Starting phenix.real_space_refine on Sat Aug 23 02:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jim_36318/08_2025/8jim_36318.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.095 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 69 5.16 5 C 5779 2.51 5 N 1538 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9051 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'AW9': 1, 'CLR': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 9051 At special positions: 0 Unit cell: (93.5, 122.4, 137.7, 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 69 16.00 O 1665 8.00 N 1538 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 183 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 351.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 33.0% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.982A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.884A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.607A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.192A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.692A pdb=" N LYS D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.766A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.752A pdb=" N PHE D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.692A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.598A pdb=" N ALA D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 351 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.840A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 54 removed outlier: 3.817A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Proline residue: E 31 - end of helix removed outlier: 4.309A pdb=" N LEU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.741A pdb=" N LEU E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 4.025A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.834A pdb=" N CYS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.552A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 4.133A pdb=" N PHE E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 4.672A pdb=" N TYR E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.971A pdb=" N ILE E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 157 Processing helix chain 'E' and resid 158 through 163 removed outlier: 5.347A pdb=" N HIS E 161 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 193 removed outlier: 4.268A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 214 removed outlier: 4.131A pdb=" N ILE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 244 removed outlier: 3.650A pdb=" N ARG E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 removed outlier: 3.590A pdb=" N VAL E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 270 removed outlier: 3.607A pdb=" N VAL E 268 " --> pdb=" O ASN E 265 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 270 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 280 removed outlier: 3.866A pdb=" N ILE E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.950A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.155A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.545A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.709A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 191 removed outlier: 3.865A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.613A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.662A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.687A pdb=" N GLU E 12 " --> pdb=" O CYS E 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.578A pdb=" N ILE E 169 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1041 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: 1.54 Time building geometry restraints manager: 1.13 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: 1462 1.31 - 1.44: 2571 1.44 - 1.57: 5114 1.57 - 1.70: 0 1.70 - 1.83: 100 Bond restraints: 9247 Sorted by residual: bond pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 1.533 1.460 0.073 1.60e-02 3.91e+03 2.07e+01 bond pdb=" C ILE E 230 " pdb=" O ILE E 230 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" CA ALA E 229 " pdb=" CB ALA E 229 " ideal model delta sigma weight residual 1.528 1.465 0.064 1.66e-02 3.63e+03 1.47e+01 bond pdb=" C ARG E 228 " pdb=" O ARG E 228 " ideal model delta sigma weight residual 1.237 1.281 -0.044 1.19e-02 7.06e+03 1.40e+01 bond pdb=" C ALA E 229 " pdb=" O ALA E 229 