Starting phenix.real_space_refine on Sun Dec 29 19:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.map" model { file = "/net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7f_12746/12_2024/7o7f_12746.cif" } resolution = 3.15 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= 0.026 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 75 5.16 5 C 7113 2.51 5 N 1882 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11170 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1767 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2440 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "I" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain: "F" Number of atoms: 1694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Conformer: "B" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} bond proxies already assigned to first conformer: 1700 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU F 148 " occ=0.73 ... (16 atoms not shown) pdb=" OE2BGLU F 148 " occ=0.27 Time building chain proxies: 8.66, per 1000 atoms: 0.78 Number of scatterers: 11170 At special positions: 0 Unit cell: (95.632, 136.776, 156.792, 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 75 16.00 O 2100 8.00 N 1882 7.00 C 7113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 34 " distance=2.03 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 113 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 219 " 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=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 20 sheets defined 34.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.868A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.811A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.702A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.699A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.927A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 58 Proline residue: C 34 - end of helix removed outlier: 3.637A pdb=" N GLY C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 91 removed outlier: 3.702A pdb=" N ILE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.683A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 132 removed outlier: 3.541A pdb=" N HIS C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 140 removed outlier: 3.518A pdb=" N ALA C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 139 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 165 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 183 through 201 removed outlier: 4.555A pdb=" N GLN C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 224 removed outlier: 3.641A pdb=" N ILE C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 260 Proline residue: C 250 - end of helix removed outlier: 3.595A pdb=" N PHE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 268 through 299 Proline residue: C 294 - end of helix Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.864A pdb=" N ASN C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 32 through 49 removed outlier: 3.615A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.524A pdb=" N LYS G 61 " --> pdb=" O PRO G 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.548A pdb=" N PHE H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 75 removed outlier: 3.994A pdb=" N GLY H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'F' and resid 104 through 108 removed outlier: 4.049A pdb=" N VAL F 108 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 152 Processing helix chain 'F' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.577A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.540A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.989A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.795A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.878A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.617A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB1, first strand: chain 'I' and resid 24 through 29 removed outlier: 6.786A pdb=" N VAL I 42 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR I 27 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 40 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AB3, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.344A pdb=" N GLY H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.344A pdb=" N