Starting phenix.real_space_refine on Sat Jun 7 19:02:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908.map" model { file = "/net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hn8_34908/06_2025/8hn8_34908_neut.cif" } resolution = 3.0 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= -0.006 sd= 0.162 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 59 5.16 5 C 5673 2.51 5 N 1489 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.17, per 1000 atoms: 0.70 Number of scatterers: 8860 At special positions: 0 Unit cell: (94.64, 122.72, 131.04, 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 59 16.00 O 1639 8.00 N 1489 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.5% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.681A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 52' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.538A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.962A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.080A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.527A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.637A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.184A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.749A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 14 through 43 removed outlier: 3.560A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 78 removed outlier: 5.598A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 85 through 118 Processing helix chain 'R' and resid 118 through 125 removed outlier: 3.684A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.525A pdb=" N ILE R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 171 through 205 removed outlier: 5.302A pdb=" N VAL R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 4.038A pdb=" N ILE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR R 198 " --> pdb=" O ASN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 327 removed outlier: 3.541A pdb=" N LEU R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.792A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.744A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 344 " --> pdb=" O TYR R 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 364 through 374 removed outlier: 3.517A pdb=" N ALA R 368 " --> pdb=" O ARG R 364 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.580A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.076A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.132A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.244A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.629A 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: 6.982A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.341A 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 removed outlier: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.512A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.207A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.179A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.559A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148 418 hydrogen bonds defined for protein. 1194 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: 2.42 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1432 1.32 - 1.44: 2575 1.44 - 1.57: 4970 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9062 Sorted by residual: bond pdb=" CG HSM R 401 " pdb=" ND1 HSM R 401 " ideal model delta sigma weight residual 1.383 1.258 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CD2 HSM R 401 " pdb=" NE2 HSM R 401 " ideal model delta sigma weight residual 1.376 1.293 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C LEU R 301 " pdb=" O LEU R 301 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" CA ALA R 298 " pdb=" CB ALA R 298 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.12e+01 bond pdb=" N ALA R 298 " pdb=" CA ALA R 298 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.92e+00 ... (remaining 9057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11917 1.48 - 2.95: 282 2.95 - 4.43: 55 4.43 - 5.91: 14 5.91 - 7.38: 5 Bond angle restraints: 12273 Sorted by residual: angle pdb=" N LEU R 293 " pdb=" CA LEU R 293 " pdb=" C LEU R 293 " ideal model delta sigma weight residual 111.28 104.04 7.24 1.09e+00 8.42e-01 4.41e+01 angle pdb=" CA LEU R 301 " pdb=" C LEU R 301 " pdb=" N ALA R 302 " ideal model delta sigma weight residual 117.04 122.25 -5.21 1.24e+00 6.50e-01 1.76e+01 angle pdb=" C LEU R 295 " pdb=" N LEU R 296 " pdb=" CA LEU R 296 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 108.14 113.31 -5.17 1.52e+00 4.33e-01 1.16e+01 angle pdb=" C LYS B 280 " pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4845 17.54 - 35.07: 414 35.07 - 52.61: 53 52.61 - 70.15: 14 70.15 - 87.69: 11 Dihedral angle restraints: 5337 sinusoidal: 2082 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -160.93 74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CB