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.26e-02 6.30e+03 1.33e+01 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 12241 2.60 - 5.21: 240 5.21 - 7.81: 22 7.81 - 10.42: 9 10.42 - 13.02: 1 Bond angle restraints: 12513 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 122.60 109.58 13.02 1.88e+00 2.83e-01 4.80e+01 angle pdb=" N ARG S 191 " pdb=" CA ARG S 191 " pdb=" C ARG S 191 " ideal model delta sigma weight residual 108.00 99.52 8.48 1.48e+00 4.57e-01 3.28e+01 angle pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 110.61 102.05 8.56 1.51e+00 4.39e-01 3.21e+01 angle pdb=" C ASN S 194 " pdb=" CA ASN S 194 " pdb=" CB ASN S 194 " ideal model delta sigma weight residual 109.89 117.74 -7.85 1.60e+00 3.91e-01 2.41e+01 angle pdb=" N ALA E 229 " pdb=" CA ALA E 229 " pdb=" C ALA E 229 " ideal model delta sigma weight residual 111.82 106.75 5.07 1.16e+00 7.43e-01 1.91e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4864 15.46 - 30.91: 514 30.91 - 46.37: 124 46.37 - 61.82: 21 61.82 - 77.28: 7 Dihedral angle restraints: 5530 sinusoidal: 2218 harmonic: 3312 Sorted by residual: dihedral pdb=" CB CYS E 18 " pdb=" SG CYS E 18 " pdb=" SG CYS E 183 " pdb=" CB CYS E 183 " ideal model delta sinusoidal sigma weight residual 93.00 49.73 43.27 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PHE E 52 " pdb=" C PHE E 52 " pdb=" N CYS E 53 " pdb=" CA CYS E 53 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 830 0.041 - 0.082: 432 0.082 - 0.123: 110 0.123 - 0.164: 29 0.164 - 0.205: 6 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL E 235 " pdb=" N VAL E 235 " pdb=" C VAL E 235 " pdb=" CB VAL E 235 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB VAL S 64 " pdb=" CA VAL S 64 " pdb=" CG1 VAL S 64 " pdb=" CG2 VAL S 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 1404 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 227 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C LYS E 227 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS E 227 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG E 228 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 105 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 192 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C MET S 192 " -0.045 2.00e-02 2.50e+03 pdb=" O MET S 192 " 0.017 2.00e-02 2.50e+03 pdb=" N SER S 193 " 0.016 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1638 2.77 - 3.30: 8251 3.30 - 3.83: 13628 3.83 - 4.37: 16317 4.37 - 4.90: 29620 Nonbonded interactions: 69454 Sorted by model distance: nonbonded pdb=" O LEU S 174 " pdb=" O ARG S 191 " model vdw 2.232 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.234 3.040 nonbonded pdb=" O SER E 214 " pdb=" OG SER E 214 " model vdw 2.257 3.040 nonbonded pdb=" OG SER S 161 " pdb=" OG1 THR S 210 " model vdw 2.261 3.040 nonbonded pdb=" NZ LYS B 89 " pdb=" OD1 ASP D 20 " model vdw 2.287 3.120 ... (remaining 69449 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: 1.010 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.007 0.073 9251 Z= 0.336 Angle : 0.907 13.021 12521 Z= 0.533 Chirality : 0.052 0.205 1407 Planarity : 0.004 0.050 1578 Dihedral : 13.511 77.278 3378 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 0.41 % Allowed : 1.01 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.23), residues: 1130 helix: -0.53 (0.28), residues: 329 sheet: -0.41 (0.31), residues: 271 loop : -2.23 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 160 TYR 0.049 0.003 TYR B 105 PHE 0.025 0.002 PHE E 52 TRP 0.025 0.003 TRP S 47 HIS 0.009 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 9247) covalent geometry : angle 0.90537 (12513) SS BOND : bond 0.00713 ( 4) SS BOND : angle 2.12812 ( 8) hydrogen bonds : bond 0.16389 ( 370) hydrogen bonds : angle 6.19889 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.366 Fit side-chains REVERT: B 217 MET cc_start: 0.7942 (ptt) cc_final: 0.7734 (ptt) REVERT: C 48 ASP cc_start: 0.6571 (p0) cc_final: 0.6366 (p0) REVERT: D 24 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7729 (ttp80) REVERT: D 270 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7866 (mtmp) REVERT: S 46 GLU cc_start: 0.7826 (pm20) cc_final: 0.7585 (pm20) REVERT: E 269 TYR cc_start: 0.7639 (m-80) cc_final: 0.7306 (m-80) REVERT: E 274 LEU cc_start: 0.7943 (tp) cc_final: 0.7734 (tm) REVERT: E 282 PHE cc_start: 0.7587 (m-80) cc_final: 0.7049 (m-10) outliers