GLY H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE H 129 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 151 removed outlier: 5.760A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 151 removed outlier: 5.760A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 178 through 181 Processing sheet with id=AB8, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.729A pdb=" N ALA F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.378A pdb=" N TRP F 60 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR F 74 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 58 " --> pdb=" O TYR F 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 139 through 143 removed outlier: 5.970A pdb=" N TYR F 198 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 178 through 180 removed outlier: 4.118A pdb=" N TRP F 173 " --> pdb=" O ARG F 180 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1554 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: 3.89 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1808 1.31 - 1.44: 3167 1.44 - 1.57: 6340 1.57 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 11420 Sorted by residual: bond pdb=" C VAL C 83 " pdb=" O VAL C 83 " ideal model delta sigma weight residual 1.238 1.181 0.057 8.50e-03 1.38e+04 4.58e+01 bond pdb=" N PCA I 0 " pdb=" CD PCA I 0 " ideal model delta sigma weight residual 1.345 1.467 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.17e-02 7.31e+03 2.60e+01 bond pdb=" C LEU C 80 " pdb=" O LEU C 80 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.29e-02 6.01e+03 1.50e+01 bond pdb=" N PRO I 3 " pdb=" CA PRO I 3 " ideal model delta sigma weight residual 1.469 1.424 0.044 1.28e-02 6.10e+03 1.20e+01 ... (remaining 11415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 15210 1.99 - 3.99: 231 3.99 - 5.98: 29 5.98 - 7.98: 5 7.98 - 9.97: 2 Bond angle restraints: 15477 Sorted by residual: angle pdb=" N MET C 287 " pdb=" CA MET C 287 " pdb=" C MET C 287 " ideal model delta sigma weight residual 111.28 104.25 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" CA THR C 288 " pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 120.55 114.14 6.41 1.06e+00 8.90e-01 3.66e+01 angle pdb=" N THR C 284 " pdb=" CA THR C 284 " pdb=" C THR C 284 " ideal model delta sigma weight residual 111.28 105.08 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" CB THR C 288 " ideal model delta sigma weight residual 110.12 118.24 -8.12 1.47e+00 4.63e-01 3.05e+01 angle pdb=" CA PHE C 41 " pdb=" C PHE C 41 " pdb=" O PHE C 41 " ideal model delta sigma weight residual 120.70 115.27 5.43 1.03e+00 9.43e-01 2.78e+01 ... (remaining 15472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6169 17.93 - 35.87: 522 35.87 - 53.80: 80 53.80 - 71.73: 19 71.73 - 89.67: 16 Dihedral angle restraints: 6806 sinusoidal: 2676 harmonic: 4130 Sorted by residual: dihedral pdb=" CB CYS I 11 " pdb=" SG CYS I 11 " pdb=" SG CYS I 50 " pdb=" CB CYS I 50 " ideal model delta sinusoidal sigma weight residual 93.00 149.38 -56.38 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PHE H 51 " pdb=" C PHE H 51 " pdb=" N GLY H 52 " pdb=" CA GLY H 52 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1412 0.046 - 0.091: 234 0.091 - 0.137: 91 0.137 - 0.183: 7 0.183 - 0.228: 3 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CB THR C 288 " pdb=" CA THR C 288 " pdb=" OG1 THR C 288 " pdb=" CG2 THR C 288 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA HIS C 289 " pdb=" N HIS C 289 " pdb=" C HIS C 289 " pdb=" CB HIS C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1744 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 78 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C PHE C 78 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE C 78 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 79 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 289 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C HIS C 289 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS C 289 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS C 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 80 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU C 80 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU C 80 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 81 " 0.014 