GLU R 165 " pdb=" CG GLU R 165 " pdb=" CD GLU R 165 " pdb=" OE1 GLU R 165 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.076: 321 0.076 - 0.115: 88 0.115 - 0.153: 18 0.153 - 0.191: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA LEU R 296 " pdb=" N LEU R 296 " pdb=" C LEU R 296 " pdb=" CB LEU R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ARG R 299 " pdb=" N ARG R 299 " pdb=" C ARG R 299 " pdb=" CB ARG R 299 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU R 293 " pdb=" CB LEU R 293 " pdb=" CD1 LEU R 293 " pdb=" CD2 LEU R 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1369 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 301 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU R 301 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 301 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 334 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO R 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.020 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1325 2.76 - 3.30: 8050 3.30 - 3.83: 13942 3.83 - 4.37: 16368 4.37 - 4.90: 29837 Nonbonded interactions: 69522 Sorted by model distance: nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.225 3.120 nonbonded pdb=" OG SER S 134 " pdb=" OE1 GLU S 234 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.328 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.336 3.040 ... (remaining 69517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 51.690 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.003 0.125 9065 Z= 0.192 Angle : 0.590 7.382 12279 Z= 0.349 Chirality : 0.042 0.191 1372 Planarity : 0.003 0.041 1543 Dihedral : 13.370 87.685 3228 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.41 % Allowed : 0.21 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.25), residues: 1102 helix: 1.69 (0.28), residues: 383 sheet: 0.46 (0.31), residues: 280 loop : -0.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE R 169 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.15579 ( 418) hydrogen bonds : angle 5.42055 ( 1194) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.72654 ( 6) covalent geometry : bond 0.00334 ( 9062) covalent geometry : angle 0.58955 (12273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 1.033 Fit side-chains REVERT: A 309 ASP cc_start: 0.7096 (m-30) cc_final: 0.6716 (m-30) REVERT: R 125 GLN cc_start: 0.6974 (tt0) cc_final: 0.6418 (tt0) REVERT: R 297 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4287 (mtt180) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 1.1249 time to fit residues: 174.8784 Evaluate side-chains 106 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 297 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.0000 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121523 restraints weight = 10101.867| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.26 r_work: 0.3286 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9065 Z= 0.106 Angle : 0.496 6.355 12279 Z= 0.264 Chirality : 0.041 0.196 1372 Planarity : 0.004 0.038 1543 Dihedral : 5.183 60.787 1220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.35 % Allowed : 9.23 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.87 (0.26), residues: 1102 helix: 2.19 (0.27), residues: 376 sheet: 0.43 (0.30), residues: 288 loop : -0.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 48 PHE 0.016 0.001 PHE R 322 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 418) hydrogen bonds : angle 4.25108 ( 1194) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.67609 ( 6) covalent geometry : bond 0.00222 ( 9062) covalent geometry : angle 0.49607 (12273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.929 Fit side-chains REVERT: A 309 ASP cc_start: 0.7052 (m-30) cc_final: 0.6650 (m-30) REVERT: A 354 PHE cc_start: 0.8151 (t80) cc_final: 0.7842 (t80) REVERT: B 247 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8364 (OUTLIER) REVERT: B 268 ASN cc_start: 0.8089 (m110) cc_final: 0.7873 (m110) REVERT: R 47 ARG cc_start: 0.8463 (mpt180) cc_final: 0.8128 (mpt180) REVERT: R 125 GLN cc_start: 0.6811 (tt0) cc_final: 0.6211 (tt0) REVERT: R 297 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4628 (mtt180) REVERT: S 11 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7835 (tt) outliers start: 13 outliers final: 6 residues processed: 125 average time/residue: 1.1525 time to fit residues: 154.6704 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.0020 chunk 87 optimal weight: 9.