start: 4 outliers final: 2 residues processed: 166 average time/residue: 0.6326 time to fit residues: 111.6475 Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 82 GLN S 194 ASN E 161 HIS E 189 HIS E 223 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.143662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105856 restraints weight = 14427.701| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.57 r_work: 0.3323 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9251 Z= 0.140 Angle : 0.639 7.850 12521 Z= 0.336 Chirality : 0.044 0.155 1407 Planarity : 0.004 0.039 1578 Dihedral : 6.301 87.870 1307 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.93 % Allowed : 10.34 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.24), residues: 1130 helix: 0.13 (0.29), residues: 339 sheet: -0.16 (0.32), residues: 278 loop : -1.98 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 251 TYR 0.020 0.002 TYR B 105 PHE 0.036 0.001 PHE E 255 TRP 0.016 0.002 TRP S 47 HIS 0.012 0.002 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9247) covalent geometry : angle 0.63819 (12513) SS BOND : bond 0.00917 ( 4) SS BOND : angle 1.73275 ( 8) hydrogen bonds : bond 0.04251 ( 370) hydrogen bonds : angle 4.74938 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.278 Fit side-chains REVERT: B 217 MET cc_start: 0.8318 (ptt) cc_final: 0.8113 (ptt) REVERT: B 258 ASP cc_start: 0.7727 (p0) cc_final: 0.7527 (p0) REVERT: D 24 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7762 (ttm170) REVERT: D 229 ASP cc_start: 0.7625 (t0) cc_final: 0.7409 (t0) REVERT: S 60 TYR cc_start: 0.8252 (m-80) cc_final: 0.7790 (m-80) REVERT: S 67 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7073 (mtm180) REVERT: E 109 MET cc_start: 0.8085 (tmt) cc_final: 0.7870 (tmt) REVERT: E 269 TYR cc_start: 0.7767 (m-80) cc_final: 0.7377 (m-80) REVERT: E 282 PHE cc_start: 0.7619 (m-80) cc_final: 0.7356 (m-10) outliers start: 19 outliers final: 8 residues processed: 144 average time/residue: 0.6095 time to fit residues: 93.3880 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 281 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN S 113 GLN E 161 HIS E 223 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104668 restraints weight = 14258.392| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.57 r_work: 0.3305 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9251 Z= 0.139 Angle : 0.612 7.431 12521 Z= 0.322 Chirality : 0.043 0.144 1407 Planarity : 0.004 0.037 1578 Dihedral : 5.803 85.089 1304 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.74 % Allowed : 12.98 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.24), residues: 1130 helix: 0.44 (0.29), residues: 341 sheet: 0.03 (0.31), residues: 281 loop : -1.87 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 251 TYR 0.017 0.001 TYR B 105 PHE 0.033 0.001 PHE E 255 TRP 0.012 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9247) covalent geometry : angle 0.61075 (12513) SS BOND : bond 0.00490 ( 4) SS BOND : angle 1.49058 ( 8) hydrogen bonds : bond 0.04143 ( 370) hydrogen bonds : angle 4.50404 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.252 Fit side-chains REVERT: D 24 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7669 (ttm170) REVERT: D 53 MET cc_start: 0.6584 (mtp) cc_final: 0.6294 (mtp) REVERT: D 229 ASP cc_start: 0.7815 (t0) cc_final: 0.7472 (t0) REVERT: S 60 TYR cc_start: 0.8325 (m-80) cc_final: 0.8121 (m-80) REVERT: S 67 ARG cc_start: 0.7492 (mtm180) cc_final: 0.7059 (mtm180) REVERT: E 269 TYR cc_start: 0.7809 (m-80) cc_final: 0.7488 (m-80) REVERT: E 282 PHE cc_start: 0.7678 (m-80) cc_final: 0.7448 (m-10) outliers start: 27 outliers final: 14 residues processed: 139 average time/residue: 0.5961 time to fit residues: 88.2058 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 281 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 161 HIS E 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.142443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103905 restraints weight = 14490.476| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.60 r_work: 0.3293 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9251 Z= 0.140 Angle : 0.605 7.761 12521 Z= 0.316 Chirality : 0.043 0.145 1407 Planarity : 0.004 0.036 1578 Dihedral : 5.670 81.032 1304 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.25 % Allowed : 14.40 