cc_start: 0.7041 (m-80) cc_final: 0.6803 (m-80) REVERT: B 313 ASN cc_start: 0.8662 (t0) cc_final: 0.8265 (t0) REVERT: B 325 MET cc_start: 0.8936 (ttp) cc_final: 0.8046 (ppp) REVERT: G 64 PHE cc_start: 0.7840 (m-10) cc_final: 0.7621 (m-10) REVERT: L 114 MET cc_start: 0.7657 (ttm) cc_final: 0.7183 (ttp) REVERT: L 123 PHE cc_start: 0.7098 (m-10) cc_final: 0.6754 (m-80) REVERT: L 190 ASP cc_start: 0.8322 (p0) cc_final: 0.8068 (p0) REVERT: H 172 TYR cc_start: 0.7790 (p90) cc_final: 0.7042 (p90) REVERT: H 196 LEU cc_start: 0.8661 (tp) cc_final: 0.8443 (tt) REVERT: R 39 MET cc_start: 0.7309 (mmp) cc_final: 0.6962 (mmm) REVERT: R 69 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7124 (mpt-90) REVERT: R 155 MET cc_start: 0.9358 (ppp) cc_final: 0.9138 (ppp) REVERT: R 207 MET cc_start: 0.8798 (tpp) cc_final: 0.7968 (tpp) REVERT: R 253 MET cc_start: 0.9393 (mmm) cc_final: 0.8900 (mmt) REVERT: R 305 ILE cc_start: 0.9392 (pt) cc_final: 0.9028 (tt) REVERT: R 309 MET cc_start: 0.8658 (mmm) cc_final: 0.8353 (mmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0975 time to fit residues: 20.3160 Evaluate side-chains 112 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 94 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.063315 restraints weight = 112686.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065382 restraints weight = 52928.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065746 restraints weight = 37100.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.066201 restraints weight = 28972.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.066666 restraints weight = 25592.245| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10689 Z= 0.134 Angle : 0.717 12.516 14516 Z= 0.362 Chirality : 0.045 0.309 1624 Planarity : 0.004 0.050 1841 Dihedral : 6.555 71.207 1488 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.26 % Allowed : 0.35 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.22), residues: 1318 helix: 0.09 (0.27), residues: 333 sheet: -1.08 (0.28), residues: 328 loop : -2.09 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 41 TYR 0.013 0.001 TYR A 296 PHE 0.035 0.002 PHE R 159 TRP 0.022 0.002 TRP R 126 HIS 0.006 0.001 HIS R 65 Details of bonding type rmsd covalent geometry : bond 0.00296 (10680) covalent geometry : angle 0.71371 (14498) SS BOND : bond 0.00474 ( 6) SS BOND : angle 1.54594 ( 12) hydrogen bonds : bond 0.04036 ( 438) hydrogen bonds : angle 5.66173 ( 1214) Misc. bond : bond 0.00650 ( 1) link_BETA1-4 : bond 0.00263 ( 1) link_BETA1-4 : angle 1.71915 ( 3) link_NAG-ASN : bond 0.00349 ( 1) link_NAG-ASN : angle 3.41776 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8749 (m-40) cc_final: 0.7340 (t0) REVERT: A 24 ARG cc_start: 0.8744 (ppt170) cc_final: 0.8269 (ttp80) REVERT: A 345 LYS cc_start: 0.8155 (ptmm) cc_final: 0.7853 (pttp) REVERT: B 111 TYR cc_start: 0.7918 (m-10) cc_final: 0.7363 (m-10) REVERT: B 253 PHE cc_start: 0.6777 (m-80) cc_final: 0.6491 (m-10) REVERT: B 262 MET cc_start: 0.6700 (mmm) cc_final: 0.6368 (mmm) REVERT: B 313 ASN cc_start: 0.8622 (t0) cc_final: 0.8233 (t0) REVERT: B 325 MET cc_start: 0.8824 (ttp) cc_final: 0.8070 (ttp) REVERT: L 114 MET cc_start: 0.7342 (ttm) cc_final: 0.7009 (ttm) REVERT: L 190 ASP cc_start: 0.8234 (p0) cc_final: 0.8018 (p0) REVERT: H 172 TYR cc_start: 0.7708 (p90) cc_final: 0.6981 (p90) REVERT: H 196 LEU cc_start: 0.8611 (tp) cc_final: 0.8375 (tt) REVERT: R 39 MET cc_start: 0.7322 (mmp) cc_final: 0.6958 (mmm) REVERT: R 69 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7269 (mtt90) REVERT: R 155 MET cc_start: 0.9375 (ppp) cc_final: 0.9140 (ppp) REVERT: R 207 MET cc_start: 0.8683 (tpp) cc_final: 0.8167 (tpp) REVERT: R 253 MET cc_start: 0.9348 (mmm) cc_final: 0.8845 (mmt) REVERT: R 305 ILE cc_start: 0.9369 (pt) cc_final: 0.8983 (tt) REVERT: R 309 MET cc_start: 0.8583 (mmm) cc_final: 0.8289 (mmm) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0995 time to fit residues: 21.7257 Evaluate side-chains 114 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.080306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064282 restraints weight = 92243.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065701 restraints weight = 46348.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.066352 restraints weight = 34838.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.066664 restraints weight = 27841.