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116587 restraints weight = 10424.248| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.25 r_work: 0.3208 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9065 Z= 0.145 Angle : 0.519 6.132 12279 Z= 0.277 Chirality : 0.043 0.213 1372 Planarity : 0.004 0.042 1543 Dihedral : 5.023 59.857 1220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 10.37 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.71 (0.25), residues: 1102 helix: 2.11 (0.27), residues: 381 sheet: 0.26 (0.30), residues: 287 loop : -0.85 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 169 TYR 0.021 0.001 TYR S 178 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 418) hydrogen bonds : angle 4.22971 ( 1194) SS BOND : bond 0.00403 ( 3) SS BOND : angle 0.69554 ( 6) covalent geometry : bond 0.00344 ( 9062) covalent geometry : angle 0.51904 (12273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.370 Fit side-chains REVERT: A 255 ASN cc_start: 0.8055 (m-40) cc_final: 0.7584 (m110) REVERT: A 309 ASP cc_start: 0.7125 (m-30) cc_final: 0.6706 (m-30) REVERT: A 354 PHE cc_start: 0.8317 (t80) cc_final: 0.7970 (t80) REVERT: B 215 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: R 47 ARG cc_start: 0.8523 (mpt180) cc_final: 0.8228 (mmt-90) REVERT: R 125 GLN cc_start: 0.7074 (tt0) cc_final: 0.6512 (tt0) REVERT: R 297 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.4969 (mtt180) REVERT: S 11 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7898 (tt) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 1.1868 time to fit residues: 156.4455 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112565 restraints weight = 10266.247| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.25 r_work: 0.3167 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9065 Z= 0.190 Angle : 0.563 6.489 12279 Z= 0.300 Chirality : 0.044 0.208 1372 Planarity : 0.004 0.044 1543 Dihedral : 4.990 58.296 1218 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.01 % Allowed : 10.79 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.47 (0.25), residues: 1102 helix: 1.90 (0.27), residues: 388 sheet: 0.09 (0.30), residues: 286 loop : -1.00 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.002 PHE B 235 TYR 0.024 0.002 TYR S 178 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 418) hydrogen bonds : angle 4.35621 ( 1194) SS BOND : bond 0.00450 ( 3) SS BOND : angle 0.65137 ( 6) covalent geometry : bond 0.00463 ( 9062) covalent geometry : angle 0.56293 (12273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 252 SER cc_start: 0.7176 (m) cc_final: 0.6956 (m) REVERT: A 255 ASN cc_start: 0.8062 (m-40) cc_final: 0.7543 (m110) REVERT: A 309 ASP cc_start: 0.7015 (m-30) cc_final: 0.6560 (m-30) REVERT: B 197 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.6800 (mtp-110) REVERT: B 217 MET cc_start: 0.8189 (pmt) cc_final: 0.7928 (pp-130) REVERT: R 47 ARG cc_start: 0.8530 (mpt180) cc_final: 0.8145 (mpt180) REVERT: R 125 GLN cc_start: 0.7072 (tt0) cc_final: 0.6567 (tt0) REVERT: R 297 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.5016 (mtt180) REVERT: R 322 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: S 11 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7867 (tt) outliers start: 29 outliers final: 12 residues processed: 131 average time/residue: 1.2421 time to fit residues: 174.0687 Evaluate side-chains 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115131 restraints weight = 10209.064| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.24 r_work: 0.3202 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9065 Z= 0.126 Angle : 0.505 6.697 12279 Z= 0.269 Chirality : 0.042 0.177 1372 Planarity : 0.004 0.041 1543 Dihedral : 4.770 59.278 1218 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.80 % Allowed : 13.07 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.25), residues: 1102 helix: 2.02 (0.27), residues: 389 sheet: 0.06 (0.30), residues: 288 loop : -0.95 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.012 0.001 PHE S 27 TYR 0.020 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 418) hydrogen bonds : angle 4.23297 ( 1194) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.59313 ( 6) covalent geometry : bond 0.00289 ( 9062) covalent geometry : angle 0.50468 (12273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8506 (ttm) cc_final: 0.8295 (ttm) REVERT: A 252 SER cc_start: 0.7131 (m) cc_final: 0.6919 (m) REVERT: A 255 ASN cc_start: 0.7938 (m-40) cc_final: 0.7485 (m110) REVERT: A 309 ASP cc_start: 0.7001 (m-30) cc_final: 0.6533 (m-30) REVERT: B 197 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.6804 (mtp-110) REVERT: B 215 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: B 268 ASN cc_start: 0.8121 (m110) cc_final: 0.7913 (m110) REVERT: R 30 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.6041 (mmt) REVERT: R 47 ARG cc_start: 0.8497 (mpt180) cc_final: 0.8108 (mmt-90) REVERT: R 125 GLN cc_start: 0.7019 (tt0) cc_final: 0.6528 (tt0) REVERT: R 297 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5007 (mtt180) REVERT: R 322 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7057 (m-80) outliers start: 27 outliers final: 10 residues processed: 131 average time/residue: 1.0804 time to fit residues: 152.0827 Evaluate side-chains 