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1130 helix: 0.53 (0.30), residues: 342 sheet: 0.08 (0.31), residues: 281 loop : -1.75 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 160 TYR 0.016 0.001 TYR B 105 PHE 0.032 0.002 PHE E 38 TRP 0.012 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9247) covalent geometry : angle 0.60446 (12513) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.38656 ( 8) hydrogen bonds : bond 0.03998 ( 370) hydrogen bonds : angle 4.39384 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.383 Fit side-chains REVERT: D 24 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7634 (ttm170) REVERT: D 53 MET cc_start: 0.6637 (mtp) cc_final: 0.6344 (mtp) REVERT: S 67 ARG cc_start: 0.7455 (mtm180) cc_final: 0.6990 (mtm180) REVERT: E 102 LEU cc_start: 0.7670 (mm) cc_final: 0.7151 (tm) REVERT: E 269 TYR cc_start: 0.7734 (m-80) cc_final: 0.7423 (m-80) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 0.5317 time to fit residues: 78.6181 Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 108 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.144520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106274 restraints weight = 14146.386| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.51 r_work: 0.3329 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9251 Z= 0.107 Angle : 0.552 7.639 12521 Z= 0.289 Chirality : 0.042 0.149 1407 Planarity : 0.003 0.036 1578 Dihedral : 5.399 79.173 1304 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.35 % Allowed : 15.82 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1130 helix: 0.73 (0.30), residues: 342 sheet: 0.13 (0.31), residues: 282 loop : -1.64 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 72 TYR 0.012 0.001 TYR S 190 PHE 0.031 0.001 PHE E 38 TRP 0.010 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9247) covalent geometry : angle 0.55102 (12513) SS BOND : bond 0.00472 ( 4) SS BOND : angle 1.15770 ( 8) hydrogen bonds : bond 0.03411 ( 370) hydrogen bonds : angle 4.21404 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.346 Fit side-chains REVERT: D 24 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7798 (ttp-110) REVERT: D 53 MET cc_start: 0.6549 (mtp) cc_final: 0.6272 (mtp) REVERT: D 248 LYS cc_start: 0.8044 (tppt) cc_final: 0.7223 (mtpm) REVERT: D 270 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8130 (mtmp) REVERT: S 67 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7017 (mtm180) REVERT: E 25 PHE cc_start: 0.7884 (t80) cc_final: 0.7605 (t80) REVERT: E 102 LEU cc_start: 0.7743 (mm) cc_final: 0.7245 (tm) REVERT: E 269 TYR cc_start: 0.7700 (m-80) cc_final: 0.7483 (m-80) outliers start: 33 outliers final: 10 residues processed: 141 average time/residue: 0.5488 time to fit residues: 82.4406 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.0770 chunk 99 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107181 restraints weight = 14159.689| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.51 r_work: 0.3342 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9251 Z= 0.101 Angle : 0.550 8.013 12521 Z= 0.286 Chirality : 0.042 0.208 1407 Planarity : 0.003 0.037 1578 Dihedral : 5.221 77.630 1304 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.94 % Allowed : 18.26 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.25), residues: 1130 helix: 0.88 (0.30), residues: 341 sheet: 0.23 (0.31), residues: 279 loop : -1.58 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 242 TYR 0.012 0.001 TYR S 190 PHE 0.034 0.001 PHE E 38 TRP 0.009 0.001 TRP B 211 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9247) covalent geometry : angle 0.54956 (12513) SS BOND : bond 0.00468 ( 4) SS BOND : angle 1.11644 ( 8) hydrogen bonds : bond 0.03237 ( 370) hydrogen bonds : angle 4.10078 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.374 Fit side-chains REVERT: D 20 ASP cc_start: 0.7826 (m-30) cc_final: 0.7607 (m-30) REVERT: D 24 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7770 (ttp-110) REVERT: D 52 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6506 (mt0) REVERT: D 53 MET cc_start: 0.6518 (mtp) cc_final: 0.6257 (mtp) REVERT: D 248 LYS cc_start: 0.8018 (tppt) cc_final: 0.7217 (mtpm) REVERT: D 270 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (mtmp) REVERT: S 67 ARG cc_start: 0.7462 (mtm180) cc_final: 0.6926 (mtm180) REVERT: S 78 THR cc_start: 0.7704 (t) cc_final: 