Starting phenix.real_space_refine on Mon Jun 9 01:09:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3z_32297/06_2025/7w3z_32297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3z_32297/06_2025/7w3z_32297.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/7w3z_32297/06_2025/7w3z_32297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3z_32297/06_2025/7w3z_32297.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3z_32297/06_2025/7w3z_32297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3z_32297/06_2025/7w3z_32297.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= 0.000 sd= 0.004 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 63 5.16 5 C 6506 2.51 5 N 1744 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 10221 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2396 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 14, 'TRANS': 286} Chain: "L" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 96 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2887 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 340} Chain: "C" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "H" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Time building chain proxies: 6.07, per 1000 atoms: 0.59 Number of scatterers: 10221 At special positions: 0 Unit cell: (111.54, 117.624, 135.876, 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 63 16.00 O 1908 8.00 N 1744 7.00 C 6506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 14 sheets defined 42.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 Proline residue: A 44 - end of helix removed outlier: 3.519A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 103 removed outlier: 3.608A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.127A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 179 removed outlier: 3.583A pdb=" N ILE A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.574A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 290 removed outlier: 3.718A pdb=" N LYS A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.668A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.823A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.823A pdb=" N ARG B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.857A pdb=" N LYS B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.580A pdb=" N ASP B 130 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.882A pdb=" N VAL B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.653A pdb=" N ILE B 217 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B 218 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 219 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.435A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.099A pdb=" N TYR B 291 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.872A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.509A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 9.004A pdb=" N VAL A 294 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS A 185 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.348A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.740A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.696A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.661A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.287A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.730A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.328A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.617A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1464 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: 3.04 Time building geometry restraints manager: 3.00 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: 1852 1.32 - 1.45: 2708 1.45 - 1.57: 5788 1.57 - 1.69: 0 1.69 - 1.82: 95 Bond restraints: 10443 Sorted by residual: bond pdb=" C ILE A 164 " pdb=" O ILE A 164 " ideal model delta sigma weight residual 1.237 1.307 -0.070 1.17e-02 7.31e+03 3.60e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.18e+01 bond pdb=" C ILE A 167 " pdb=" O ILE A 167 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.05e+01 bond pdb=" C ALA A 263 " pdb=" O ALA A 263 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.15e-02 7.56e+03 2.01e+01 bond pdb=" C LEU A 170 " pdb=" O LEU A 170 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.90e+01 ... (remaining 10438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11813 1.65 - 3.30: 2008 3.30 - 4.95: 278 4.95 - 6.60: 38 6.60 - 8.25: 13 Bond angle restraints: 14150 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.10 8.25 1.36e+00 5.41e-01 