Starting phenix.real_space_refine on Thu Jul 2 15:55:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew3_31346/07_2026/7ew3_31346.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 48 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 68 5.16 5 C 5794 2.51 5 N 1531 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "R" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2294 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {'PLM': 4, 'S1P': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.57, per 1000 atoms: 0.17 Number of scatterers: 9072 At special positions: 0 Unit cell: (94.76, 124.2, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 1 15.00 O 1678 8.00 N 1531 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 178 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 269 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 312.7 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 36.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.983A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.536A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.627A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.519A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.032A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.857A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.558A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.608A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'R' and resid 17 through 26 Processing helix chain 'R' and resid 40 through 67 removed outlier: 3.972A pdb=" N ASN R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 99 removed outlier: 3.788A pdb=" N PHE R 77 " --> pdb=" O ARG R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.545A pdb=" N MET R 118 " --> pdb=" O ARG R 114 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU R 129 " --> pdb=" O SER R 125 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 130 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 171 removed outlier: 3.642A pdb=" N PHE R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.581A pdb=" N GLY R 175 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 193 through 229 removed outlier: 3.726A pdb=" N ILE R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR R 219 " --> pdb=" O TYR R 215 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 269 removed outlier: 3.763A pdb=" N CYS R 255 " --> pdb=" O VAL R 251 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 274 through 279 Processing helix chain 'R' and resid 280 through 298 removed outlier: 4.087A pdb=" N LEU R 286 " --> pdb=" O TRP R 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.528A pdb=" N TYR R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 312 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.638A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.936A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.182A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.527A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.718A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.265A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.903A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.056A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.886A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.971A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.720A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE S 177 " --> pdb=" O TYR S 228 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 428 hydrogen bonds defined for protein. 1209 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: 0.94 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2904 1.35 - 1.46: 2234 1.46 - 1.58: 4010 1.58 - 1.70: 1 1.70 - 1.82: 99 Bond restraints: 9248 Sorted by residual: bond pdb=" C14 S1P R 401 " pdb=" C15 S1P R 401 " ideal model delta sigma weight residual 1.532 1.443 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C13 S1P R 401 " pdb=" C14 S1P R 401 " ideal model delta sigma weight residual 1.533 1.451 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C8 S1P R 401 " pdb=" C9 S1P R 401 " ideal model delta sigma weight residual 1.531 1.452 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C3 S1P R 401 " pdb=" O3 S1P R 401 " ideal model delta sigma weight residual 1.445 1.367 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O25 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.530 1.452 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12421 2.75 - 5.51: 51 5.51 - 8.26: 3 8.26 - 11.02: 5 11.02 - 13.77: 4 Bond angle restraints: 12484 Sorted by residual: angle pdb=" C3 S1P R 401 " pdb=" C2 S1P R 401 " pdb=" N2 S1P R 401 " ideal model delta sigma weight residual 112.93 99.16 13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C7 S1P R 401 " pdb=" C8 S1P R 401 " pdb=" C9 S1P R 401 " ideal model delta sigma weight residual 115.70 102.32 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C13 S1P R 401 " pdb=" C14 S1P R 401 " pdb=" C15 S1P R 401 " ideal model delta sigma weight residual 115.37 103.46 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C11 S1P R 401 " pdb=" C10 S1P R 401 " pdb=" C9 S1P R 401 " ideal model delta sigma weight residual 114.40 102.61 11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O23 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O24 S1P R 401 " ideal model delta sigma weight residual 114.79 103.89 10.90 3.00e+00 1.11e-01 1.32e+01 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 5406 34.06 - 68.12: 111 68.12 - 102.18: 12 102.18 - 136.24: 2 136.24 - 170.30: 2 Dihedral angle restraints: 5533 sinusoidal: 2201 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS R 178 " pdb=" SG CYS R 178 " pdb=" SG CYS R 185 " pdb=" CB CYS R 185 " ideal model delta sinusoidal sigma weight residual 93.00 50.01 42.99 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" N2 S1P R 401 " pdb=" C1 S1P R 401 " pdb=" C2 S1P R 401 " pdb=" O1 S1P R 401 " ideal model delta sinusoidal sigma weight residual 286.07 115.77 170.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C3 S1P R 401 " pdb=" C1 S1P R 401 " pdb=" C2 S1P R 401 " pdb=" O1 S1P R 401 " ideal model delta sinusoidal sigma weight residual 52.36 -137.45 -170.19 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1265 0.063 - 0.127: 146 0.127 - 0.190: 1 0.190 - 0.253: 0 0.253 - 0.316: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" C2 S1P R 401 " pdb=" C1 S1P R 401 " pdb=" C3 S1P R 401 " pdb=" N2 S1P R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.74 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PRO R 172 " pdb=" N PRO R 172 " pdb=" C PRO R 172 " pdb=" CB PRO R 172 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1410 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG S 180 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO S 181 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO S 181 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 181 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 236 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 246 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ASP B 246 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP B 246 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP B 247 " -0.008 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2165 2.80 - 3.32: 7885 3.32 - 3.85: 13921 3.85 - 4.37: 15789 4.37 - 4.90: 29201 Nonbonded interactions: 68961 Sorted by model distance: nonbonded pdb=" O LEU R 168 " pdb=" OH TYR R 196 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.320 3.040 nonbonded pdb=" O PHE S 32 " pdb=" NH2 ARG S 72 " model vdw 2.330 3.120 nonbonded pdb=" NH1 ARG S 87 " pdb=" OE2 GLU S 89 " model vdw 2.340 3.120 ... (remaining 68956 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9251 Z= 0.179 Angle : 0.556 13.771 12490 Z= 0.274 Chirality : 0.039 0.316 1413 Planarity : 0.003 0.038 1566 Dihedral : 15.136 170.301 3372 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1133 helix: 2.58 (0.26), residues: 385 sheet: 1.16 (0.32), residues: 270 loop : -0.70 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 18 TYR 0.005 0.001 TYR S 190 PHE 0.010 0.001 PHE R 260 TRP 0.018 0.001 TRP R 111 HIS 0.001 0.000 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 ( 9248) covalent geometry : angle 0.55576 / 0.27 (12484) SS BOND : bond 0.00182 / 0.10 ( 3) SS BOND : angle 0.93972 / 0.46 ( 6) hydrogen bonds : bond 0.18264 / 11.86 ( 428) hydrogen bonds : angle 5.20608 / 3.60 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.272 Fit side-chains REVERT: A 229 ASP cc_start: 0.7905 (m-30) cc_final: 0.7553 (m-30) REVERT: C 21 MET cc_start: 0.7835 (mmm) cc_final: 0.6929 (ptm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0733 time to fit residues: 13.3286 Evaluate side-chains 109 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133213 restraints weight = 10624.480| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.47 r_work: 0.3285 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9251 Z= 0.103 Angle : 0.475 5.549 12490 Z= 0.249 Chirality : 0.041 0.141 1413 Planarity : 0.003 0.038 1566 Dihedral : 10.536 179.573 1321 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.51 % Allowed : 7.16 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1133 helix: 2.92 (0.27), residues: 384 sheet: 0.95 (0.32), residues: 273 loop : -0.77 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 67 TYR 0.014 0.001 TYR S 190 PHE 0.009 0.001 PHE B 199 TRP 0.011 0.001 TRP R 111 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 9248) covalent geometry : angle 0.47445 / 0.25 (12484) SS BOND : bond 0.00438 / 0.22 ( 3) SS BOND : angle 1.18984 / 0.66 ( 6) hydrogen bonds : bond 0.03979 / 2.64 ( 428) hydrogen bonds : angle 4.01361 / 2.75 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.290 Fit side-chains REVERT: A 350 ASP cc_start: 0.6545 (m-30) cc_final: 0.6269 (m-30) REVERT: C 21 MET cc_start: 0.8011 (mmm) cc_final: 0.6986 (ptm) REVERT: R 192 TYR cc_start: 0.5600 (m-10) cc_final: 0.5317 (m-10) REVERT: S 186 GLN cc_start: 0.6981 (mm110) cc_final: 0.6178 (tt0) outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 0.0830 time to fit residues: 12.5482 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 34 optimal weight: 0.0070 chunk 80 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** R 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132478 restraints weight = 10591.226| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.46 r_work: 0.3290 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9251 Z= 0.089 Angle : 0.434 6.936 12490 Z= 0.229 Chirality : 0.040 0.144 1413 Planarity : 0.003 0.037 1566 Dihedral : 10.020 171.119 1321 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.72 % Allowed : 8.80 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1133 helix: 3.09 (0.27), residues: 384 sheet: 0.96 (0.32), residues: 273 loop : -0.77 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 87 TYR 0.014 0.001 TYR S 190 PHE 0.010 0.001 PHE B 199 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 9248) covalent geometry : angle 0.43378 / 0.23 (12484) SS BOND : bond 0.00310 / 0.16 ( 3) SS BOND : angle 1.07541 / 0.59 ( 6) hydrogen bonds : bond 0.03594 / 2.38 ( 428) hydrogen bonds : angle 3.82109 / 2.61 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.212 Fit side-chains REVERT: B 215 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 21 MET cc_start: 0.8016 (mmm) cc_final: 0.6909 (ptm) REVERT: R 150 LYS cc_start: 0.5910 (ptmt) cc_final: 0.5598 (ttpt) REVERT: R 192 TYR cc_start: 0.5750 (m-10) cc_final: 0.5495 (m-10) outliers start: 7 outliers final: 5 residues processed: 104 average time/residue: 0.0766 time to fit residues: 11.1389 Evaluate side-chains 100 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN R 21 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129429 restraints weight = 10649.616| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.61 r_work: 0.3219 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9251 Z= 0.113 Angle : 0.465 6.375 12490 Z= 0.246 Chirality : 0.041 0.143 1413 Planarity : 0.003 0.037 1566 Dihedral : 9.462 164.956 1321 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.02 % Allowed : 10.44 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.26), residues: 1133 helix: 3.14 (0.27), residues: 383 sheet: 0.88 (0.32), residues: 280 loop : -0.85 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 87 TYR 0.012 0.001 TYR S 190 PHE 0.014 0.001 PHE B 199 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9248) covalent geometry : angle 0.46456 / 0.25 (12484) SS BOND : bond 0.00356 / 0.18 ( 3) SS BOND : angle 1.16570 / 0.63 ( 6) hydrogen bonds : bond 0.04232 / 2.82 ( 428) hydrogen bonds : angle 3.90250 / 2.66 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.221 Fit side-chains REVERT: B 215 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7014 (mm-30) REVERT: C 21 MET cc_start: 0.8099 (mmm) cc_final: 0.6911 (ptm) REVERT: R 150 LYS cc_start: 0.5984 (ptmt) cc_final: 0.5712 (ttpt) REVERT: S 186 GLN cc_start: 0.6888 (mm110) cc_final: 0.6119 (tt0) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.0938 time to fit residues: 13.8215 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124700 restraints weight = 10576.062| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.80 r_work: 0.3137 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9251 Z= 0.177 Angle : 0.544 9.248 12490 Z= 0.287 Chirality : 0.043 0.144 1413 Planarity : 0.003 0.037 1566 Dihedral : 9.502 162.200 1321 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.84 % Allowed : 11.77 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1133 helix: 2.86 (0.27), residues: 389 sheet: 0.89 (0.31), residues: 277 loop : -1.00 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 