0.7430 (m) REVERT: E 25 PHE cc_start: 0.7893 (t80) cc_final: 0.7685 (t80) REVERT: E 52 PHE cc_start: 0.6335 (m-10) cc_final: 0.6105 (OUTLIER) REVERT: E 102 LEU cc_start: 0.7710 (mm) cc_final: 0.7186 (tm) REVERT: E 269 TYR cc_start: 0.7644 (m-80) cc_final: 0.7418 (m-80) outliers start: 29 outliers final: 13 residues processed: 145 average time/residue: 0.5397 time to fit residues: 83.8406 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.6980 chunk 93 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.142733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104083 restraints weight = 14149.280| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.50 r_work: 0.3286 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9251 Z= 0.148 Angle : 0.607 8.239 12521 Z= 0.316 Chirality : 0.044 0.201 1407 Planarity : 0.004 0.038 1578 Dihedral : 5.398 76.133 1304 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 19.37 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1130 helix: 0.83 (0.30), residues: 344 sheet: 0.20 (0.31), residues: 277 loop : -1.55 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 242 TYR 0.017 0.002 TYR B 105 PHE 0.034 0.002 PHE E 255 TRP 0.011 0.001 TRP E 152 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9247) covalent geometry : angle 0.60648 (12513) SS BOND : bond 0.00552 ( 4) SS BOND : angle 1.26453 ( 8) hydrogen bonds : bond 0.03910 ( 370) hydrogen bonds : angle 4.18512 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.258 Fit side-chains REVERT: B 220 GLN cc_start: 0.7635 (mt0) cc_final: 0.7287 (mt0) REVERT: D 24 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7869 (ttp-110) REVERT: D 52 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6504 (mt0) REVERT: D 53 MET cc_start: 0.6498 (mtp) cc_final: 0.6248 (mtp) REVERT: D 270 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8254 (mtmp) REVERT: S 60 TYR cc_start: 0.8255 (m-80) cc_final: 0.8026 (m-80) REVERT: S 78 THR cc_start: 0.7682 (t) cc_final: 0.7442 (m) REVERT: E 102 LEU cc_start: 0.7683 (mm) cc_final: 0.7204 (tm) REVERT: E 220 MET cc_start: 0.8132 (tpp) cc_final: 0.7730 (tpp) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 0.5497 time to fit residues: 81.6735 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105013 restraints weight = 14107.266| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.51 r_work: 0.3303 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9251 Z= 0.130 Angle : 0.595 8.718 12521 Z= 0.308 Chirality : 0.043 0.191 1407 Planarity : 0.004 0.039 1578 Dihedral : 5.338 74.542 1304 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.84 % Allowed : 20.18 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1130 helix: 0.89 (0.30), residues: 341 sheet: 0.29 (0.32), residues: 270 loop : -1.56 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 242 TYR 0.014 0.001 TYR S 95 PHE 0.033 0.001 PHE E 38 TRP 0.011 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9247) covalent geometry : angle 0.59462 (12513) SS BOND : bond 0.00523 ( 4) SS BOND : angle 1.35581 ( 8) hydrogen bonds : bond 0.03680 ( 370) hydrogen bonds : angle 4.18682 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.363 Fit side-chains REVERT: B 220 GLN cc_start: 0.7603 (mt0) cc_final: 0.7241 (mt0) REVERT: D 24 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7905 (ttp-110) REVERT: D 52 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6403 (mt0) REVERT: D 53 MET cc_start: 0.6482 (mtp) cc_final: 0.6232 (mtp) REVERT: D 248 LYS cc_start: 0.8014 (tppt) cc_final: 0.7211 (mtpm) REVERT: D 270 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8271 (mtmp) REVERT: S 60 TYR cc_start: 0.8290 (m-80) cc_final: 0.8062 (m-80) REVERT: S 78 THR cc_start: 0.7653 (t) cc_final: 0.7408 (m) REVERT: E 102 LEU cc_start: 0.7728 (mm) cc_final: 0.7220 (tm) outliers start: 28 outliers final: 18 residues processed: 131 average time/residue: 0.6246 time to fit residues: 87.2996 Evaluate side-chains 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105605 restraints weight = 14042.723| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.54 r_work: 0.3317 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9251 Z= 0.115 Angle : 0.580 8.991 12521 Z= 0.299 Chirality : 0.043 0.191 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.215 71.965 1304 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.33 % Allowed : 20.79 