3.68e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.88 6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.93 3.95 7.80e-01 1.64e+00 2.56e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.43 107.05 6.38 1.26e+00 6.30e-01 2.56e+01 angle pdb=" C LEU A 170 " pdb=" N LEU A 171 " pdb=" CA LEU A 171 " ideal model delta sigma weight residual 120.44 114.00 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 14145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5675 16.73 - 33.46: 452 33.46 - 50.19: 93 50.19 - 66.93: 16 66.93 - 83.66: 2 Dihedral angle restraints: 6238 sinusoidal: 2460 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.38 56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" N PRO H 236 " pdb=" CA PRO H 236 " ideal model delta harmonic sigma weight residual 0.00 29.05 -29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N TYR C 111 " pdb=" CA TYR C 111 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 6235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 999 0.065 - 0.130: 415 0.130 - 0.195: 127 0.195 - 0.260: 37 0.260 - 0.325: 11 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA CYS A 158 " pdb=" N CYS A 158 " pdb=" C CYS A 158 " pdb=" CB CYS A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1586 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS C 127 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C VAL C 315 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2139 2.79 - 3.32: 9678 3.32 - 3.85: 16570 3.85 - 4.37: 20760 4.37 - 4.90: 34262 Nonbonded interactions: 83409 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.291 3.040 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 3.120 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.323 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.338 3.040 ... (remaining 83404 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: 0.680 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: 0.080 Set scattering table: 0.100 Process input model: 25.380 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 0.105 10447 Z= 0.703 Angle : 1.251 8.252 14156 Z= 0.903 Chirality : 0.083 0.325 1589 Planarity : 0.006 0.053 1801 Dihedral : 12.512 83.657 3795 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.61 % Allowed : 3.93 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.23 (0.22), residues: 1281 helix: 0.81 (0.23), residues: 486 sheet: 0.00 (0.31), residues: 294 loop : -1.14 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 PHE 0.030 0.003 PHE C 199 TYR 0.056 0.003 TYR H 175 ARG 0.013 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.17432 ( 513) hydrogen bonds : angle 6.69857 ( 1464) SS BOND : bond 0.02117 ( 3) SS BOND : angle 3.05859 ( 6) covalent geometry : bond 0.01007 (10443) covalent geometry : angle 1.24918 (14150) Misc. bond : bond 0.10547 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 GLU cc_start: 0.6980 (tp30) cc_final: 0.6667 (tp30) REVERT: B 332 THR cc_start: 0.8243 (t) cc_final: 0.7598 (m) REVERT: B 337 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7538 (mp) REVERT: C 228 ASP cc_start: 0.7555 (m-30) cc_final: 0.6636 (m-30) REVERT: H 109 ASP cc_start: 0.7307 (p0) cc_final: 0.6975 (p0) REVERT: H 234 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7229 (mt-10) outliers start: 18 outliers final: 6 residues processed: 211 average time/residue: 1.3822 time to fit residues: 310.9858 Evaluate side-chains 137 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain H residue 63 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.0020 chunk 74 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 239 GLN A 280 ASN A 334 ASN B 274 ASN C 36 ASN C 88 ASN C 110 ASN C 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.181632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139107 restraints weight = 11044.357| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.00 r_work: 0.3477 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10447 Z= 0.124 Angle : 0.568 8.430 14156 Z= 0.299 Chirality : 0.041 0.137 1589 Planarity : 0.004 0.053 1801 Dihedral : 5.017 55.115 1426 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.39 % Allowed : 11.96 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.22), residues: 1281 helix: 1.97 (0.22), residues: 498 sheet: 0.15 (0.30), residues: 278 loop : -0.82 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE C 199 TYR 0.031 0.001 TYR B 80 ARG 0.010 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 513) hydrogen bonds : angle 4.58749 ( 1464) SS BOND : bond 0.00886 ( 3) SS BOND : angle 1.08568 ( 6) covalent geometry : bond 0.00253 (10443) covalent geometry : angle 0.56806 (14150) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.2387 (OUTLIER) cc_final: 0.2078 (pt) REVERT: A 331 LYS cc_start: 0.7613 (tttt) cc_final: 0.7140 (mmpt) REVERT: B 87 MET cc_start: 0.7757 (tpt) cc_final: 0.7358 (tpt) REVERT: B 94 MET cc_start: 0.4840 (mmt) cc_final: 0.4431 (mmt) REVERT: B 277 ASP cc_start: 0.7632 (m-30) cc_final: 0.6333 (m-30) REVERT: B 281 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: B 337 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7377 (mp) REVERT: C 129 ARG cc_start: 0.7668 (tmm160) cc_final: 0.7312 (ttm-80) REVERT: C 325 MET cc_start: 0.8583 (mmt) cc_final: 0.8118 (mmt) REVERT: D 47 GLU cc_start: 0.8357 (mp0) cc_final: 0.8093 (mt-10) REVERT: H 18 ARG cc_start: 0.7115 (tpp80) cc_final: 0.6838 (tpt-90) REVERT: H 109 ASP cc_start: 0.7820 (p0) cc_final: 0.7591 (p0) outliers start: 38 outliers final: 16 residues processed: 175 average time/residue: 1.5470 time to fit residues: 289.0433 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN L 19 ASN C 36 ASN C 110 ASN C 237 ASN C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135462 restraints weight = 11148.615| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.08 r_work: 0.3424 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10447 Z= 0.129 Angle : 0.544 6.510 14156 Z= 0.286 Chirality : 0.041 0.139 1589 Planarity : 0.004 0.052 1801 Dihedral : 4.972 59.372 1425 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.77 % Allowed : 15.09 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.01 (0.22), residues: 1281 helix: 2.29 (0.22), residues: 498 sheet: 0.40 (0.31), residues: 271 loop : -0.82 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 218 PHE 0.016 0.002 PHE C 199 TYR 0.029 0.001 TYR B 80 ARG 0.008 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 513) hydrogen bonds : angle 4.33391 ( 1464) SS BOND : bond 0.00699 ( 3) SS BOND : angle 1.45769 ( 6) covalent geometry : bond 0.00283 (10443) covalent geometry : angle 0.54351 (14150) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.7595 (tttt) cc_final: 0.7104 (mmpt) REVERT: B 87 MET cc_start: 0.7779 (tpt) cc_final: 0.7387 (tpt) REVERT: B 90 MET cc_start: 0.6742 (ttp) cc_final: 0.6384 (ttp) REVERT: B 94 MET cc_start: 0.4608 (mmt) cc_final: 0.4287 (mmt) REVERT: B 210 ARG cc_start: 0.8292 (ptp-110) cc_final: 0.8086 (ptp-110) REVERT: B 281 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: B 337 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7347 (pp) REVERT: D 47 GLU cc_start: 0.8260 (mp0) cc_final: 0.8036 (mt-10) REVERT: H 109 ASP cc_start: 0.7500 (p0) cc_final: 0.7298 (p0) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 1.3689 time to fit residues: 229.1800 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 36 ASN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133984 restraints weight = 11031.619| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.04 r_work: 0.3330 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10447 Z= 0.131 Angle : 0.535 6.550 14156 Z= 0.281 Chirality : 0.041 0.215 1589 Planarity : 0.004 0.049 1801 Dihedral : 4.840 58.645 1424 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.30 % Allowed : 16.07 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.08 (0.23), residues: 1281 helix: 2.35 (0.23), residues: 500 sheet: 0.43 (0.30), residues: 270 loop : -0.79 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 327 PHE 0.016 0.002 PHE C 199 TYR 0.031 0.002 TYR B 80 ARG 0.008 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 513) hydrogen bonds : angle 4.23052 ( 1464) SS BOND : bond 0.00673 ( 3) SS BOND : angle 1.34738 ( 6) covalent geometry : bond 0.00293 (10443) covalent geometry : angle 0.53434 (14150) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.7502 (tttt) cc_final: 0.6978 (mmpt) REVERT: L 19 ASN cc_start: 0.6331 (OUTLIER) cc_final: 0.5988 (p0) REVERT: B 87 MET cc_start: 0.7795 (tpt) cc_final: 0.7446 (tpt) REVERT: B 90 MET cc_start: 0.6722 (ttp) cc_final: 0.6372 (ttp) REVERT: B 94 MET cc_start: 0.4766 (mmt) cc_final: 0.4517 (mmt) REVERT: B 124 PHE cc_start: 0.3201 (OUTLIER) cc_final: 0.2606 (t80) REVERT: B 277 ASP cc_start: 0.7720 (m-30) cc_final: 0.6332 (m-30) REVERT: B 281 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 285 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6610 (p90) REVERT: B 321 ASP cc_start: 0.8011 (t0) cc_final: 0.7769 (t0) REVERT: H 109 ASP cc_start: 0.7826 (p0) cc_final: 0.7607 (p0) outliers start: 37 outliers final: 20 residues processed: 152 average time/residue: 1.7649 time to fit residues: 