Starting phenix.real_space_refine on Fri Feb 14 21:19:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qno_4598/02_2025/6qno_4598_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qno_4598/02_2025/6qno_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_4598/02_2025/6qno_4598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qno_4598/02_2025/6qno_4598.map" model { file = "/net/cci-nas-00/data/ceres_data/6qno_4598/02_2025/6qno_4598_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qno_4598/02_2025/6qno_4598_neut.cif" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.70, per 1000 atoms: 0.64 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: 2.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.18 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: 3.28 Time building geometry restraints manager: 2.71 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: 2.040 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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 10680 Z= 0.652 Angle : 1.248 12.112 14498 Z= 0.683 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 : 12.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.066 0.006 TRP B 297 HIS 0.027 0.005 HIS H 54 PHE 0.042 0.005 PHE A 215 TYR 0.041 0.004 TYR R 257 ARG 0.010 0.002 ARG H 57 *********************** 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 : 1.151 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: 0.7306 (t0) REVERT: A 304 GLN cc_start: 0.7462 (tt0) cc_final: 0.7188 (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: 0.7526 (t) REVERT: B 313 ASN cc_start: 0.8473 (t0) cc_final: 0.8100 (t0) REVERT: G 36 CYS cc_start: 0.8316 (m) cc_final: 0.7326 (m) REVERT: G 39 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8751 (mt-10) 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: 0.7986 (mt-10) REVERT: H 172 TYR cc_start: 0.7838 (p90) cc_final: 0.7177 (p90) REVERT: R 39 MET cc_start: 0.7449 (mmp) cc_final: 0.7203 (mmm) REVERT: R 69 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7608 (ptp-170) REVERT: R 207 MET cc_start: 0.9121 (mmm) cc_final: 0.8705 (tpp) REVERT: R 253 MET cc_start: 0.9315 (mmm) cc_final: 0.8899 (mmm) REVERT: R 308 MET cc_start: 0.8799 (mtp) cc_final: 0.8479 (mtp) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.2753 time to fit residues: 81.2276 Evaluate side-chains 119 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 B 62 HIS B 91 HIS B 176 GLN 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 = 0.3811 r_free = 0.3811 target = 0.079750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.062946 restraints weight = 115684.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064852 restraints weight = 58819.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065335 restraints weight = 41628.460| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 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 = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10680 Z= 0.208 Angle : 0.763 8.397 14498 Z= 0.405 Chirality : 0.046 0.232 1624 Planarity : 0.006 0.075 1841 Dihedral : 7.855 68.567 1488 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.52 % Allowed : 3.91 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1318 helix: -0.74 (0.26), residues: 329 sheet: -1.54 (0.27), residues: 321 loop : -2.68 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.007 0.002 HIS R 65 PHE 0.016 0.002 PHE A 215 TYR 0.030 0.002 TYR R 301 ARG 0.006 0.001 ARG B 134 *********************** 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 189 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 1.213 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: 0.8800 (m-40) cc_final: 0.7648 (t0) REVERT: A 24 ARG cc_start: 0.8479 (ppt170) cc_final: 0.8225 (ttp80) REVERT: A 304 GLN cc_start: 0.7427 (tt0) cc_final: 0.7117 (tm-30) REVERT: A 305 CYS cc_start: 0.7923 (m) cc_final: 