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1130 helix: 0.96 (0.30), residues: 345 sheet: 0.31 (0.31), residues: 278 loop : -1.51 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 242 TYR 0.012 0.001 TYR S 190 PHE 0.034 0.001 PHE E 38 TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9247) covalent geometry : angle 0.57944 (12513) SS BOND : bond 0.00489 ( 4) SS BOND : angle 1.25262 ( 8) hydrogen bonds : bond 0.03399 ( 370) hydrogen bonds : angle 4.11812 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.385 Fit side-chains REVERT: B 220 GLN cc_start: 0.7485 (mt0) cc_final: 0.7146 (mt0) REVERT: D 24 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7843 (ttp-110) REVERT: D 52 GLN cc_start: 0.6589 (OUTLIER) cc_final: 0.6374 (mt0) REVERT: D 53 MET cc_start: 0.6454 (mtp) cc_final: 0.6187 (mtp) REVERT: D 248 LYS cc_start: 0.7959 (tppt) cc_final: 0.7161 (mtpm) REVERT: D 270 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8205 (mtmp) REVERT: S 60 TYR cc_start: 0.8329 (m-80) cc_final: 0.8085 (m-80) REVERT: S 78 THR cc_start: 0.7593 (t) cc_final: 0.7347 (m) REVERT: E 102 LEU cc_start: 0.7672 (mm) cc_final: 0.7167 (tm) REVERT: E 220 MET cc_start: 0.8165 (tpp) cc_final: 0.7747 (tpp) outliers start: 23 outliers final: 16 residues processed: 129 average time/residue: 0.6188 time to fit residues: 85.1899 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 102 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105611 restraints weight = 14092.292| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.51 r_work: 0.3324 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9251 Z= 0.114 Angle : 0.576 9.261 12521 Z= 0.299 Chirality : 0.043 0.189 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.166 70.367 1304 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.03 % Allowed : 21.20 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.25), residues: 1130 helix: 0.98 (0.30), residues: 345 sheet: 0.33 (0.32), residues: 272 loop : -1.47 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 242 TYR 0.014 0.001 TYR S 95 PHE 0.033 0.001 PHE E 38 TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9247) covalent geometry : angle 0.57537 (12513) SS BOND : bond 0.00488 ( 4) SS BOND : angle 1.19090 ( 8) hydrogen bonds : bond 0.03371 ( 370) hydrogen bonds : angle 4.07917 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.442 Fit side-chains REVERT: B 220 GLN cc_start: 0.7569 (mt0) cc_final: 0.7238 (mt0) REVERT: D 24 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: D 52 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6247 (mt0) REVERT: D 53 MET cc_start: 0.6424 (mtp) cc_final: 0.6163 (mtp) REVERT: D 248 LYS cc_start: 0.8068 (tppt) cc_final: 0.7259 (mtpm) REVERT: D 270 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (mtmp) REVERT: S 60 TYR cc_start: 0.8352 (m-80) cc_final: 0.8100 (m-80) REVERT: S 78 THR cc_start: 0.7630 (t) cc_final: 0.7386 (m) REVERT: E 102 LEU cc_start: 0.7731 (mm) cc_final: 0.7213 (tm) REVERT: E 220 MET cc_start: 0.8165 (tpp) cc_final: 0.7722 (tpp) outliers start: 20 outliers final: 17 residues processed: 126 average time/residue: 0.6289 time to fit residues: 84.4975 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.0000 chunk 73 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.144949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106494 restraints weight = 13908.920| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.50 r_work: 0.3326 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9251 Z= 0.111 Angle : 0.574 9.266 12521 Z= 0.296 Chirality : 0.042 0.188 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.087 68.009 1304 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.43 % Allowed : 20.69 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.25), residues: 1130 helix: 1.04 (0.30), residues: 344 sheet: 0.28 (0.31), residues: 280 loop : -1.44 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 242 TYR 0.014 0.001 TYR S 95 PHE 0.033 0.001 PHE E 38 TRP 0.009 0.001 TRP B 211 HIS 0.011 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9247) covalent geometry : angle 0.57304 (12513) SS BOND : bond 0.00475 ( 4) SS BOND : angle 1.12722 ( 8) hydrogen bonds : bond 0.03281 ( 370) hydrogen bonds : angle 4.05830 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.98 seconds wall clock time: 65 minutes 37.78 seconds (3937.78 seconds total)