136 TYR 0.012 0.001 TYR S 190 PHE 0.016 0.002 PHE B 199 TRP 0.011 0.002 TRP S 36 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 9248) covalent geometry : angle 0.54358 / 0.29 (12484) SS BOND : bond 0.00403 / 0.20 ( 3) SS BOND : angle 1.38074 / 0.74 ( 6) hydrogen bonds : bond 0.05466 / 3.66 ( 428) hydrogen bonds : angle 4.18696 / 2.85 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.216 Fit side-chains REVERT: B 338 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (mp) REVERT: C 21 MET cc_start: 0.8113 (mmm) cc_final: 0.6947 (ptm) REVERT: R 140 MET cc_start: 0.8548 (mmm) cc_final: 0.8313 (mmm) REVERT: S 38 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7845 (ttm170) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 0.0851 time to fit residues: 12.6507 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123985 restraints weight = 10646.539| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.73 r_work: 0.3133 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9251 Z= 0.167 Angle : 0.536 8.225 12490 Z= 0.283 Chirality : 0.043 0.144 1413 Planarity : 0.003 0.037 1566 Dihedral : 9.367 161.636 1321 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 11.87 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1133 helix: 2.94 (0.27), residues: 383 sheet: 0.77 (0.31), residues: 278 loop : -1.09 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 202 TYR 0.012 0.001 TYR S 190 PHE 0.017 0.002 PHE B 199 TRP 0.011 0.001 TRP S 36 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 9248) covalent geometry : angle 0.53452 / 0.28 (12484) SS BOND : bond 0.00405 / 0.20 ( 3) SS BOND : angle 1.75823 / 0.89 ( 6) hydrogen bonds : bond 0.05273 / 3.55 ( 428) hydrogen bonds : angle 4.18384 / 2.85 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.305 Fit side-chains REVERT: B 215 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 338 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 21 MET cc_start: 0.8046 (mmm) cc_final: 0.6831 (ptm) REVERT: R 118 MET cc_start: 0.6966 (tpt) cc_final: 0.6747 (mmm) REVERT: R 140 MET cc_start: 0.8496 (mmm) cc_final: 0.8240 (mmm) REVERT: S 38 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7815 (ttp-170) outliers start: 22 outliers final: 15 residues processed: 109 average time/residue: 0.1262 time to fit residues: 18.2733 Evaluate side-chains 108 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127083 restraints weight = 10620.317| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.72 r_work: 0.3181 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9251 Z= 0.120 Angle : 0.482 6.692 12490 Z= 0.255 Chirality : 0.041 0.145 1413 Planarity : 0.003 0.038 1566 Dihedral : 8.894 159.904 1321 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.54 % Allowed : 12.59 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1133 helix: 3.07 (0.27), residues: 383 sheet: 0.81 (0.31), residues: 278 loop : -1.05 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 136 TYR 0.013 0.001 TYR S 190 PHE 0.014 0.001 PHE B 241 TRP 0.009 0.001 TRP S 36 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9248) covalent geometry : angle 0.48141 / 0.25 (12484) SS BOND : bond 0.00366 / 0.19 ( 3) SS BOND : angle 1.35582 / 0.69 ( 6) hydrogen bonds : bond 0.04401 / 2.95 ( 428) hydrogen bonds : angle 4.01597 / 2.74 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.368 Fit side-chains REVERT: B 215 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 338 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 21 MET cc_start: 0.8066 (mmm) cc_final: 0.6860 (ptm) REVERT: R 118 MET cc_start: 0.6862 (tpt) cc_final: 0.6656 (mmm) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.1157 time to fit residues: 16.5135 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124808 restraints weight = 10605.564| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.82 r_work: 0.3145 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9251 Z= 0.171 Angle : 0.544 8.575 12490 Z= 0.285 Chirality : 0.043 0.145 1413 Planarity : 0.003 0.038 1566 Dihedral : 8.996 161.729 1321 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.74 % Allowed : 13.20 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1133 helix: 2.95 (0.27), residues: 384 sheet: 0.72 (0.31), residues: 278 loop : -1.09 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 202 TYR 0.012 0.001 TYR S 190 PHE 0.017 0.002 PHE B 199 TRP 0.010 0.001 TRP S 36 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 9248) covalent geometry : angle 0.54352 / 0.28 (12484) SS BOND : bond 0.00401 / 0.20 ( 3) SS BOND : angle 1.56339 / 