0.7504 (t) REVERT: B 58 ILE cc_start: 0.8944 (mt) cc_final: 0.8288 (pt) REVERT: B 76 ASP cc_start: 0.8369 (p0) cc_final: 0.8081 (t0) REVERT: B 91 HIS cc_start: 0.7169 (m90) cc_final: 0.6801 (m170) REVERT: B 111 TYR cc_start: 0.8196 (m-10) cc_final: 0.7564 (m-10) REVERT: B 160 SER cc_start: 0.8714 (p) cc_final: 0.8199 (p) REVERT: B 187 VAL cc_start: 0.7475 (t) cc_final: 0.7201 (t) REVERT: B 217 MET cc_start: 0.7157 (mpp) cc_final: 0.6877 (mpp) REVERT: B 313 ASN cc_start: 0.8529 (t0) cc_final: 0.8186 (t0) REVERT: G 36 CYS cc_start: 0.8344 (m) cc_final: 0.6785 (m) REVERT: G 39 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8767 (mt-10) REVERT: L 34 THR cc_start: 0.8805 (m) cc_final: 0.8350 (p) REVERT: L 37 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7919 (mt-10) REVERT: L 172 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8287 (mtmm) REVERT: L 190 ASP cc_start: 0.8248 (p0) cc_final: 0.8004 (p0) REVERT: H 22 GLN cc_start: 0.7762 (mp10) cc_final: 0.7484 (mp10) REVERT: H 129 PHE cc_start: 0.8658 (t80) cc_final: 0.8346 (t80) REVERT: H 172 TYR cc_start: 0.8028 (p90) cc_final: 0.7334 (p90) REVERT: R 69 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7262 (mpt-90) REVERT: R 183 MET cc_start: 0.8782 (mtm) cc_final: 0.8420 (mmm) REVERT: R 207 MET cc_start: 0.8928 (mmm) cc_final: 0.8563 (tpp) REVERT: R 253 MET cc_start: 0.9434 (mmm) cc_final: 0.9000 (mmt) REVERT: R 302 ASN cc_start: 0.8810 (m110) cc_final: 0.8203 (m110) REVERT: R 305 ILE cc_start: 0.9324 (pt) cc_final: 0.9000 (tt) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.2586 time to fit residues: 65.9574 Evaluate side-chains 127 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.077583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.061855 restraints weight = 94482.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.062931 restraints weight = 45279.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063568 restraints weight = 32460.172| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 10680 Z= 0.305 Angle : 0.765 9.451 14498 Z= 0.406 Chirality : 0.047 0.221 1624 Planarity : 0.005 0.049 1841 Dihedral : 7.514 67.551 1488 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.52 % Allowed : 3.22 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1318 helix: -0.74 (0.26), residues: 347 sheet: -1.27 (0.28), residues: 306 loop : -2.57 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 297 HIS 0.010 0.002 HIS B 54 PHE 0.034 0.002 PHE R 85 TYR 0.018 0.002 TYR A 287 ARG 0.008 0.001 ARG B 134 *********************** 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 160 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 1.230 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 24 ARG cc_start: 0.8605 (ppt170) cc_final: 0.8228 (ttp80) REVERT: A 53 MET cc_start: 0.5126 (ttp) cc_final: 0.4873 (ttp) REVERT: A 305 CYS cc_start: 0.7775 (m) cc_final: 0.7283 (t) REVERT: B 58 ILE cc_start: 0.8981 (mt) cc_final: 0.8514 (pt) REVERT: B 91 HIS cc_start: 0.6952 (m90) cc_final: 0.6732 (m170) REVERT: B 325 MET cc_start: 0.7881 (tmm) cc_final: 0.6970 (tmm) REVERT: G 36 CYS cc_start: 0.8101 (m) cc_final: 0.7307 (m) REVERT: L 34 THR cc_start: 0.8909 (m) cc_final: 0.8482 (p) REVERT: L 37 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7770 (mt-10) REVERT: L 114 MET cc_start: 0.7555 (ttm) cc_final: 0.6933 (ttm) REVERT: H 172 TYR cc_start: 0.7850 (p90) cc_final: 0.7168 (p90) REVERT: R 69 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7447 (mtt90) REVERT: R 183 MET cc_start: 0.8802 (mtm) cc_final: 0.8471 (mmm) REVERT: R 253 MET cc_start: 0.9331 (mmm) cc_final: 0.8828 (mmt) REVERT: R 305 ILE cc_start: 0.9342 (pt) cc_final: 0.9055 (tt) outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 0.2448 time to fit residues: 53.8445 Evaluate side-chains 115 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 15 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 311 HIS ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.063315 restraints weight = 125569.