287.4021 Evaluate side-chains 144 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 64 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 30 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN C 36 ASN C 110 ASN C 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136417 restraints weight = 11046.341| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.87 r_work: 0.3375 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10447 Z= 0.107 Angle : 0.510 8.174 14156 Z= 0.266 Chirality : 0.040 0.135 1589 Planarity : 0.004 0.051 1801 Dihedral : 4.399 34.448 1422 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.04 % Allowed : 17.50 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.26 (0.23), residues: 1281 helix: 2.54 (0.23), residues: 499 sheet: 0.54 (0.30), residues: 274 loop : -0.76 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 63 PHE 0.014 0.001 PHE C 199 TYR 0.033 0.001 TYR B 80 ARG 0.008 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 513) hydrogen bonds : angle 4.05723 ( 1464) SS BOND : bond 0.00586 ( 3) SS BOND : angle 1.17110 ( 6) covalent geometry : bond 0.00230 (10443) covalent geometry : angle 0.50922 (14150) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.7953 (tt) cc_final: 0.7752 (pt) REVERT: A 331 LYS cc_start: 0.7661 (tttt) cc_final: 0.7084 (mmpt) REVERT: L 19 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.6166 (p0) REVERT: B 87 MET cc_start: 0.7702 (tpt) cc_final: 0.7349 (tpt) REVERT: B 90 MET cc_start: 0.6716 (ttp) cc_final: 0.6360 (ttp) REVERT: B 124 PHE cc_start: 0.3222 (OUTLIER) cc_final: 0.2614 (t80) REVERT: B 277 ASP cc_start: 0.7740 (m-30) cc_final: 0.6347 (m-30) REVERT: B 281 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: D 21 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6786 (tmm) REVERT: H 109 ASP cc_start: 0.7747 (p0) cc_final: 0.7514 (p0) outliers start: 34 outliers final: 17 residues processed: 155 average time/residue: 1.5843 time to fit residues: 263.3803 Evaluate side-chains 145 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 334 ASN C 36 ASN C 142 HIS C 237 ASN H 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.174825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131388 restraints weight = 11054.372| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.00 r_work: 0.3301 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10447 Z= 0.178 Angle : 0.593 8.949 14156 Z= 0.311 Chirality : 0.043 0.139 1589 Planarity : 0.005 0.055 1801 Dihedral : 4.654 38.466 1419 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.39 % Allowed : 19.38 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.00 (0.23), residues: 1281 helix: 2.27 (0.23), residues: 499 sheet: 0.44 (0.30), residues: 269 loop : -0.85 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 36 HIS 0.007 0.001 HIS B 327 PHE 0.023 0.002 PHE C 199 TYR 0.034 0.002 TYR B 80 ARG 0.011 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 513) hydrogen bonds : angle 4.27298 ( 1464) SS BOND : bond 0.00856 ( 3) SS BOND : angle 1.48712 ( 6) covalent geometry : bond 0.00417 (10443) covalent geometry : angle 0.59224 (14150) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6997 (mt) REVERT: A 331 LYS cc_start: 0.7480 (tttt) cc_final: 0.7018 (tptt) REVERT: L 19 ASN cc_start: 0.6658 (OUTLIER) cc_final: 0.6349 (p0) REVERT: B 87 MET cc_start: 0.7767 (tpt) cc_final: 0.7370 (tpt) REVERT: B 90 MET cc_start: 0.6747 (ttp) cc_final: 0.6413 (ttp) REVERT: B 124 PHE cc_start: 0.3293 (OUTLIER) cc_final: 0.2628 (t80) REVERT: B 277 ASP cc_start: 0.7841 (m-30) cc_final: 0.6339 (m-30) REVERT: B 281 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: B 285 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6972 (p90) REVERT: C 226 GLU cc_start: 0.8309 (pt0) cc_final: 0.8024 (mt-10) REVERT: C 228 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: D 21 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6832 (tmm) REVERT: H 109 ASP cc_start: 0.7904 (p0) cc_final: 0.7684 (p0) outliers start: 38 outliers final: 19 residues processed: 150 average time/residue: 1.8079 time to fit residues: 291.5576 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.175313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132584 restraints weight = 11175.552| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.10 r_work: 0.3272 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10447 Z= 0.138 Angle : 0.553 9.938 14156 Z= 0.288 Chirality : 0.041 0.139 1589 Planarity : 0.004 0.052 1801 Dihedral : 4.546 35.742 1419 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.12 % Allowed : 