Starting phenix.real_space_refine on Thu Mar 13 19:13:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jim_36318/03_2025/8jim_36318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jim_36318/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jim_36318/03_2025/8jim_36318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jim_36318/03_2025/8jim_36318.map" model { file = "/net/cci-nas-00/data/ceres_data/8jim_36318/03_2025/8jim_36318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jim_36318/03_2025/8jim_36318_neut.cif" } resolution = 2.98 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= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.01, per 1000 atoms: 0.66 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 2.52 Time building geometry restraints manager: 2.95 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: 1.130 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.350 Find NCS groups from input model: 0.120 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:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- 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 9247 Z= 0.453 Angle : 0.905 13.021 12513 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 : 10.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.025 0.003 TRP S 47 HIS 0.009 0.002 HIS S 35 PHE 0.025 0.002 PHE E 52 TYR 0.049 0.003 TYR B 105 ARG 0.007 0.001 ARG S 160 *********************** 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 : 1.041 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: 1.3572 time to fit residues: 240.0277 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 : 1.104 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.143836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105954 restraints weight = 14303.166| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.57 r_work: 0.3324 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.201 Angle : 0.641 7.791 12513 Z= 0.338 Chirality : 0.044 0.151 1407 Planarity : 0.004 0.039 1578 Dihedral : 6.356 89.595 1307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 9.74 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1130 helix: 0.12 (0.29), residues: 341 sheet: -0.18 (0.31), residues: 278 loop : -2.01 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.011 0.002 HIS E 161 PHE 0.035 0.001 PHE E 255 TYR 0.019 0.002 TYR B 105 ARG 0.004 0.000 ARG S 160 *********************** 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 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.291 Fit side-chains REVERT: C 48 ASP cc_start: 0.7359 (p0) cc_final: 0.7024 (p0) REVERT: D 24 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7759 (ttp80) REVERT: D 229 ASP cc_start: 0.7669 (t0) cc_final: 0.7466 (t0) REVERT: S 60 TYR cc_start: 0.8303 (m-80) cc_final: 0.8053 (m-80) REVERT: S 67 ARG cc_start: 0.7513 (mtm180) cc_final: 0.6980 (mtm180) REVERT: S 93 MET cc_start: 0.8375 (ttt) cc_final: 0.8077 (ttt) REVERT: E 269 TYR cc_start: 0.7745 (m-80) cc_final: 0.7374 (m-80) REVERT: E 270 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7600 (mpp80) REVERT: E 282 PHE cc_start: 0.7598 (m-80) cc_final: 0.7287 (m-10) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 1.4474 time to fit residues: 215.6872 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 D residue 190 THR 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 257 LEU Chi-restraints excluded: chain E residue 270 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 E 161 HIS E 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105989 restraints weight = 14367.849| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.58 r_work: 0.3325 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9247 Z= 0.183 Angle : 0.592 7.327 12513 Z= 0.311 Chirality : 0.043 0.155 1407 Planarity : 0.004 0.036 1578 Dihedral : 5.745 89.480 1304 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 12.68 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.94 (0.25), residues: 1130 helix: 0.55 (0.30), residues: 340 sheet: 0.03 (0.31), residues: 281 loop : -1.85 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.010 0.001 HIS E 161 PHE 0.029 0.001 PHE E 38 TYR 0.013 0.001 TYR B 105 ARG 0.002 0.000 ARG S 160 *********************** 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 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 1.318 Fit side-chains REVERT: C 48 ASP cc_start: 0.7612 (p0) cc_final: 0.7314 (p0) REVERT: D 24 ARG cc_start: 0.8056 (ttp-110) cc_final: 0.7748 (ttm170) REVERT: D 53 MET cc_start: 0.6629 (mtp) cc_final: 0.6353 (mtp) REVERT: D 229 ASP cc_start: 0.7783 (t0) cc_final: 0.7489 (t0) REVERT: S 60 TYR cc_start: 0.8280 (m-80) cc_final: 0.7997 (m-80) REVERT: S 67 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7027 (mtm180) REVERT: S 83 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: E 192 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7080 (ttm) REVERT: E 269 TYR cc_start: 0.7746 (m-80) cc_final: 0.7389 (m-80) REVERT: E 270 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (mpp80) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 1.4948 time to fit residues: 218.4719 Evaluate side-chains 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 LEU 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 270 ARG Chi-restraints excluded: chain E residue 274 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN E 161 HIS E 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104628 restraints weight = 14182.117| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.58 r_work: 0.3299 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.209 Angle : 0.593 7.269 12513 Z= 0.310 Chirality : 0.043 0.144 1407 Planarity : 0.004 0.037 1578 Dihedral : 5.601 84.030 1304 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.35 % Allowed : 13.49 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.77 (0.25), residues: 1130 helix: 0.67 (0.30), residues: 342 sheet: 0.10 (0.31), residues: 280 loop : -1.70 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.031 0.001 PHE E 255 TYR 0.015 0.001 TYR B 105 ARG 0.002 0.000 ARG D 242 *********************** 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 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.017 Fit side-chains