Starting phenix.real_space_refine on Tue Apr 29 16:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1a_35915/04_2025/8j1a_35915_neut.cif" } resolution = 3.24 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5640 2.51 5 N 1528 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8845 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1759 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 5.62, per 1000 atoms: 0.64 Number of scatterers: 8845 At special positions: 0 Unit cell: (88.992, 119.48, 124.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1618 8.00 N 1528 7.00 C 5640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.03 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 39.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.539A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.980A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.359A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.582A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.627A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.625A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 13 through 15 No H-bonds generated for 'chain 'R' and resid 13 through 15' Processing helix chain 'R' and resid 16 through 48 removed outlier: 4.197A pdb=" N TYR R 21 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 Processing helix chain 'R' and resid 53 through 71 removed outlier: 4.033A pdb=" N LEU R 58 " --> pdb=" O ARG R 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 89 through 124 removed outlier: 3.651A pdb=" N ARG R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 133 removed outlier: 3.598A pdb=" N VAL R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 153 removed outlier: 3.557A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Proline residue: R 157 - end of helix No H-bonds generated for 'chain 'R' and resid 154 through 159' Processing helix chain 'R' and resid 175 through 215 removed outlier: 3.734A pdb=" N TYR R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 342 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 347 through 349 No H-bonds generated for 'chain 'R' and resid 347 through 349' Processing helix chain 'R' and resid 350 through 371 removed outlier: 3.838A pdb=" N LEU R 354 " --> pdb=" O VAL R 350 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP R 360 " --> pdb=" O ALA R 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU R 361 " --> pdb=" O ASN R 357 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 387 Processing helix chain 'R' and resid 387 through 392 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.168A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.951A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.149A 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: 7.550A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.562A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.650A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.406A 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: 6.147A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.721A 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 150 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.789A 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: 6.818A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.665A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.739A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 161 through 162 removed outlier: 4.159A pdb=" N VAL R 162 " --> pdb=" O THR R 167 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR R 167 " --> pdb=" O VAL R 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.916A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.486A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1552 1.33 - 1.45: 2399 1.45 - 1.57: 4996 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9029 Sorted by residual: bond pdb=" C TYR A 287 " pdb=" O TYR A 287 " ideal model delta sigma weight residual 1.244 1.203 0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" C ASN G 59 " pdb=" N PRO G 60 " ideal model delta sigma weight residual 1.336 1.369 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" CA ARG R 176 " pdb=" C ARG R 176 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" C ASP B 163 " pdb=" N THR B 164 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.24e-02 6.50e+03 9.02e+00 bond pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.35e-02 5.49e+03 6.82e+00 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11882 1.52 - 3.03: 280 3.03 - 4.55: 57 4.55 - 6.07: 8 6.07 - 7.58: 8 Bond angle restraints: 12235 Sorted by residual: angle pdb=" N TYR R 332 " pdb=" CA TYR R 332 " pdb=" C TYR R 332 " ideal model delta sigma weight residual 113.12 120.45 -7.33 1.25e+00 6.40e-01 3.43e+01 angle pdb=" CA ASP B 163 " pdb=" C ASP B 163 " pdb=" O ASP B 163 " ideal model delta sigma weight residual 120.55 114.60 5.95 1.21e+00 6.83e-01 2.42e+01 angle pdb=" N GLU A 289 " pdb=" CA GLU A 289 " pdb=" C GLU A 289 " ideal model delta sigma weight residual 110.97 105.99 4.98 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 111.22 104.32 6.90 1.58e+00 4.01e-01 1.91e+01 angle pdb=" N SER A 293 " pdb=" CA SER A 293 " pdb=" C SER A 293 " ideal model delta sigma weight residual 109.46 102.24 7.22 1.66e+00 3.63e-01 1.89e+01 ... (remaining 12230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4749 17.58 - 35.16: 456 35.16 - 52.74: 108 52.74 - 70.32: 30 70.32 - 87.90: 8 Dihedral angle restraints: 5351 sinusoidal: 