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 87 2.53 - 3.12: 8740 3.12 - 3.71: 16834 3.71 - 4.31: 24341 4.31 - 4.90: 41735 Nonbonded interactions: 91737 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 1.932 3.040 nonbonded pdb=" OH TYR C 187 " pdb=" O CYS I 34 " model vdw 1.955 3.040 nonbonded pdb=" OG1 THR A 324 " pdb=" OD1 ASN A 331 " model vdw 1.970 3.040 nonbonded pdb=" OG1 THR C 65 " pdb=" OD2 ASP C 125 " model vdw 1.973 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 1.984 3.040 ... (remaining 91732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.27 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: 4.630 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.550 Find NCS groups from input model: 0.160 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.004 0.122 11420 Z= 0.237 Angle : 0.637 9.970 15477 Z= 0.401 Chirality : 0.042 0.228 1747 Planarity : 0.003 0.051 1959 Dihedral : 14.025 89.666 4120 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.16 % Allowed : 0.40 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.48 (0.23), residues: 1405 helix: 1.58 (0.25), residues: 425 sheet: 0.05 (0.27), residues: 378 loop : -0.32 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 188 HIS 0.010 0.001 HIS C 289 PHE 0.024 0.001 PHE C 41 TYR 0.017 0.001 TYR A 296 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6420 (tm-30) cc_final: 0.5940 (tm-30) REVERT: A 269 ASN cc_start: 0.8496 (m110) cc_final: 0.8292 (m-40) REVERT: C 54 ILE cc_start: 0.7939 (mm) cc_final: 0.7694 (mm) REVERT: C 182 PHE cc_start: 0.5716 (m-80) cc_final: 0.5346 (m-80) REVERT: C 198 ILE cc_start: 0.8489 (tt) cc_final: 0.8278 (tt) REVERT: C 273 ASN cc_start: 0.6768 (m-40) cc_final: 0.6468 (m-40) REVERT: C 274 ARG cc_start: 0.7667 (ttm110) cc_final: 0.6815 (ttp-170) REVERT: G 24 LYS cc_start: 0.8260 (ttmt) cc_final: 0.8059 (ttmt) REVERT: H 198 GLN cc_start: 0.6900 (tt0) cc_final: 0.6063 (pp30) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2984 time to fit residues: 89.4587 Evaluate side-chains 181 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 244 HIS B 237 ASN C 194 GLN C 293 ASN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11420 Z= 0.264 Angle : 0.600 8.419 15477 Z= 0.319 Chirality : 0.044 0.197 1747 Planarity : 0.004 0.057 1959 Dihedral : 4.536 31.135 1537 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.29 % Allowed : 7.66 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.56 (0.23), residues: 1405 helix: 1.62 (0.25), residues: 430 sheet: 0.20 (0.27), residues: 371 loop : -0.35 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS C 289 PHE 0.021 0.002 PHE F 160 TYR 0.016 0.002 TYR B 59 ARG 0.006 0.001 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5886 (tm-30) REVERT: A 342 VAL cc_start: 0.8355 (t) cc_final: 0.7996 (t) REVERT: B 234 PHE cc_start: 0.5435 (p90) cc_final: 0.5167 (p90) REVERT: C 52 ILE cc_start: 0.8336 (pt) cc_final: 0.8002 (mt) REVERT: C 54 ILE cc_start: 0.7530 (mm) cc_final: 0.7093 (mm) REVERT: C 182 PHE cc_start: 0.5986 (m-80) cc_final: 0.5482 (m-80) REVERT: C 274 ARG cc_start: 0.7769 (ttm110) cc_final: 0.6875 (ttp-170) REVERT: G 24 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7898 (ttmt) REVERT: H 198 GLN cc_start: 0.6859 (tt0) cc_final: 0.5981 (pp30) REVERT: H 204 MET cc_start: 0.7937 (ptp) cc_final: 0.7731 (ptm) REVERT: F 217 TYR cc_start: 0.6453 (m-80) cc_final: 0.6110 (m-80) outliers start: 16 outliers final: 9 residues processed: 210 average time/residue: 0.2804 time to fit residues: 79.9389 Evaluate side-chains 184 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 chunk 125 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11420 Z= 0.256 Angle : 0.577 7.185 15477 Z= 0.306 Chirality : 0.043 0.180 1747 Planarity : 0.004 0.051 1959 Dihedral : 4.490 31.494 1537 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.77 % Allowed : 10.80 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.48 (0.23), residues: 1405 helix: 1.56 (0.25), residues: 431 sheet: 0.13 (0.27), residues: 367 loop : -0.38 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS C 289 PHE 0.024 0.002 PHE C 304 TYR 0.016 0.002 TYR C 187 ARG 0.006 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5949 (tm-30) REVERT: B 234 PHE cc_start: 0.5525 (p90) cc_final: 0.5232 (p90) REVERT: C 52 ILE cc_start: 0.8243 (pt) cc_final: 