REVERT: D 24 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7646 (ttm170) REVERT: D 53 MET cc_start: 0.6534 (mtp) cc_final: 0.6272 (mtp) REVERT: S 67 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7034 (mtm180) REVERT: S 93 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8093 (tpp) REVERT: E 104 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8322 (mp) REVERT: E 269 TYR cc_start: 0.7682 (m-80) cc_final: 0.7346 (m-80) REVERT: E 270 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7614 (mpp80) outliers start: 33 outliers final: 13 residues processed: 139 average time/residue: 1.1804 time to fit residues: 175.7071 Evaluate side-chains 131 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 205 LEU 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 270 ARG 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 13 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.145211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106597 restraints weight = 14086.131| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.57 r_work: 0.3328 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9247 Z= 0.151 Angle : 0.551 7.375 12513 Z= 0.289 Chirality : 0.042 0.157 1407 Planarity : 0.003 0.036 1578 Dihedral : 5.338 80.121 1304 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.74 % Allowed : 16.43 % 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 (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: -0.58 (0.25), residues: 1130 helix: 0.86 (0.30), residues: 341 sheet: 0.11 (0.31), residues: 282 loop : -1.57 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.012 0.001 TYR S 190 ARG 0.002 0.000 ARG S 72 *********************** 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 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.051 Fit side-chains REVERT: D 24 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: D 53 MET cc_start: 0.6532 (mtp) cc_final: 0.6308 (mtp) REVERT: D 248 LYS cc_start: 0.7982 (tppt) cc_final: 0.7168 (mtpm) REVERT: D 270 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8090 (mtmp) REVERT: S 60 TYR cc_start: 0.8103 (m-80) cc_final: 0.7886 (m-80) REVERT: S 67 ARG cc_start: 0.7455 (mtm180) cc_final: 0.7041 (mtm180) REVERT: E 269 TYR cc_start: 0.7621 (m-80) cc_final: 0.7340 (m-80) outliers start: 27 outliers final: 9 residues processed: 135 average time/residue: 1.2253 time to fit residues: 177.2403 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 104 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 111 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN E 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106005 restraints weight = 13949.022| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.49 r_work: 0.3323 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9247 Z= 0.172 Angle : 0.567 7.614 12513 Z= 0.294 Chirality : 0.043 0.205 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.299 78.628 1304 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.45 % Allowed : 17.04 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.53 (0.25), residues: 1130 helix: 0.90 (0.30), residues: 341 sheet: 0.13 (0.31), residues: 282 loop : -1.52 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.012 0.001 TYR S 95 ARG 0.003 0.000 ARG E 270 *********************** 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 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.954 Fit side-chains REVERT: B 220 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: D 24 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: D 52 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6495 (mt0) REVERT: D 53 MET cc_start: 0.6520 (mtp) cc_final: 0.6280 (mtp) REVERT: D 227 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8270 (pt) REVERT: D 248 LYS cc_start: 0.8048 (tppt) cc_final: 0.7254 (mtpm) REVERT: S 60 TYR cc_start: 0.8261 (m-80) cc_final: 0.8014 (m-80) REVERT: S 67 ARG cc_start: 0.7483 (mtm180) cc_final: 0.6962 (mtm180) REVERT: S 78 THR cc_start: 0.7733 (t) cc_final: 0.7458 (m) REVERT: E 290 ASP cc_start: 0.7285 (t0) cc_final: 0.6977 (t0) outliers start: 34 outliers final: 13 residues processed: 141 average time/residue: 1.1683 time to fit residues: 176.4538 Evaluate side-chains 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 220 GLN 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 227 LEU Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 197 SER 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 281 SER 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 43 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 0.0030 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106103 restraints weight = 14095.428| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.50 r_work: 0.3322 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9247 Z= 0.170 Angle : 0.570 8.287 12513 Z= 0.297 Chirality : 0.043 0.194 1407 Planarity : 0.004 0.051 1578 Dihedral : 5.274 77.238 1304 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.94 % Allowed : 18.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.50 (0.25), residues: 1130 helix: 0.93 (0.30), residues: 342 sheet: 0.15 (0.31), residues: 283 loop : -1.51 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.011 0.001 TYR S 190 ARG 0.007 0.000 ARG D 242 *********************** 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 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.998 Fit side-chains REVERT: B 220 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: D 24 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7864 (ttp-110) REVERT: D 53 MET cc_start: 0.6512 (mtp) cc_final: 0.6204 (mtp) REVERT: D 227 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8297 (pt) REVERT: S 67 ARG cc_start: 0.7479 (mtm180) cc_final: 0.6970 (mtm180) REVERT: S 78 THR cc_start: 0.7706 (t) cc_final: 0.7454 (m) REVERT: E 25 PHE cc_start: 0.7736 (t80) cc_final: 0.7513 (t80) outliers start: 29 outliers final: 15 residues processed: 136 average time/residue: 1.3135 time to fit residues: 192.3864 Evaluate side-chains 131 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 220 GLN 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 227 LEU Chi-restraints excluded: chain D residue 276 GLU 