2061 harmonic: 3290 Sorted by residual: dihedral pdb=" N SER B 331 " pdb=" C SER B 331 " pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta harmonic sigma weight residual 122.80 113.84 8.96 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 40.06 49.94 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " pdb=" CG ASP B 290 " pdb=" OD1 ASP B 290 " ideal model delta sinusoidal sigma weight residual -30.00 -90.91 60.91 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1174 0.054 - 0.107: 180 0.107 - 0.161: 35 0.161 - 0.215: 6 0.215 - 0.268: 4 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA TYR R 332 " pdb=" N TYR R 332 " pdb=" C TYR R 332 " pdb=" CB TYR R 332 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG R 176 " pdb=" N ARG R 176 " pdb=" C ARG R 176 " pdb=" CB ARG R 176 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA SER A 293 " pdb=" N SER A 293 " pdb=" C SER A 293 " pdb=" CB SER A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1396 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.057 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO S 14 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 333 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ASP B 333 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP B 333 " 0.021 2.00e-02 2.50e+03 pdb=" N SER B 334 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C GLY R 175 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.016 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 82 2.56 - 3.15: 7341 3.15 - 3.73: 13430 3.73 - 4.32: 18841 4.32 - 4.90: 33050 Nonbonded interactions: 72744 Sorted by model distance: nonbonded pdb=" CD1 LEU R 98 " pdb=" CE3 TRP R 156 " model vdw 1.976 3.760 nonbonded pdb=" CD2 LEU R 98 " pdb=" CE2 TYR R 159 " model vdw 2.136 3.760 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.174 3.040 nonbonded pdb=" CD1 LEU R 98 " pdb=" CZ3 TRP R 156 " model vdw 2.189 3.760 nonbonded pdb=" OH TYR R 12 " pdb=" OE2 GLU R 14 " model vdw 2.268 3.040 ... (remaining 72739 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: 0.990 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 0.058 9032 Z= 0.214 Angle : 0.615 7.584 12241 Z= 0.371 Chirality : 0.044 0.268 1399 Planarity : 0.005 0.084 1543 Dihedral : 15.324 87.901 3222 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.63 % Allowed : 16.37 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.26), residues: 1119 helix: 1.87 (0.28), residues: 370 sheet: -0.56 (0.30), residues: 287 loop : -0.48 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE S 32 TYR 0.016 0.001 TYR S 227 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.12777 ( 444) hydrogen bonds : angle 5.95467 ( 1242) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.78411 ( 6) covalent geometry : bond 0.00384 ( 9029) covalent geometry : angle 0.61537 (12235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7603 (mt0) REVERT: B 259 GLN cc_start: 0.8480 (pt0) cc_final: 0.8270 (pt0) REVERT: B 260 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: S 160 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7036 (mtp85) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.2796 time to fit residues: 36.3679 Evaluate side-chains 95 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain R residue 359 THR Chi-restraints excluded: chain R residue 390 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN R 352 HIS R 362 ASN S 82 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.176776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132526 restraints weight = 9742.858| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.15 r_work: 0.3189 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9032 Z= 0.175 Angle : 0.572 7.652 12241 Z= 0.306 Chirality : 0.043 0.151 1399 Planarity : 0.004 0.047 1543 Dihedral : 5.060 62.271 1244 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.31 % Allowed : 15.84 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.26), residues: 1119 helix: 1.72 (0.27), residues: 380 sheet: -0.53 (0.30), residues: 282 loop : -0.50 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 169 HIS 0.004 0.001 HIS S 232 PHE 0.015 0.002 PHE B 292 TYR 0.016 0.001 TYR B 59 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 444) hydrogen bonds : angle 4.99565 ( 1242) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.71781 ( 6) covalent geometry : bond 0.00416 ( 9029) covalent geometry : angle 0.57234 (12235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7583 (mt0) outliers start: 22 outliers final: 14 residues processed: 127 average time/residue: 0.2613 time to fit residues: 45.3979 Evaluate side-chains 110 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129983 restraints weight = 9878.335| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.23 r_work: 0.3177 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9032 Z= 0.215 Angle : 0.589 8.141 12241 Z= 0.313 Chirality : 0.043 0.145 1399 Planarity : 0.004 0.040 1543 Dihedral : 4.871 60.425 1237 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.46 % Allowed : 17.21 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.12 (0.25), residues: 1119 helix: 1.60 (0.27), residues: 378 sheet: -0.73 (0.30), residues: 289 loop : -0.57 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 169 HIS 0.004 0.001 HIS S 232 PHE 0.017 0.002 PHE B 292 TYR 0.012 0.002 TYR R 159 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 444) hydrogen bonds : angle 5.02110 ( 1242) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.62470 ( 6) covalent geometry : bond 0.00522 ( 9029) covalent geometry : angle 0.58931 (12235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: B 259 GLN cc_start: 0.8561 (pt0) cc_final: 0.8293 (pt0) REVERT: B 312 ASP cc_start: 0.8612 (t0) cc_final: 0.8407 (t0) REVERT: R 191 LEU cc_start: 0.7397 (tt) cc_final: 0.7189 (tp) REVERT: S 160 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7060 (mtp85) outliers start: 33 outliers final: 25 residues processed: 127 average time/residue: 0.2424 time to fit residues: 41.3847 Evaluate side-chains 123 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132729 restraints weight = 9686.707| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.12 r_work: 0.3221 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9032 Z= 0.145 Angle : 0.534 8.196 12241 Z= 0.284 Chirality : 0.041 0.136 1399 Planarity : 0.004 0.039 1543 Dihedral : 4.732 57.831 1237 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.83 % Allowed : 19.10 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.25), residues: 1119 helix: 1.77 (0.27), residues: 376 sheet: -0.70 (0.30), residues: 278 loop : -0.59 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.026 0.002 PHE S 68 TYR 0.012 0.001 TYR B 59 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 444) hydrogen bonds : angle 4.87160 ( 1242) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.63643 ( 6) covalent geometry : bond 0.00344 ( 9029) covalent geometry : angle 0.53433 (12235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: B 312 ASP cc_start: 0.8530 (t0) cc_final: 0.8194 (t0) REVERT: S 160 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7147 (mtp85) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 0.2983 time to fit residues: 48.8376 Evaluate side-chains 113 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 17 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134797 restraints weight = 9710.041| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.16 r_work: 0.3290 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.128 Angle : 0.516 8.260 12241 Z= 0.273 Chirality : 0.041 0.135 1399 Planarity : 0.004 0.040 1543 Dihedral : 4.031 17.939 1234 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.94 % Allowed : 18.99 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.25 (0.25), residues: 1119 helix: 1.87 (0.27), residues: 377 sheet: -0.76 (0.30), residues: 271 loop : -0.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE S 68 TYR 0.010 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 444) hydrogen bonds : angle 4.73209 ( 1242) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.74469 ( 6) covalent geometry : bond 0.00299 ( 9029) covalent geometry : angle 0.51551 (12235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: B 86 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 312 ASP cc_start: 0.8568 (t0) cc_final: 0.8180 (t0) outliers start: 28 outliers final: 20 residues processed: 128 average time/residue: 0.2404 time to fit residues: 42.9113 Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.178478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133092 restraints weight = 9696.632| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.13 r_work: 0.3267 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9032 Z= 0.167 Angle : 0.544 8.462 12241 Z= 0.287 Chirality : 0.042 0.143 1399 Planarity : 0.004 0.042 1543 Dihedral : 4.102 17.993 1234 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.83 % Allowed : 19.41 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.81 (0.27), residues: 376 sheet: -0.89 (0.30), residues: 272 loop : -0.61 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.032 0.002 PHE S 68 TYR 0.012 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 444) hydrogen bonds : angle 4.80870 ( 1242) SS BOND : bond 0.00115 ( 3) SS BOND : angle 1.02915 ( 6) covalent geometry : bond 0.00402 ( 9029) covalent geometry : angle 0.54409 (12235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 312 ASP cc_start: 0.8602 (t0) cc_final: 0.8186 (t0) outliers start: 27 outliers final: 22 residues processed: 127 average time/residue: 0.2232 time to fit residues: 39.2648 Evaluate side-chains 121 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133559 restraints weight = 9714.853| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.08 r_work: 0.3292 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9032 Z= 0.134 Angle : 0.521 8.786 12241 Z= 0.274 Chirality : 0.041 0.133 1399 Planarity : 0.003 0.039 1543 Dihedral : 4.015 18.035 1234 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.94 % Allowed : 19.94 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.85 (0.27), residues: 377 sheet: -0.94 (0.30), residues: 274 loop : -0.58 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.020 0.001 PHE S 68 TYR 0.016 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 444) hydrogen bonds : angle 4.71489 ( 1242) SS BOND : bond 0.00577 ( 3) SS BOND : angle 1.47640 ( 6) covalent geometry : bond 0.00316 ( 9029) covalent geometry : angle 0.51961 (12235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7002 (tp) REVERT: B 86 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 312 ASP cc_start: 0.8660 (t0) cc_final: 0.8291 (t0) REVERT: R 61 ASN cc_start: 0.8443 (t0) cc_final: 0.8221 (t0) REVERT: S 82 GLN cc_start: 0.7547 (tp40) cc_final: 0.7295 (tp40) outliers start: 28 outliers final: 25 residues processed: 125 average time/residue: 0.2246 time to fit residues: 38.3554 Evaluate