0.7936 (mt) REVERT: C 120 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7396 (mp) REVERT: C 182 PHE cc_start: 0.5936 (m-80) cc_final: 0.5495 (m-80) REVERT: C 274 ARG cc_start: 0.7778 (ttm110) cc_final: 0.6880 (ttp-170) REVERT: G 24 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7887 (ttmt) REVERT: H 38 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7880 (ttpp) REVERT: H 204 MET cc_start: 0.8003 (ptp) cc_final: 0.7765 (ptm) REVERT: F 44 ARG cc_start: 0.7829 (ptp-110) cc_final: 0.7616 (ptp-110) REVERT: F 217 TYR cc_start: 0.6472 (m-80) cc_final: 0.6045 (m-80) outliers start: 22 outliers final: 13 residues processed: 199 average time/residue: 0.2884 time to fit residues: 77.9308 Evaluate side-chains 188 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 0.0030 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11420 Z= 0.228 Angle : 0.565 12.503 15477 Z= 0.297 Chirality : 0.042 0.157 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.392 31.060 1537 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 12.57 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.49 (0.23), residues: 1405 helix: 1.53 (0.25), residues: 431 sheet: 0.21 (0.27), residues: 367 loop : -0.40 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS C 289 PHE 0.014 0.001 PHE F 160 TYR 0.016 0.001 TYR B 59 ARG 0.006 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6462 (tm-30) cc_final: 0.6142 (tm-30) REVERT: B 234 PHE cc_start: 0.5515 (p90) cc_final: 0.5184 (p90) REVERT: C 52 ILE cc_start: 0.8293 (pt) cc_final: 0.7983 (mt) REVERT: C 94 TRP cc_start: 0.3870 (t-100) cc_final: 0.3638 (t-100) REVERT: C 120 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7405 (mp) REVERT: C 182 PHE cc_start: 0.5995 (m-80) cc_final: 0.5588 (m-80) REVERT: C 274 ARG cc_start: 0.7779 (ttm110) cc_final: 0.6949 (mmt180) REVERT: C 304 PHE cc_start: 0.7907 (t80) cc_final: 0.7695 (t80) REVERT: F 44 ARG cc_start: 0.7819 (ptp-110) cc_final: 0.7618 (ptp-110) REVERT: F 217 TYR cc_start: 0.6484 (m-80) cc_final: 0.5988 (m-80) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 0.2796 time to fit residues: 75.1605 Evaluate side-chains 186 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11420 Z= 0.229 Angle : 0.565 10.795 15477 Z= 0.296 Chirality : 0.043 0.178 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.393 30.720 1537 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.82 % Allowed : 12.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.43 (0.23), residues: 1405 helix: 1.48 (0.25), residues: 434 sheet: 0.18 (0.27), residues: 365 loop : -0.45 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS C 289 PHE 0.020 0.002 PHE C 311 TYR 0.016 0.001 TYR C 37 ARG 0.008 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.346 Fit side-chains REVERT: A 245 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6157 (tm-30) REVERT: B 198 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7712 (pp) REVERT: C 41 PHE cc_start: 0.6348 (t80) cc_final: 0.6078 (t80) REVERT: C 52 ILE cc_start: 0.8334 (pt) cc_final: 0.7988 (mt) REVERT: C 120 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7400 (mp) REVERT: C 182 PHE cc_start: 0.6099 (m-80) cc_final: 0.5721 (m-80) REVERT: C 274 ARG cc_start: 0.7691 (ttm110) cc_final: 0.6859 (mmt180) REVERT: C 304 PHE cc_start: 0.7969 (t80) cc_final: 0.7727 (t80) REVERT: F 200 MET cc_start: 0.7318 (tpt) cc_final: 0.6585 (tpt) outliers start: 35 outliers final: 21 residues processed: 205 average time/residue: 0.2704 time to fit residues: 75.9815 Evaluate side-chains 188 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 0.0980 chunk 61 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN H 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11420 Z= 0.190 Angle : 0.544 9.608 15477 Z= 0.285 Chirality : 0.042 0.155 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.286 28.965 1537 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 13.46 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.52 (0.23), residues: 1405 helix: 1.62 (0.25), residues: 435 sheet: 0.18 (0.27), residues: 365 loop : -0.42 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 57 HIS 0.006 0.001 HIS C 289 PHE 0.015 0.001 PHE C 311 TYR 0.016 0.001 TYR B 59 ARG 0.009 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.331 Fit side-chains REVERT: A 245 