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.065801 restraints weight = 63487.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.066096 restraints weight = 40198.335| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10680 Z= 0.189 Angle : 0.683 7.943 14498 Z= 0.360 Chirality : 0.045 0.236 1624 Planarity : 0.005 0.055 1841 Dihedral : 7.016 68.583 1488 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.26 % Allowed : 2.96 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.22), residues: 1318 helix: -0.33 (0.27), residues: 344 sheet: -1.15 (0.29), residues: 305 loop : -2.33 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 175 HIS 0.006 0.001 HIS R 211 PHE 0.021 0.002 PHE A 215 TYR 0.015 0.002 TYR R 178 ARG 0.007 0.001 ARG A 242 *********************** 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 172 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.281 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: 0.8790 (m-40) cc_final: 0.7337 (t0) REVERT: A 24 ARG cc_start: 0.8524 (ppt170) cc_final: 0.8172 (ttp80) REVERT: A 53 MET cc_start: 0.5232 (ttp) cc_final: 0.4816 (ttp) REVERT: A 242 ARG cc_start: 0.5711 (mtt-85) cc_final: 0.4669 (mmp80) REVERT: A 304 GLN cc_start: 0.7560 (tt0) cc_final: 0.7357 (tm-30) REVERT: A 305 CYS cc_start: 0.7851 (m) cc_final: 0.7488 (t) REVERT: A 345 LYS cc_start: 0.8269 (ptmm) cc_final: 0.8037 (pttp) REVERT: B 75 GLN cc_start: 0.8835 (mm110) cc_final: 0.8576 (mm-40) REVERT: B 91 HIS cc_start: 0.7069 (m90) cc_final: 0.6819 (m170) REVERT: B 111 TYR cc_start: 0.8062 (m-10) cc_final: 0.7484 (m-10) REVERT: B 253 PHE cc_start: 0.6761 (m-80) cc_final: 0.6475 (m-80) REVERT: B 313 ASN cc_start: 0.8486 (t0) cc_final: 0.8056 (t0) REVERT: B 325 MET cc_start: 0.8254 (tmm) cc_final: 0.7342 (tmm) REVERT: G 31 MET cc_start: 0.7360 (ppp) cc_final: 0.6967 (tpp) REVERT: G 36 CYS cc_start: 0.8128 (m) cc_final: 0.7434 (m) REVERT: H 129 PHE cc_start: 0.8689 (t80) cc_final: 0.8440 (t80) REVERT: H 172 TYR cc_start: 0.7853 (p90) cc_final: 0.7136 (p90) REVERT: H 198 GLN cc_start: 0.8949 (tp40) cc_final: 0.8542 (tp40) REVERT: R 69 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7420 (mtt90) REVERT: R 183 MET cc_start: 0.8767 (mtm) cc_final: 0.8480 (mmm) REVERT: R 189 ILE cc_start: 0.8727 (pt) cc_final: 0.8381 (mp) REVERT: R 207 MET cc_start: 0.8722 (tpp) cc_final: 0.8336 (tpp) REVERT: R 253 MET cc_start: 0.9290 (mmm) cc_final: 0.8846 (mmt) REVERT: R 305 ILE cc_start: 0.9300 (pt) cc_final: 0.8978 (tt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2541 time to fit residues: 59.6065 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 : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 1 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 115 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.079780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063678 restraints weight = 110641.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064961 restraints weight = 53791.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.065803 restraints weight = 39238.706| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10680 Z= 0.211 Angle : 0.692 10.204 14498 Z= 0.358 Chirality : 0.045 0.259 1624 Planarity : 0.005 0.050 1841 Dihedral : 6.811 69.129 1488 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.35 % Allowed : 2.26 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1318 helix: 0.01 (0.27), residues: 329 sheet: -1.09 (0.29), residues: 305 loop : -2.27 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 126 HIS 0.008 0.001 HIS B 54 PHE 0.018 0.002 PHE L 123 TYR 0.013 0.002 TYR R 178 ARG 0.005 0.001 ARG L 44 *********************** 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 161 