0.80 ( 6) hydrogen bonds : bond 0.05305 / 3.56 ( 428) hydrogen bonds : angle 4.18744 / 2.85 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.360 Fit side-chains REVERT: B 215 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 338 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8539 (mp) REVERT: C 21 MET cc_start: 0.8047 (mmm) cc_final: 0.6833 (ptm) REVERT: R 118 MET cc_start: 0.6919 (tpt) cc_final: 0.6715 (mmm) REVERT: R 140 MET cc_start: 0.8542 (mmm) cc_final: 0.8293 (mmm) REVERT: S 38 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7770 (ttp-170) REVERT: S 140 MET cc_start: 0.6906 (mmt) cc_final: 0.6151 (mmt) outliers start: 17 outliers final: 13 residues processed: 104 average time/residue: 0.1179 time to fit residues: 16.4358 Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 257 SER Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126938 restraints weight = 10579.002| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.75 r_work: 0.3196 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9251 Z= 0.104 Angle : 0.477 11.529 12490 Z= 0.248 Chirality : 0.041 0.218 1413 Planarity : 0.003 0.038 1566 Dihedral : 8.719 162.728 1321 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.33 % Allowed : 13.82 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1133 helix: 3.14 (0.26), residues: 383 sheet: 0.82 (0.32), residues: 269 loop : -1.04 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 19 TYR 0.013 0.001 TYR S 190 PHE 0.013 0.001 PHE B 241 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 9248) covalent geometry : angle 0.47640 / 0.25 (12484) SS BOND : bond 0.00340 / 0.17 ( 3) SS BOND : angle 1.20936 / 0.61 ( 6) hydrogen bonds : bond 0.03941 / 2.64 ( 428) hydrogen bonds : angle 3.94936 / 2.69 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.348 Fit side-chains REVERT: B 215 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 21 MET cc_start: 0.8073 (mmm) cc_final: 0.6880 (ptm) REVERT: S 140 MET cc_start: 0.6864 (mmt) cc_final: 0.6147 (mmt) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.1057 time to fit residues: 15.0791 Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127492 restraints weight = 10565.614| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.66 r_work: 0.3207 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9251 Z= 0.105 Angle : 0.489 12.143 12490 Z= 0.251 Chirality : 0.041 0.209 1413 Planarity : 0.003 0.038 1566 Dihedral : 8.596 160.385 1321 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.82 % Allowed : 14.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1133 helix: 3.19 (0.26), residues: 383 sheet: 0.86 (0.32), residues: 268 loop : -1.05 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 19 TYR 0.013 0.001 TYR S 190 PHE 0.014 0.001 PHE B 241 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 9248) covalent geometry : angle 0.48817 / 0.25 (12484) SS BOND : bond 0.00330 / 0.17 ( 3) SS BOND : angle 1.22136 / 0.62 ( 6) hydrogen bonds : bond 0.03962 / 2.66 ( 428) hydrogen bonds : angle 3.92432 / 2.67 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.360 Fit side-chains REVERT: B 215 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 21 MET cc_start: 0.8078 (mmm) cc_final: 0.6883 (ptm) REVERT: S 140 MET cc_start: 0.6835 (mmt) cc_final: 0.6144 (mmt) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.1168 time to fit residues: 15.8420 Evaluate side-chains 101 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 217 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 111 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126390 restraints weight = 10506.030| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.66 r_work: 0.3182 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9251 Z= 0.129 Angle : 0.511 12.521 12490 Z= 0.262 Chirality : 0.042 0.214 1413 Planarity : 0.003 0.038 1566 Dihedral : 8.566 159.773 1321 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.92 % Allowed : 14.33 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1133 helix: 3.11 (0.26), residues: 385 sheet: 0.83 (0.32), residues: 268 loop : -1.04 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 202 TYR 0.013 0.001 TYR S 190 PHE 0.016 0.001 PHE B 241 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9248) covalent geometry : angle 0.51029 / 0.26 (12484) SS BOND : bond 0.00362 / 0.18 ( 3) SS BOND : angle 1.36003 / 0.69 ( 6) hydrogen bonds : bond 0.04422 / 2.96 ( 428) hydrogen bonds : angle 3.98764 / 2.71 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.19 seconds wall clock time: 41 minutes 34.17 seconds (2494.17 seconds total)