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6174 (tm-30) REVERT: B 198 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7682 (pp) REVERT: C 41 PHE cc_start: 0.6310 (t80) cc_final: 0.6021 (t80) REVERT: C 52 ILE cc_start: 0.8268 (pt) cc_final: 0.7910 (mt) REVERT: C 120 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7388 (mp) REVERT: C 144 PHE cc_start: 0.6360 (t80) cc_final: 0.6048 (t80) REVERT: C 182 PHE cc_start: 0.6158 (m-80) cc_final: 0.5819 (m-80) REVERT: C 274 ARG cc_start: 0.7602 (ttm110) cc_final: 0.6803 (mmt180) REVERT: C 283 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: C 304 PHE cc_start: 0.8050 (t80) cc_final: 0.7791 (t80) REVERT: F 200 MET cc_start: 0.7299 (tpt) cc_final: 0.6655 (tpt) outliers start: 28 outliers final: 23 residues processed: 197 average time/residue: 0.2781 time to fit residues: 74.7301 Evaluate side-chains 192 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11420 Z= 0.257 Angle : 0.583 9.342 15477 Z= 0.304 Chirality : 0.043 0.200 1747 Planarity : 0.004 0.052 1959 Dihedral : 4.401 31.390 1537 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.50 % Allowed : 14.10 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.43 (0.23), residues: 1405 helix: 1.57 (0.25), residues: 435 sheet: 0.09 (0.26), residues: 377 loop : -0.48 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 94 HIS 0.006 0.001 HIS C 289 PHE 0.014 0.002 PHE C 311 TYR 0.017 0.001 TYR B 59 ARG 0.010 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.335 Fit side-chains REVERT: A 25 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6644 (tt0) REVERT: A 245 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6202 (tm-30) REVERT: A 273 LEU cc_start: 0.8495 (tp) cc_final: 0.8285 (tp) REVERT: B 198 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7735 (pp) REVERT: C 41 PHE cc_start: 0.6354 (t80) cc_final: 0.6077 (t80) REVERT: C 52 ILE cc_start: 0.8325 (pt) cc_final: 0.7984 (mt) REVERT: C 120 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7393 (mp) REVERT: C 144 PHE cc_start: 0.6372 (t80) cc_final: 0.6068 (t80) REVERT: C 182 PHE cc_start: 0.6241 (m-80) cc_final: 0.5878 (m-80) REVERT: C 274 ARG cc_start: 0.7647 (ttm110) cc_final: 0.6843 (mmt180) REVERT: C 283 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: C 304 PHE cc_start: 0.8102 (t80) cc_final: 0.7827 (t80) REVERT: F 200 MET cc_start: 0.7348 (tpt) cc_final: 0.6642 (tpt) outliers start: 31 outliers final: 22 residues processed: 195 average time/residue: 0.2855 time to fit residues: 76.1720 Evaluate side-chains 192 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 120 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: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11420 Z= 0.257 Angle : 0.581 9.330 15477 Z= 0.304 Chirality : 0.043 0.193 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.421 32.097 1537 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.26 % Allowed : 15.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.33 (0.23), residues: 1405 helix: 1.51 (0.25), residues: 436 sheet: -0.00 (0.26), residues: 378 loop : -0.52 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 PHE 0.017 0.002 PHE C 311 TYR 0.016 0.001 TYR B 59 ARG 0.011 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.330 Fit side-chains REVERT: A 245 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6208 (tm-30) REVERT: A 273 LEU cc_start: 0.8491 (tp) cc_final: 0.8282 (tp) REVERT: B 198 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7722 (pp) REVERT: C 31 ARG cc_start: 0.6610 (ttp80) cc_final: 0.6308 (tmm160) REVERT: C 41 PHE cc_start: 0.6373 (t80) cc_final: 0.6121 (t80) REVERT: C 52 ILE cc_start: 0.8213 (pt) cc_final: 0.7956 (mt) REVERT: C 120 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 144 PHE cc_start: 0.6352 (t80) cc_final: 0.6142 (t80) REVERT: C 182 PHE cc_start: 0.6207 (m-80) cc_final: 0.5837 (m-80) REVERT: C 274 ARG cc_start: 0.7685 (ttm110) cc_final: 0.6870 (mmt180) REVERT: C 283 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: C 304 PHE cc_start: 0.8198 (t80) cc_final: 0.7970 (t80) REVERT: F 200 MET cc_start: 0.7348 (tpt) cc_final: 0.6584 (tpt) outliers start: 28 outliers final: 21 residues processed: 195 average time/residue: 0.2789 time to fit residues: 74.2739 Evaluate side-chains 193 