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.126 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: 0.8798 (m-40) cc_final: 0.7370 (t0) REVERT: A 24 ARG cc_start: 0.8601 (ppt170) cc_final: 0.8167 (ttp80) REVERT: A 38 LEU cc_start: 0.7493 (mp) cc_final: 0.7222 (mp) REVERT: A 305 CYS cc_start: 0.7692 (m) cc_final: 0.7340 (t) REVERT: A 345 LYS cc_start: 0.8257 (ptmm) cc_final: 0.8025 (pttp) REVERT: B 75 GLN cc_start: 0.8898 (mm110) cc_final: 0.8652 (mm-40) REVERT: B 91 HIS cc_start: 0.7167 (m90) cc_final: 0.6887 (m170) REVERT: B 111 TYR cc_start: 0.8140 (m-10) cc_final: 0.7574 (m-10) REVERT: B 313 ASN cc_start: 0.8575 (t0) cc_final: 0.8264 (t0) REVERT: B 325 MET cc_start: 0.8270 (tmm) cc_final: 0.7401 (tmm) REVERT: G 35 LYS cc_start: 0.8269 (tptt) cc_final: 0.7270 (ptmt) REVERT: L 37 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8362 (pt0) REVERT: L 115 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6800 (pp30) REVERT: L 123 PHE cc_start: 0.6940 (m-10) cc_final: 0.6697 (m-80) REVERT: H 172 TYR cc_start: 0.7876 (p90) cc_final: 0.7132 (p90) REVERT: R 69 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7380 (mtt90) REVERT: R 183 MET cc_start: 0.8821 (mtm) cc_final: 0.8548 (mmm) REVERT: R 189 ILE cc_start: 0.8727 (pt) cc_final: 0.8425 (mp) REVERT: R 207 MET cc_start: 0.8798 (tpp) cc_final: 0.8511 (tpp) REVERT: R 253 MET cc_start: 0.9327 (mmm) cc_final: 0.8874 (mmt) REVERT: R 305 ILE cc_start: 0.9320 (pt) cc_final: 0.8983 (tt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2393 time to fit residues: 53.3548 Evaluate side-chains 120 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.080837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066281 restraints weight = 75829.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066202 restraints weight = 44072.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066891 restraints weight = 37213.960| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10680 Z= 0.179 Angle : 0.675 9.860 14498 Z= 0.351 Chirality : 0.045 0.254 1624 Planarity : 0.004 0.052 1841 Dihedral : 6.667 71.092 1488 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.35 % Allowed : 0.87 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1318 helix: -0.02 (0.27), residues: 336 sheet: -0.98 (0.29), residues: 301 loop : -2.15 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 297 HIS 0.007 0.001 HIS B 54 PHE 0.014 0.001 PHE R 159 TYR 0.013 0.001 TYR R 178 ARG 0.005 0.000 ARG A 205 *********************** 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 168 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.998 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: 0.8796 (m-40) cc_final: 0.7386 (t0) REVERT: A 24 ARG cc_start: 0.8559 (ppt170) cc_final: 0.8119 (ttp80) REVERT: A 186 GLU cc_start: 0.8356 (pt0) cc_final: 0.7749 (mp0) REVERT: A 188 HIS cc_start: 0.8533 (m-70) cc_final: 0.7984 (m-70) REVERT: A 242 ARG cc_start: 0.5754 (mtt-85) cc_final: 0.4704 (mmp-170) REVERT: A 304 GLN cc_start: 0.7387 (tt0) cc_final: 0.7071 (tp40) REVERT: A 305 CYS cc_start: 0.7565 (m) cc_final: 0.7295 (t) REVERT: A 345 LYS cc_start: 0.8217 (ptmm) cc_final: 0.7961 (pttp) REVERT: B 59 TYR cc_start: 0.7490 (m-80) cc_final: 0.7200 (m-80) REVERT: B 111 TYR cc_start: 0.7758 (m-10) cc_final: 0.7291 (m-10) REVERT: B 313 ASN cc_start: 0.8649 (t0) cc_final: 0.8350 (t0) REVERT: B 325 MET cc_start: 0.8232 (tmm) cc_final: 0.7220 (tmm) REVERT: L 114 MET cc_start: 0.7466 (ttm) cc_final: 0.7008 (ttp) REVERT: L 123 PHE cc_start: 0.6779 (m-10) cc_final: 0.6514 (m-80) REVERT: H 25 GLU cc_start: 0.8679 (mp0) cc_final: 0.8466 (mp0) REVERT: H 172 TYR cc_start: 0.7804 (p90) cc_final: 0.7156 (p90) REVERT: H 196 LEU cc_start: 0.8620 (tp) cc_final: 0.8392 (tt) REVERT: H 198 GLN cc_start: 0.8967 (tp40) cc_final: 0.8552 (tp40) REVERT: R 69 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7403 (mtt90) REVERT: R 155 MET cc_start: 0.9332 (ppp) cc_final: 0.9115 (ppp) REVERT: R 183 MET cc_start: 0.8774 (mtm) cc_final: 0.8519 (mmm) REVERT: R 207 MET cc_start: 0.8902 (tpp) cc_final: 0.8647 (tpp) REVERT: R 253 MET cc_start: 0.9304 (mmm) cc_final: 0.8831 (mmt) REVERT: R 305 ILE cc_start: 0.9282 (pt) cc_final: 0.8990 (tt) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2555 time to fit residues: 58.7766 Evaluate side-chains 121 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.080383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065398 restraints weight = 67965.