19.82 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.05 (0.23), residues: 1281 helix: 2.36 (0.23), residues: 499 sheet: 0.44 (0.30), residues: 270 loop : -0.87 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 327 PHE 0.021 0.002 PHE A 329 TYR 0.033 0.001 TYR B 80 ARG 0.011 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 513) hydrogen bonds : angle 4.16861 ( 1464) SS BOND : bond 0.00705 ( 3) SS BOND : angle 1.28646 ( 6) covalent geometry : bond 0.00315 (10443) covalent geometry : angle 0.55208 (14150) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8003 (tt) cc_final: 0.7686 (pt) REVERT: A 283 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6958 (mt) REVERT: A 331 LYS cc_start: 0.7634 (tttt) cc_final: 0.7024 (mmpt) REVERT: L 19 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6321 (p0) REVERT: B 87 MET cc_start: 0.7802 (tpt) cc_final: 0.7395 (tpt) REVERT: B 90 MET cc_start: 0.6760 (ttp) cc_final: 0.6436 (ttp) REVERT: B 124 PHE cc_start: 0.3271 (OUTLIER) cc_final: 0.2606 (t80) REVERT: B 190 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 277 ASP cc_start: 0.7867 (m-30) cc_final: 0.6386 (m-30) REVERT: B 281 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: B 285 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6970 (p90) REVERT: C 215 GLU cc_start: 0.7489 (mp0) cc_final: 0.7207 (mp0) REVERT: C 228 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: D 21 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6857 (tmm) REVERT: H 109 ASP cc_start: 0.7892 (p0) cc_final: 0.7658 (p0) outliers start: 35 outliers final: 21 residues processed: 150 average time/residue: 1.4918 time to fit residues: 238.1219 Evaluate side-chains 147 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 32 GLN C 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.177063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134160 restraints weight = 11068.699| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.89 r_work: 0.3331 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10447 Z= 0.125 Angle : 0.539 10.129 14156 Z= 0.281 Chirality : 0.041 0.136 1589 Planarity : 0.004 0.053 1801 Dihedral : 4.444 34.386 1419 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.21 % Allowed : 19.73 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.12 (0.23), residues: 1281 helix: 2.45 (0.23), residues: 499 sheet: 0.46 (0.30), residues: 279 loop : -0.88 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 PHE 0.016 0.001 PHE C 199 TYR 0.033 0.001 TYR B 80 ARG 0.012 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 513) hydrogen bonds : angle 4.07395 ( 1464) SS BOND : bond 0.00666 ( 3) SS BOND : angle 1.23134 ( 6) covalent geometry : bond 0.00282 (10443) covalent geometry : angle 0.53858 (14150) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6946 (mt) REVERT: A 331 LYS cc_start: 0.7654 (tttt) cc_final: 0.7029 (mmpt) REVERT: L 19 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 87 MET cc_start: 0.7761 (tpt) cc_final: 0.7382 (tpt) REVERT: B 90 MET cc_start: 0.6681 (ttp) cc_final: 0.6377 (ttp) REVERT: B 124 PHE cc_start: 0.3187 (OUTLIER) cc_final: 0.2443 (t80) REVERT: B 234 GLU cc_start: 0.8136 (tt0) cc_final: 0.7732 (tm-30) REVERT: B 277 ASP cc_start: 0.7928 (m-30) cc_final: 0.6432 (m-30) REVERT: B 281 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: B 285 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6966 (p90) REVERT: C 228 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: D 21 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6928 (tmm) REVERT: H 109 ASP cc_start: 0.7893 (p0) cc_final: 0.7654 (p0) outliers start: 36 outliers final: 23 residues processed: 144 average time/residue: 1.3909 time to fit residues: 214.1718 Evaluate side-chains 143 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.176292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133414 restraints weight = 11133.118| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.90 r_work: 0.3321 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10447 Z= 0.138 Angle : 0.560 10.241 14156 Z= 0.290 Chirality : 0.041 0.136 1589 Planarity : 0.004 0.063 1801 Dihedral : 4.510 35.397 1419 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.21 % Allowed : 20.00 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.10 (0.23), residues: 1281 helix: 2.45 (0.23), residues: 498 sheet: 0.47 (0.30), residues: 280 loop : -0.90 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 327 PHE 0.017 0.002 PHE C 199 TYR 0.034 0.001 TYR B 80 ARG 0.012 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 513) hydrogen