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11420 Z= 0.251 Angle : 0.582 10.139 15477 Z= 0.304 Chirality : 0.043 0.190 1747 Planarity : 0.004 0.054 1959 Dihedral : 4.432 32.198 1537 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 15.87 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.28 (0.23), residues: 1405 helix: 1.46 (0.25), residues: 436 sheet: -0.05 (0.26), residues: 378 loop : -0.54 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 PHE 0.016 0.001 PHE A 189 TYR 0.015 0.001 TYR B 59 ARG 0.009 0.000 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.244 Fit side-chains REVERT: A 245 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6179 (tm-30) REVERT: A 273 LEU cc_start: 0.8498 (tp) cc_final: 0.8294 (tp) REVERT: B 198 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7723 (pp) REVERT: C 41 PHE cc_start: 0.6348 (t80) cc_final: 0.6096 (t80) REVERT: C 52 ILE cc_start: 0.8265 (pt) cc_final: 0.7993 (mt) REVERT: C 120 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7378 (mp) REVERT: C 182 PHE cc_start: 0.6206 (m-80) cc_final: 0.5778 (m-80) REVERT: C 274 ARG cc_start: 0.7659 (ttm110) cc_final: 0.6743 (mmt180) REVERT: C 283 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: C 304 PHE cc_start: 0.8196 (t80) cc_final: 0.7912 (t80) REVERT: F 200 MET cc_start: 0.7355 (tpt) cc_final: 0.6534 (tpt) REVERT: F 217 TYR cc_start: 0.6360 (m-80) cc_final: 0.5836 (m-80) outliers start: 26 outliers final: 23 residues processed: 189 average time/residue: 0.2722 time to fit residues: 70.3649 Evaluate side-chains 197 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11420 Z= 0.306 Angle : 0.612 10.671 15477 Z= 0.319 Chirality : 0.044 0.197 1747 Planarity : 0.004 0.055 1959 Dihedral : 4.559 35.125 1537 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.18 % Allowed : 15.55 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.15 (0.22), residues: 1405 helix: 1.32 (0.25), residues: 434 sheet: -0.07 (0.26), residues: 378 loop : -0.61 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 94 HIS 0.005 0.001 HIS C 289 PHE 0.017 0.002 PHE A 189 TYR 0.017 0.002 TYR B 59 ARG 0.013 0.001 ARG C 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.327 Fit side-chains REVERT: A 245 GLU cc_start: 0.6554 (tm-30) cc_final: 0.6219 (tm-30) REVERT: A 273 LEU cc_start: 0.8452 (tp) cc_final: 0.8251 (tp) REVERT: B 46 ARG cc_start: 0.7113 (mtm-85) cc_final: 0.6790 (mtm180) REVERT: B 198 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7713 (pp) REVERT: C 31 ARG cc_start: 0.6692 (ttp80) cc_final: 0.6321 (tmm160) REVERT: C 41 PHE cc_start: 0.6453 (t80) cc_final: 0.6186 (t80) REVERT: C 52 ILE cc_start: 0.8223 (pt) cc_final: 0.8010 (mt) REVERT: C 120 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7383 (mp) REVERT: C 182 PHE cc_start: 0.6197 (m-80) cc_final: 0.5797 (m-80) REVERT: C 274 ARG cc_start: 0.7682 (ttm110) cc_final: 0.6723 (mmt180) REVERT: C 283 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: C 304 PHE cc_start: 0.8282 (t80) cc_final: 0.8041 (t80) REVERT: G 41 ARG cc_start: 0.8504 (tmm-80) cc_final: 0.8252 (tmm-80) REVERT: F 200 MET cc_start: 0.7395 (tpt) cc_final: 0.6554 (tpt) outliers start: 27 outliers final: 21 residues processed: 189 average time/residue: 0.2966 time to fit residues: 75.9637 Evaluate side-chains 192 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 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 331 ASN B 156 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.187680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155576 restraints weight = 26410.235| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 4.96 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11420 Z= 0.248 Angle : 0.597 11.258 15477 Z= 0.311 Chirality : 0.043 0.198 1747 Planarity : 0.004 0.055 1959 Dihedral : 4.488 33.808 1537 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.18 % Allowed : 15.87 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.17 (0.22), residues: 1405 helix: 1.37 (0.25), residues: 434 sheet: -0.09 (0.26), residues: 368 loop : -0.60 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.005 0.001 HIS C 289 PHE 0.017 0.002 PHE C 311 TYR 0.022 0.001 TYR C 307 ARG 0.013 0.001 ARG C 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.85 seconds wall clock time: 49 minutes 15.03 seconds (2955.03 seconds total)