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.065869 restraints weight = 41145.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.066528 restraints weight = 31245.614| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10680 Z= 0.194 Angle : 0.670 9.038 14498 Z= 0.348 Chirality : 0.044 0.202 1624 Planarity : 0.004 0.046 1841 Dihedral : 6.446 71.801 1488 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.35 % Allowed : 1.13 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.23), residues: 1318 helix: 0.18 (0.27), residues: 336 sheet: -0.98 (0.28), residues: 335 loop : -2.07 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 175 HIS 0.006 0.001 HIS R 65 PHE 0.020 0.002 PHE R 159 TYR 0.014 0.001 TYR R 178 ARG 0.004 0.000 ARG B 134 *********************** 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 154 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.152 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: 0.8781 (m-40) cc_final: 0.7389 (t0) REVERT: A 24 ARG cc_start: 0.8639 (ppt170) cc_final: 0.8158 (ttp80) REVERT: A 186 GLU cc_start: 0.8209 (pt0) cc_final: 0.7769 (mp0) REVERT: A 188 HIS cc_start: 0.8527 (m-70) cc_final: 0.7895 (m-70) REVERT: A 242 ARG cc_start: 0.5944 (mtt-85) cc_final: 0.4758 (mmp-170) REVERT: A 304 GLN cc_start: 0.7516 (tt0) cc_final: 0.7204 (tp40) REVERT: A 305 CYS cc_start: 0.7443 (m) cc_final: 0.7172 (t) REVERT: A 345 LYS cc_start: 0.8214 (ptmm) cc_final: 0.7943 (pttp) REVERT: B 111 TYR cc_start: 0.7767 (m-10) cc_final: 0.7379 (m-10) REVERT: B 313 ASN cc_start: 0.8674 (t0) cc_final: 0.8337 (t0) REVERT: B 325 MET cc_start: 0.8067 (tmm) cc_final: 0.7156 (tmm) REVERT: L 114 MET cc_start: 0.7812 (ttm) cc_final: 0.7208 (ttp) REVERT: L 123 PHE cc_start: 0.6711 (m-10) cc_final: 0.6439 (m-80) REVERT: H 172 TYR cc_start: 0.7801 (p90) cc_final: 0.7113 (p90) REVERT: H 196 LEU cc_start: 0.8625 (tp) cc_final: 0.8395 (tt) REVERT: H 198 GLN cc_start: 0.8929 (tp40) cc_final: 0.8509 (tp40) REVERT: R 69 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7428 (mtt90) REVERT: R 155 MET cc_start: 0.9325 (ppp) cc_final: 0.9093 (ppp) REVERT: R 253 MET cc_start: 0.9320 (mmm) cc_final: 0.8796 (mmt) REVERT: R 305 ILE cc_start: 0.9323 (pt) cc_final: 0.8947 (tt) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2476 time to fit residues: 53.0087 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 : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.081289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065404 restraints weight = 91815.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.067591 restraints weight = 51279.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067862 restraints weight = 37504.100| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10680 Z= 0.169 Angle : 0.662 10.706 14498 Z= 0.341 Chirality : 0.044 0.195 1624 Planarity : 0.004 0.050 1841 Dihedral : 6.335 74.180 1488 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.35 % Allowed : 0.61 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1318 helix: 0.24 (0.27), residues: 336 sheet: -0.95 (0.30), residues: 303 loop : -1.98 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 175 HIS 0.006 0.001 HIS R 65 PHE 0.038 0.001 PHE R 159 TYR 0.011 0.001 TYR A 296 ARG 0.005 0.000 ARG G 41 *********************** 