side-chains 126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 58 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.183119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140589 restraints weight = 9695.432| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.87 r_work: 0.3378 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9032 Z= 0.106 Angle : 0.498 8.869 12241 Z= 0.263 Chirality : 0.040 0.132 1399 Planarity : 0.003 0.040 1543 Dihedral : 3.843 18.071 1234 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.62 % Allowed : 20.15 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.94 (0.27), residues: 378 sheet: -0.86 (0.30), residues: 273 loop : -0.53 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE S 68 TYR 0.011 0.001 TYR R 159 ARG 0.010 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 444) hydrogen bonds : angle 4.54574 ( 1242) SS BOND : bond 0.00184 ( 3) SS BOND : angle 1.11482 ( 6) covalent geometry : bond 0.00240 ( 9029) covalent geometry : angle 0.49789 (12235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7028 (tp) REVERT: A 276 GLU cc_start: 0.7404 (pm20) cc_final: 0.7042 (pm20) REVERT: B 86 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 205 ASP cc_start: 0.8137 (p0) cc_final: 0.7924 (p0) REVERT: B 312 ASP cc_start: 0.8595 (t0) cc_final: 0.8243 (t0) REVERT: S 82 GLN cc_start: 0.7482 (tp40) cc_final: 0.7151 (tp-100) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.2296 time to fit residues: 38.6488 Evaluate side-chains 119 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.181224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137114 restraints weight = 9824.781| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.13 r_work: 0.3230 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9032 Z= 0.129 Angle : 0.518 9.035 12241 Z= 0.273 Chirality : 0.041 0.136 1399 Planarity : 0.003 0.043 1543 Dihedral : 3.880 18.065 1234 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.73 % Allowed : 20.36 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.26 (0.25), residues: 1119 helix: 1.91 (0.27), residues: 379 sheet: -0.88 (0.30), residues: 273 loop : -0.53 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE S 68 TYR 0.012 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 444) hydrogen bonds : angle 4.56622 ( 1242) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.27651 ( 6) covalent geometry : bond 0.00303 ( 9029) covalent geometry : angle 0.51778 (12235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6929 (tp) REVERT: A 276 GLU cc_start: 0.7387 (pm20) cc_final: 0.7028 (pm20) REVERT: B 86 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 312 ASP cc_start: 0.8669 (t0) cc_final: 0.8280 (t0) REVERT: S 82 GLN cc_start: 0.7468 (tp40) cc_final: 0.7118 (tp-100) outliers start: 26 outliers final: 23 residues processed: 124 average time/residue: 0.2236 time to fit residues: 38.1164 Evaluate side-chains 129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 0.0030 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138326 restraints weight = 9758.159| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.14 r_work: 0.3266 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9032 Z= 0.115 Angle : 0.508 9.155 12241 Z= 0.268 Chirality : 0.041 0.133 1399 Planarity : 0.003 0.041 1543 Dihedral : 3.827 17.992 1234 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.62 % Allowed : 20.36 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.98 (0.27), residues: 378 sheet: -0.83 (0.30), residues: 274 loop : -0.50 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE S 68 TYR 0.011 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 444) hydrogen bonds : angle 4.52333 ( 1242) SS BOND : bond 0.00260 ( 3) SS BOND : angle 1.04367 ( 6) covalent geometry : bond 0.00263 ( 9029) covalent geometry : angle 0.50720 (12235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6917 (tp) REVERT: A 276 GLU cc_start: 0.7379 (pm20) cc_final: 0.7043 (pm20) REVERT: B 86 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8512 (p) REVERT: B 312 ASP cc_start: 0.8657 (t0) cc_final: 0.8254 (t0) REVERT: R 171 ASP cc_start: 0.7488 (t0) cc_final: 0.7258 (t0) REVERT: S 82 GLN cc_start: 0.7452 (tp40) cc_final: 0.7139 (tp-100) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.2376 time to fit residues: 40.0537 Evaluate side-chains 126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN B 119 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.184141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138691 restraints weight = 9793.978| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.11 r_work: 0.3351 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9032 Z= 0.104 Angle : 0.500 9.105 12241 Z= 0.264 Chirality : 0.041 0.323 1399 Planarity : 0.003 0.040 1543 Dihedral : 3.747 18.080 1234 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.31 % Allowed : 20.57 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.25), residues: 1119 helix: 2.00 (0.27), residues: 380 sheet: -0.75 (0.30), residues: 272 loop : -0.51 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE S 68 TYR 0.010 0.001 TYR R 159 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 444) hydrogen bonds : angle 4.46471 ( 1242) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.99481 ( 6) covalent geometry : bond 0.00234 ( 9029) covalent geometry : angle 0.50001 (12235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5772.19 seconds wall clock time: 102 minutes 1.83 seconds (6121.83 seconds total)