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 92 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 104 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 45 ASN E 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106206 restraints weight = 14323.349| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.58 r_work: 0.3326 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9247 Z= 0.155 Angle : 0.569 8.316 12513 Z= 0.295 Chirality : 0.043 0.190 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.191 75.814 1304 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.04 % Allowed : 19.07 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.44 (0.25), residues: 1130 helix: 0.97 (0.30), residues: 343 sheet: 0.16 (0.31), residues: 282 loop : -1.46 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.014 0.001 TYR S 95 ARG 0.006 0.000 ARG D 242 *********************** 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 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.124 Fit side-chains REVERT: D 24 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.7789 (ttp-110) REVERT: D 52 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6410 (mt0) REVERT: D 53 MET cc_start: 0.6480 (mtp) cc_final: 0.6220 (mtp) REVERT: D 227 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8171 (pt) REVERT: D 248 LYS cc_start: 0.7982 (tppt) cc_final: 0.7186 (mtpm) REVERT: S 67 ARG cc_start: 0.7473 (mtm180) cc_final: 0.6944 (mtm180) REVERT: S 78 THR cc_start: 0.7602 (t) cc_final: 0.7361 (m) REVERT: E 220 MET cc_start: 0.8102 (tpp) cc_final: 0.7716 (tpp) outliers start: 30 outliers final: 12 residues processed: 136 average time/residue: 1.4537 time to fit residues: 211.9511 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 : 0.961 ------------------------------------------------------------------------------- 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 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 227 LEU Chi-restraints excluded: chain S residue 64 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.144423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106078 restraints weight = 13972.357| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.50 r_work: 0.3325 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9247 Z= 0.175 Angle : 0.580 8.862 12513 Z= 0.300 Chirality : 0.043 0.187 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.190 73.835 1304 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.64 % Allowed : 20.18 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.40 (0.25), residues: 1130 helix: 1.01 (0.30), residues: 343 sheet: 0.20 (0.31), residues: 282 loop : -1.44 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.013 0.001 TYR S 95 ARG 0.005 0.000 ARG D 242 *********************** 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: 26 poor density : 112 time to evaluate : 0.941 Fit side-chains REVERT: D 24 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: D 52 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.6233 (mt0) REVERT: D 53 MET cc_start: 0.6450 (mtp) cc_final: 0.6133 (mtp) REVERT: D 227 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (pt) REVERT: D 248 LYS cc_start: 0.8013 (tppt) cc_final: 0.7221 (mtpm) REVERT: D 270 LYS cc_start: 0.8586 (mttp) cc_final: 0.8331 (mttm) REVERT: S 78 THR cc_start: 0.7643 (t) cc_final: 0.7400 (m) REVERT: E 220 MET cc_start: 0.8119 (tpp) cc_final: 0.7693 (tpp) outliers start: 26 outliers final: 13 residues processed: 130 average time/residue: 1.4145 time to fit residues: 196.8564 Evaluate side-chains 126 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain S residue 64 VAL 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 23 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.107050 restraints weight = 14049.726| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.55 r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9247 Z= 0.153 Angle : 0.567 9.282 12513 Z= 0.293 Chirality : 0.042 0.187 1407 Planarity : 0.003 0.040 1578 Dihedral : 5.084 71.199 1304 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.52 % Allowed : 21.20 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.25), residues: 1130 helix: 1.06 (0.30), residues: 343 sheet: 0.21 (0.31), residues: 283 loop : -1.42 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.014 0.001 TYR S 95 ARG 0.005 0.000 ARG D 242 ********************** 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 128 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: D 24 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7781 (ttp-110) REVERT: D 25 GLU cc_start: 0.8064 (tt0) cc_final: 0.7694 (mt-10) REVERT: D 52 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6327 (mt0) REVERT: D 53 MET cc_start: 0.6403 (mtp) cc_final: 0.6141 (mtp) REVERT: D 248 LYS cc_start: 0.7972 (tppt) cc_final: 0.7173 (mtpm) REVERT: D 270 LYS cc_start: 0.8520 (mttp) cc_final: 0.8254 (mttm) REVERT: S 78 THR cc_start: 0.7585 (t) cc_final: 0.7345 (m) REVERT: E 106 MET cc_start: 0.7297 (mmp) cc_final: 0.7066 (mmp) REVERT: E 220 MET cc_start: 0.8124 (tpp) cc_final: 0.7662 (tpp) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 1.5632 time to fit residues: 203.4305 Evaluate side-chains 122 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 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 S residue 64 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR 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 104 optimal weight: 0.0370 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107609 restraints weight = 13875.808| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.56 r_work: 0.3348 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9247 Z= 0.145 Angle : 0.568 8.995 12513 Z= 0.293 Chirality : 0.042 0.185 1407 Planarity : 0.003 0.041 1578 Dihedral : 4.967 67.705 1304 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.62 % Allowed : 21.10 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1130 helix: 1.13 (0.31), residues: 341 sheet: 0.29 (0.31), residues: 280 loop : -1.38 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.014 0.001 TYR S 95 ARG 0.005 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8485.79 seconds wall clock time: 149 minutes 49.62 seconds (8989.62 seconds total)