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 155 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.283 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 18 MET cc_start: 0.8558 (mmp) cc_final: 0.7434 (tmm) REVERT: A 22 ASN cc_start: 0.8790 (m-40) cc_final: 0.7448 (t0) REVERT: A 24 ARG cc_start: 0.8644 (ppt170) cc_final: 0.8261 (ttp80) REVERT: A 188 HIS cc_start: 0.8488 (m-70) cc_final: 0.8031 (m-70) REVERT: A 242 ARG cc_start: 0.5834 (mtt-85) cc_final: 0.4709 (mmp-170) REVERT: A 304 GLN cc_start: 0.7564 (tt0) cc_final: 0.7302 (tp40) REVERT: A 305 CYS cc_start: 0.7398 (m) cc_final: 0.7105 (t) REVERT: A 345 LYS cc_start: 0.8183 (ptmm) cc_final: 0.7899 (pttp) REVERT: B 75 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: B 111 TYR cc_start: 0.7931 (m-10) cc_final: 0.7410 (m-10) REVERT: B 253 PHE cc_start: 0.6600 (m-80) cc_final: 0.6398 (m-80) REVERT: B 262 MET cc_start: 0.7103 (mmm) cc_final: 0.6804 (mmm) REVERT: B 313 ASN cc_start: 0.8515 (t0) cc_final: 0.8180 (t0) REVERT: B 325 MET cc_start: 0.8179 (tmm) cc_final: 0.7317 (tmm) REVERT: H 172 TYR cc_start: 0.7757 (p90) cc_final: 0.7115 (p90) REVERT: H 196 LEU cc_start: 0.8593 (tp) cc_final: 0.8345 (tt) REVERT: H 198 GLN cc_start: 0.8979 (tp40) cc_final: 0.8560 (tp40) REVERT: R 69 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7390 (mtt90) REVERT: R 155 MET cc_start: 0.9360 (ppp) cc_final: 0.9105 (ppp) REVERT: R 207 MET cc_start: 0.8715 (tpt) cc_final: 0.8192 (tpp) REVERT: R 253 MET cc_start: 0.9265 (mmm) cc_final: 0.8763 (mmt) REVERT: R 294 PHE cc_start: 0.8725 (m-80) cc_final: 0.8485 (m-80) REVERT: R 305 ILE cc_start: 0.9284 (pt) cc_final: 0.8823 (tt) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2496 time to fit residues: 53.4261 Evaluate side-chains 118 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 75 optimal weight: 0.0060 chunk 7 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 chunk 102 optimal weight: 6.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.081173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064070 restraints weight = 93360.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.066038 restraints weight = 43227.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066918 restraints weight = 28634.081| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10680 Z= 0.164 Angle : 0.702 13.670 14498 Z= 0.353 Chirality : 0.045 0.372 1624 Planarity : 0.004 0.049 1841 Dihedral : 6.258 76.873 1488 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1318 helix: 0.33 (0.28), residues: 337 sheet: -0.92 (0.29), residues: 305 loop : -1.89 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 175 HIS 0.005 0.001 HIS R 211 PHE 0.038 0.001 PHE R 159 TYR 0.013 0.001 TYR R 268 ARG 0.008 0.000 ARG G 41 *********************** 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 159 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.227 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 18 MET cc_start: 0.8495 (mmp) cc_final: 0.7453 (tmm) REVERT: A 22 ASN cc_start: 0.8740 (m-40) cc_final: 0.7441 (t0) REVERT: A 188 HIS cc_start: 0.8312 (m-70) cc_final: 0.8045 (m-70) REVERT: A 304 GLN cc_start: 0.7400 (tt0) cc_final: 0.7126 (tp40) REVERT: A 305 CYS cc_start: 0.7345 (m) cc_final: 0.7047 (t) REVERT: A 345 LYS cc_start: 0.8100 (ptmm) cc_final: 0.7812 (pttp) REVERT: B 111 TYR cc_start: 0.7718 (m-10) cc_final: 0.7344 (m-10) REVERT: B 253 PHE cc_start: 0.6977 (m-80) cc_final: 0.6657 (m-80) REVERT: B 262 MET cc_start: 0.6957 (mmm) cc_final: 0.6624 (mmm) REVERT: B 313 ASN cc_start: 0.8539 (t0) cc_final: 0.8194 (t0) REVERT: B 325 MET cc_start: 0.8200 (tmm) cc_final: 0.6530 (tmm) REVERT: L 190 ASP cc_start: 0.8268 (p0) cc_final: 0.8002 (p0) REVERT: H 172 TYR cc_start: 0.7738 (p90) cc_final: 0.7069 (p90) REVERT: H 196 LEU cc_start: 0.8664 (tp) cc_final: 0.8387 (tt) REVERT: H 198 GLN cc_start: 0.9012 (tp40) cc_final: 