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066998 restraints weight = 25055.917| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10689 Z= 0.140 Angle : 0.750 17.713 14516 Z= 0.379 Chirality : 0.046 0.384 1624 Planarity : 0.005 0.054 1841 Dihedral : 6.498 71.589 1488 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.26 % Allowed : 0.17 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.22), residues: 1318 helix: 0.25 (0.27), residues: 333 sheet: -1.10 (0.28), residues: 323 loop : -2.07 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 41 TYR 0.011 0.001 TYR R 178 PHE 0.034 0.002 PHE R 159 TRP 0.022 0.002 TRP R 175 HIS 0.015 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00307 (10680) covalent geometry : angle 0.74758 (14498) SS BOND : bond 0.00878 ( 6) SS BOND : angle 1.47643 ( 12) hydrogen bonds : bond 0.04167 ( 438) hydrogen bonds : angle 5.71578 ( 1214) Misc. bond : bond 0.01029 ( 1) link_BETA1-4 : bond 0.00253 ( 1) link_BETA1-4 : angle 1.73919 ( 3) link_NAG-ASN : bond 0.00332 ( 1) link_NAG-ASN : angle 3.33387 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8760 (m-40) cc_final: 0.7344 (t0) REVERT: A 24 ARG cc_start: 0.8730 (ppt170) cc_final: 0.8202 (ttp80) REVERT: A 198 MET cc_start: 0.7595 (mmm) cc_final: 0.7290 (mmm) REVERT: A 242 ARG cc_start: 0.5759 (mtt-85) cc_final: 0.4666 (mmp-170) REVERT: A 345 LYS cc_start: 0.8150 (ptmm) cc_final: 0.7838 (pttp) REVERT: B 111 TYR cc_start: 0.7784 (m-10) cc_final: 0.7388 (m-10) REVERT: B 253 PHE cc_start: 0.6483 (m-80) cc_final: 0.6238 (m-10) REVERT: B 262 MET cc_start: 0.6670 (mmm) cc_final: 0.6431 (mmm) REVERT: B 313 ASN cc_start: 0.8534 (t0) cc_final: 0.8259 (t0) REVERT: B 325 MET cc_start: 0.8730 (ttp) cc_final: 0.8177 (ppp) REVERT: G 41 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8435 (mtt90) REVERT: L 190 ASP cc_start: 0.8185 (p0) cc_final: 0.7946 (p0) REVERT: H 112 MET cc_start: 0.7865 (tpt) cc_final: 0.7425 (tpt) REVERT: H 172 TYR cc_start: 0.7533 (p90) cc_final: 0.6932 (p90) REVERT: H 196 LEU cc_start: 0.8489 (tp) cc_final: 0.8279 (tt) REVERT: H 198 GLN cc_start: 0.8876 (tp40) cc_final: 0.8468 (tp40) REVERT: R 39 MET cc_start: 0.7280 (mmp) cc_final: 0.6769 (mmm) REVERT: R 69 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7172 (mpt-90) REVERT: R 155 MET cc_start: 0.9358 (ppp) cc_final: 0.9110 (ppp) REVERT: R 207 MET cc_start: 0.8518 (tpp) cc_final: 0.8072 (tpp) REVERT: R 253 MET cc_start: 0.9264 (mmm) cc_final: 0.8721 (mmt) REVERT: R 305 ILE cc_start: 0.9366 (pt) cc_final: 0.8970 (tt) REVERT: R 309 MET cc_start: 0.8528 (mmm) cc_final: 0.8251 (mmm) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1022 time to fit residues: 21.9428 Evaluate side-chains 112 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 9.9990 chunk 96 optimal weight: 0.0970 chunk 95 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.079053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062537 restraints weight = 127067.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.064441 restraints weight = 68705.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064861 restraints weight = 48203.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065661 restraints weight = 34872.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.066516 restraints weight = 29500.629| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10689 Z= 0.173 Angle : 0.718 9.816 14516 Z= 0.375 Chirality : 0.046 0.207 1624 Planarity : 0.005 0.052 1841 Dihedral : 6.794 71.555 1488 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.22), residues: 1318 helix: 0.15 (0.27), residues: 333 sheet: -1.10 (0.27), residues: 341 loop : -2.10 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 32 TYR 0.014 0.002 TYR H 202 PHE 0.031 0.002 PHE R 159 TRP 0.031 0.002 TRP B 297 HIS 0.012 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00380 (10680) covalent geometry : angle 0.71495 (14498) SS BOND : bond 0.00877 ( 6) SS BOND : angle 1.63765 ( 12) hydrogen bonds : bond 0.04259 ( 438) hydrogen bonds : angle 5.74696 ( 1214) Misc. bond : bond 0.00152 ( 1) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.79692 ( 3) link_NAG-ASN : bond 0.00313 ( 1) link_NAG-ASN : angle 3.45562 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.71 seconds wall clock time: 32 minutes 42.10 seconds (1962.10 seconds total)