122 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** R 347 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 = 0.3787 r_free = 0.3787 target = 0.155619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117715 restraints weight = 10181.652| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.24 r_work: 0.3233 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9065 Z= 0.104 Angle : 0.481 6.926 12279 Z= 0.255 Chirality : 0.041 0.196 1372 Planarity : 0.003 0.040 1543 Dihedral : 4.590 59.789 1218 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.90 % Allowed : 13.28 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.25), residues: 1102 helix: 2.26 (0.27), residues: 383 sheet: 0.06 (0.30), residues: 294 loop : -0.84 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.016 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 418) hydrogen bonds : angle 4.10930 ( 1194) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.57118 ( 6) covalent geometry : bond 0.00229 ( 9062) covalent geometry : angle 0.48091 (12273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8505 (ttm) cc_final: 0.8283 (ttm) REVERT: A 252 SER cc_start: 0.6967 (m) cc_final: 0.6765 (m) REVERT: B 197 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.6733 (mtp-110) REVERT: B 215 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 219 ARG cc_start: 0.7606 (tpt-90) cc_final: 0.7232 (tpt170) REVERT: B 268 ASN cc_start: 0.8130 (m110) cc_final: 0.7906 (m110) REVERT: R 30 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.6098 (mmt) REVERT: R 47 ARG cc_start: 0.8438 (mpt180) cc_final: 0.8085 (mpt180) REVERT: R 125 GLN cc_start: 0.6953 (tt0) cc_final: 0.6527 (tt0) REVERT: R 297 ARG cc_start: 0.5536 (OUTLIER) cc_final: 0.4961 (mtt180) REVERT: R 322 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: S 150 SER cc_start: 0.7941 (m) cc_final: 0.7333 (p) outliers start: 28 outliers final: 11 residues processed: 135 average time/residue: 1.1354 time to fit residues: 164.7433 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** R 347 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 = 0.3763 r_free = 0.3763 target = 0.153433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115362 restraints weight = 10328.837| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.26 r_work: 0.3203 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9065 Z= 0.134 Angle : 0.512 6.703 12279 Z= 0.271 Chirality : 0.042 0.220 1372 Planarity : 0.004 0.041 1543 Dihedral : 4.608 59.445 1218 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.70 % Allowed : 13.90 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.61 (0.25), residues: 1102 helix: 2.08 (0.27), residues: 390 sheet: 0.03 (0.29), residues: 294 loop : -0.89 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.012 0.001 PHE S 27 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 418) hydrogen bonds : angle 4.17219 ( 1194) SS BOND : bond 0.00387 ( 3) SS BOND : angle 0.51470 ( 6) covalent geometry : bond 0.00316 ( 9062) covalent geometry : angle 0.51209 (12273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8491 (ttm) cc_final: 0.8257 (ttm) REVERT: A 255 ASN cc_start: 0.7940 (m-40) cc_final: 0.7483 (m110) REVERT: A 309 ASP cc_start: 0.7062 (m-30) cc_final: 0.6609 (m-30) REVERT: B 197 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.6793 (mtp-110) REVERT: B 268 ASN cc_start: 0.8187 (m110) cc_final: 0.7960 (m110) REVERT: R 30 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.6077 (mmt) REVERT: R 125 GLN cc_start: 0.7060 (tt0) cc_final: 0.6589 (tt0) REVERT: R 297 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.4985 (mtt180) REVERT: R 322 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7043 (m-80) outliers start: 26 outliers final: 16 residues processed: 129 average time/residue: 1.1800 time to fit residues: 163.5841 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116865 restraints weight = 10461.953| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.28 r_work: 0.3224 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9065 Z= 0.110 Angle : 0.490 6.917 12279 Z= 0.259 Chirality : 0.041 0.209 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.545 59.953 1218 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.70 % Allowed : 14.52 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.73 (0.25), residues: 1102 helix: 2.29 (0.27), residues: 380 sheet: 0.07 (0.30), residues: 289 loop : -0.85 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.017 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 418) hydrogen bonds : angle 4.12396 ( 1194) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.53208 ( 6) covalent geometry : bond 0.00247 ( 9062) covalent geometry : angle 0.49023 (12273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8486 (ttm) cc_final: 0.8252 (ttm) REVERT: B 197 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.6752 (mtp-110) REVERT: B 268 ASN cc_start: 0.8195 (m110) cc_final: 0.7966 (m110) REVERT: R 30 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.6188 (mmt) REVERT: R 47 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8240 (mmt-90) REVERT: R 125 GLN cc_start: 0.6995 (tt0) cc_final: 0.6574 (tt0) REVERT: R 297 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5035 (mtt180) REVERT: R 322 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: S 150 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7268 (p) outliers start: 26 outliers final: 14 residues processed: 129 average time/residue: 1.0950 time to fit residues: 152.0513 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116686 restraints weight = 10353.190| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.27 r_work: 0.3228 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9065 Z= 0.114 Angle : 0.497 6.264 12279 Z= 0.264 Chirality : 0.042 0.231 1372 Planarity : 0.004 0.039 1543 Dihedral : 4.498 59.727 1218 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 14.73 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.72 (0.25), residues: 1102 helix: 2.20 (0.27), residues: 386 sheet: 0.08 (0.30), residues: 289 loop : -0.83 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.012 0.001 PHE R 27 TYR 0.018 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 418) hydrogen bonds : angle 4.11391 ( 1194) SS BOND : bond 0.00351 ( 3) SS BOND : angle 0.47261 ( 6) covalent geometry : bond 0.00259 ( 9062) covalent geometry : angle 0.49733 (12273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8488 (ttm) cc_final: 0.8253 (ttm) REVERT: B 197 ARG cc_start: 0.7630 (ttm-80) cc_final: 0.6751 (mtp-110) REVERT: B 268 ASN cc_start: 0.8222 (m110) cc_final: 0.7996 (m110) REVERT: R 30 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6178 (mmt) REVERT: R 125 GLN cc_start: 0.6999 (tt0) cc_final: 0.6569 (tt0) REVERT: R 297 ARG cc_start: 0.5529 (OUTLIER) cc_final: 0.4989 (mtt180) REVERT: R 322 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7122 (m-80) outliers start: 26 outliers final: 17 residues processed: 128 average time/residue: 1.3262 time to fit residues: 181.5474 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115262 restraints weight = 10329.949| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.26 r_work: 0.3207 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9065 Z= 0.135 Angle : 0.520 6.047 12279 Z= 0.276 Chirality : 0.043 0.248 1372 Planarity : 0.004 0.040 1543 Dihedral : 4.580 59.822 1218 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.60 (0.25), residues: 1102 helix: 2.01 (0.27), residues: 392 sheet: 0.06 (0.30), residues: 289 loop : -0.87 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.012 0.001 PHE S 27 TYR 0.020 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 418) hydrogen bonds : angle 4.15626 ( 1194) SS BOND : bond 0.00384 ( 3) SS BOND : angle 0.44411 ( 6) covalent geometry : bond 0.00318 ( 9062) covalent geometry : angle 0.52000 (12273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8498 (ttm) cc_final: 0.8265 (ttm) REVERT: A 255 ASN cc_start: 0.7969 (m-40) cc_final: 0.7543 (m110) REVERT: B 197 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.6800 (mtp-110) REVERT: B 219 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7363 (tpt170) REVERT: B 268 ASN cc_start: 0.8238 (m110) cc_final: 0.8023 (m110) REVERT: R 30 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6234 (mmt) REVERT: R 47 ARG cc_start: 0.8577 (mpt180) cc_final: 0.8232 (mmt-90) REVERT: R 125 GLN cc_start: 0.7050 (tt0) cc_final: 0.6649 (tt0) REVERT: R 297 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.4987 (mtt180) REVERT: R 322 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7128 (m-80) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 1.1630 time to fit residues: 158.4816 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 36 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118247 restraints weight = 10290.560| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.26 r_work: 0.3248 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9065 Z= 0.102 Angle : 0.487 5.884 12279 Z= 0.257 Chirality : 0.041 0.230 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.425 58.645 1218 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.28 % Allowed : 15.46 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.25), residues: 1102 helix: 2.28 (0.27), residues: 385 sheet: 0.10 (0.30), residues: 289 loop : -0.80 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.015 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 418) hydrogen bonds : angle 4.05290 ( 1194) SS BOND : bond 0.00320 ( 3) SS BOND : angle 0.51670 ( 6) covalent geometry : bond 0.00223 ( 9062) covalent geometry : angle 0.48678 (12273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7040.74 seconds wall clock time: 122 minutes 12.38 seconds (7332.38 seconds total)