0.8613 (tp40) REVERT: R 69 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7271 (mtt90) REVERT: R 155 MET cc_start: 0.9377 (ppp) cc_final: 0.9147 (ppp) REVERT: R 207 MET cc_start: 0.8853 (tpt) cc_final: 0.8486 (tpp) REVERT: R 253 MET cc_start: 0.9388 (mmm) cc_final: 0.8885 (mmt) REVERT: R 305 ILE cc_start: 0.9261 (pt) cc_final: 0.8832 (tt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2398 time to fit residues: 53.5108 Evaluate side-chains 119 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 97 optimal weight: 0.0770 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 91 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064967 restraints weight = 75289.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.066614 restraints weight = 40537.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067189 restraints weight = 29904.365| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10680 Z= 0.182 Angle : 0.718 17.339 14498 Z= 0.363 Chirality : 0.045 0.387 1624 Planarity : 0.004 0.053 1841 Dihedral : 6.215 77.813 1488 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1318 helix: 0.39 (0.28), residues: 337 sheet: -0.96 (0.28), residues: 335 loop : -1.82 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 82 HIS 0.006 0.001 HIS R 65 PHE 0.034 0.002 PHE R 159 TYR 0.010 0.001 TYR R 178 ARG 0.005 0.001 ARG G 41 ********************** 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 155 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.256 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 18 MET cc_start: 0.8563 (mmp) cc_final: 0.7437 (tmm) REVERT: A 22 ASN cc_start: 0.8764 (m-40) cc_final: 0.7452 (t0) REVERT: A 24 ARG cc_start: 0.9011 (ttp-170) cc_final: 0.8485 (ttp80) REVERT: A 188 HIS cc_start: 0.8245 (m-70) cc_final: 0.8006 (m90) REVERT: A 345 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7819 (pttp) REVERT: B 111 TYR cc_start: 0.7860 (m-10) cc_final: 0.7317 (m-10) REVERT: B 253 PHE cc_start: 0.6936 (m-80) cc_final: 0.6648 (m-80) REVERT: B 313 ASN cc_start: 0.8554 (t0) cc_final: 0.8190 (t0) REVERT: B 325 MET cc_start: 0.8566 (tmm) cc_final: 0.7838 (tmm) REVERT: L 190 ASP cc_start: 0.8291 (p0) cc_final: 0.8012 (p0) REVERT: H 112 MET cc_start: 0.7876 (tpt) cc_final: 0.7544 (tpt) REVERT: H 172 TYR cc_start: 0.7659 (p90) cc_final: 0.7003 (p90) REVERT: H 196 LEU cc_start: 0.8606 (tp) cc_final: 0.8332 (tt) REVERT: H 198 GLN cc_start: 0.9065 (tp40) cc_final: 0.8672 (tp40) REVERT: R 69 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7297 (mtt90) REVERT: R 155 MET cc_start: 0.9376 (ppp) cc_final: 0.9140 (ppp) REVERT: R 207 MET cc_start: 0.8671 (tpt) cc_final: 0.8332 (tpp) REVERT: R 253 MET cc_start: 0.9362 (mmm) cc_final: 0.8813 (mmt) REVERT: R 294 PHE cc_start: 0.9048 (m-80) cc_final: 0.8630 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2463 time to fit residues: 53.2436 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 : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.081129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.063943 restraints weight = 122209.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066736 restraints weight = 55864.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067058 restraints weight = 35788.514| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10680 Z= 0.186 Angle : 0.695 14.123 14498 Z= 0.356 Chirality : 0.045 0.312 1624 Planarity : 0.004 0.061 1841 Dihedral : 6.112 67.441 1488 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1318 helix: 0.55 (0.28), residues: 330 sheet: -0.87 (0.28), residues: 322 loop : -1.77 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 82 HIS 0.005 0.001 HIS H 226 PHE 0.035 0.002 PHE R 159 TYR 0.010 0.001 TYR R 178 ARG 0.004 0.000 ARG G 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.44 seconds wall clock time: 65 minutes 25.81 seconds (3925.81 seconds total)