bonds : angle 4.11264 ( 1464) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.37749 ( 6) covalent geometry : bond 0.00315 (10443) covalent geometry : angle 0.55910 (14150) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.7955 (tt) cc_final: 0.7681 (pt) REVERT: A 283 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6943 (mt) REVERT: A 331 LYS cc_start: 0.7638 (tttt) cc_final: 0.7126 (tptt) REVERT: L 19 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6579 (p0) REVERT: B 87 MET cc_start: 0.7765 (tpt) cc_final: 0.7361 (tpt) REVERT: B 90 MET cc_start: 0.6760 (ttp) cc_final: 0.6449 (ttp) REVERT: B 124 PHE cc_start: 0.3134 (OUTLIER) cc_final: 0.2369 (t80) REVERT: B 234 GLU cc_start: 0.8205 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 277 ASP cc_start: 0.7928 (m-30) cc_final: 0.6354 (m-30) REVERT: B 281 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: B 285 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6995 (p90) REVERT: C 228 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: D 21 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6838 (tmm) REVERT: H 109 ASP cc_start: 0.7908 (p0) cc_final: 0.7658 (p0) outliers start: 36 outliers final: 23 residues processed: 137 average time/residue: 1.4318 time to fit residues: 209.5296 Evaluate side-chains 141 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 81 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS B 88 GLN C 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134346 restraints weight = 11178.251| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.97 r_work: 0.3336 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10447 Z= 0.115 Angle : 0.544 12.358 14156 Z= 0.281 Chirality : 0.041 0.134 1589 Planarity : 0.004 0.063 1801 Dihedral : 4.402 34.208 1419 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.12 % Allowed : 20.18 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.18 (0.23), residues: 1281 helix: 2.50 (0.23), residues: 499 sheet: 0.55 (0.30), residues: 287 loop : -0.90 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE A 329 TYR 0.034 0.001 TYR B 80 ARG 0.014 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 513) hydrogen bonds : angle 4.02812 ( 1464) SS BOND : bond 0.00621 ( 3) SS BOND : angle 1.18229 ( 6) covalent geometry : bond 0.00254 (10443) covalent geometry : angle 0.54318 (14150) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.7323 (mm) cc_final: 0.7069 (mt) REVERT: A 331 LYS cc_start: 0.7630 (tttt) cc_final: 0.7118 (tptt) REVERT: L 19 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6500 (p0) REVERT: B 87 MET cc_start: 0.7361 (tpt) cc_final: 0.7063 (tpt) REVERT: B 90 MET cc_start: 0.6696 (ttp) cc_final: 0.6329 (ttp) REVERT: B 124 PHE cc_start: 0.3178 (OUTLIER) cc_final: 0.2419 (t80) REVERT: B 234 GLU cc_start: 0.8162 (tt0) cc_final: 0.7742 (tm-30) REVERT: B 277 ASP cc_start: 0.7864 (m-30) cc_final: 0.6339 (m-30) REVERT: B 281 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: B 285 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6991 (p90) REVERT: C 228 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: D 21 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6778 (tmm) REVERT: H 109 ASP cc_start: 0.7877 (p0) cc_final: 0.7630 (p0) outliers start: 35 outliers final: 22 residues processed: 143 average time/residue: 1.3860 time to fit residues: 211.6860 Evaluate side-chains 145 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 21 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS C 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134175 restraints weight = 11063.914| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.88 r_work: 0.3305 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10447 Z= 0.126 Angle : 0.558 13.147 14156 Z= 0.289 Chirality : 0.041 0.136 1589 Planarity : 0.004 0.065 1801 Dihedral : 4.419 34.003 1419 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.95 % Allowed : 20.98 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 1.16 (0.23), residues: 1281 helix: 2.47 (0.23), residues: 499 sheet: 0.53 (0.30), residues: 278 loop : -0.86 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 PHE 0.015 0.001 PHE C 199 TYR 0.034 0.001 TYR B 80 ARG 0.014 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 513) hydrogen bonds : angle 4.10795 ( 1464) SS BOND : bond 0.00654 ( 3) SS BOND : angle 1.31976 ( 6) covalent geometry : bond 0.00284 (10443) covalent geometry : angle 0.55741 (14150) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8989.03 seconds wall clock time: 157 minutes 55.39 seconds (9475.39 seconds total)