Starting phenix.real_space_refine on Thu Feb 13 16:24:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jim_36318/02_2025/8jim_36318_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jim_36318/02_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_36318/02_2025/8jim_36318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jim_36318/02_2025/8jim_36318.map" model { file = "/net/cci-nas-00/data/ceres_data/8jim_36318/02_2025/8jim_36318_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jim_36318/02_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-5592/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: 5.73, per 1000 atoms: 0.63 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: 2.41 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: 1.01 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: 2.38 Time building geometry restraints manager: 2.76 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- 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 : 0.933 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: 1.2628 time to fit residues: 224.0411 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 : 0.962 ------------------------------------------------------------------------------- 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 = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105959 restraints weight = 14303.115| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.57 r_work: 0.3322 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 89.596 1307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.77 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 : 1.066 Fit side-chains REVERT: C 48 ASP cc_start: 0.7371 (p0) cc_final: 0.7040 (p0) REVERT: D 24 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7760 (ttp80) REVERT: D 229 ASP cc_start: 0.7670 (t0) cc_final: 0.7468 (t0) REVERT: S 60 TYR cc_start: 0.8306 (m-80) cc_final: 0.8056 (m-80) REVERT: S 67 ARG cc_start: 0.7516 (mtm180) cc_final: 0.6982 (mtm180) REVERT: S 93 MET cc_start: 0.8387 (ttt) cc_final: 0.8087 (ttt) REVERT: E 269 TYR cc_start: 0.7739 (m-80) cc_final: 0.7367 (m-80) REVERT: E 270 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7593 (mpp80) REVERT: E 282 PHE cc_start: 0.7599 (m-80) cc_final: 0.7291 (m-10) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 1.2470 time to fit residues: 185.3537 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 : 1.016 ------------------------------------------------------------------------------- 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: 0.5980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.143795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105544 restraints weight = 14363.027| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.58 r_work: 0.3319 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1992 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= 0.194 Angle : 0.598 7.367 12513 Z= 0.315 Chirality : 0.043 0.157 1407 Planarity : 0.004 0.036 1578 Dihedral : 5.754 86.754 1304 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.43 % Allowed : 12.47 % Favored : 85.09 % 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: -0.96 (0.25), residues: 1130 helix: 0.52 (0.30), residues: 341 sheet: 0.01 (0.31), residues: 280 loop : -1.84 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.029 0.001 PHE E 38 TYR 0.015 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 150 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.022 Fit side-chains REVERT: C 48 ASP cc_start: 0.7621 (p0) cc_final: 0.7321 (p0) REVERT: D 24 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7748 (ttm170) REVERT: D 53 MET cc_start: 0.6644 (mtp) cc_final: 0.6369 (mtp) REVERT: D 229 ASP cc_start: 0.7762 (t0) cc_final: 0.7463 (t0) REVERT: S 60 TYR cc_start: 0.8294 (m-80) cc_final: 0.8075 (m-80) REVERT: S 67 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7019 (mtm180) REVERT: E 269 TYR cc_start: 0.7767 (m-80) cc_final: 0.7399 (m-80) REVERT: E 270 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7601 (mpp80) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 1.2827 time to fit residues: 187.4224 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.0070 chunk 81 optimal weight: 10.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 B 340 ASN 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 = 0.4008 r_free = 0.4008 target = 0.144880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109213 restraints weight = 14173.349| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.52 r_work: 0.3352 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9247 Z= 0.158 Angle : 0.563 7.563 12513 Z= 0.293 Chirality : 0.042 0.144 1407 Planarity : 0.003 0.035 1578 Dihedral : 5.475 86.584 1304 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.74 % Allowed : 13.59 % Favored : 83.67 % 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: -0.71 (0.25), residues: 1130 helix: 0.71 (0.30), residues: 342 sheet: 0.13 (0.31), residues: 281 loop : -1.67 (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 0.011 0.001 TYR S 190 ARG 0.002 0.000 ARG S 72 *********************** 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 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.918 Fit side-chains REVERT: D 24 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7618 (ttm170) REVERT: D 53 MET cc_start: 0.6523 (mtp) cc_final: 0.6287 (mtp) REVERT: D 195 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7180 (t70) REVERT: S 60 TYR cc_start: 0.8251 (m-80) cc_final: 0.8002 (m-80) REVERT: S 67 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6882 (mtm180) REVERT: E 104 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8419 (mp) REVERT: E 269 TYR cc_start: 0.7618 (m-80) cc_final: 0.7353 (m-80) outliers start: 27 outliers final: 11 residues processed: 137 average time/residue: 1.2151 time to fit residues: 178.2029 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS 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 281 SER 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: 0.0470 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107341 restraints weight = 14140.374| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.57 r_work: 0.3341 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9247 Z= 0.141 Angle : 0.539 7.681 12513 Z= 0.281 Chirality : 0.041 0.146 1407 Planarity : 0.003 0.034 1578 Dihedral : 5.241 80.904 1304 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.74 % Allowed : 16.13 % Favored : 81.14 % 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: -0.56 (0.25), residues: 1130 helix: 0.86 (0.30), residues: 342 sheet: 0.14 (0.31), residues: 282 loop : -1.54 (0.25), residues: 506 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 0.032 0.001 PHE E 38 TYR 0.012 0.001 TYR S 190 ARG 0.008 0.000 ARG E 270 *********************** 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 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.035 Fit side-chains REVERT: D 24 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: D 53 MET cc_start: 0.6536 (mtp) cc_final: 0.6307 (mtp) REVERT: D 195 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7266 (t70) REVERT: D 248 LYS cc_start: 0.7997 (tppt) cc_final: 0.7181 (mtpm) REVERT: S 67 ARG cc_start: 0.7409 (mtm180) cc_final: 0.6884 (mtm180) REVERT: E 25 PHE cc_start: 0.7907 (t80) cc_final: 0.7667 (t80) REVERT: E 104 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (mp) outliers start: 27 outliers final: 8 residues processed: 138 average time/residue: 1.1516 time to fit residues: 170.7521 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 HIS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain E residue 104 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 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102136 restraints weight = 13969.741| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.49 r_work: 0.3251 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9247 Z= 0.339 Angle : 0.659 8.072 12513 Z= 0.343 Chirality : 0.046 0.170 1407 Planarity : 0.004 0.036 1578 Dihedral : 5.652 77.521 1304 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.55 % Allowed : 17.34 % Favored : 79.11 % 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: -0.71 (0.25), residues: 1130 helix: 0.70 (0.30), residues: 342 sheet: 0.10 (0.31), residues: 275 loop : -1.62 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 47 HIS 0.011 0.002 HIS E 133 PHE 0.031 0.002 PHE E 38 TYR 0.027 0.002 TYR B 105 ARG 0.004 0.000 ARG E 128 *********************** 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 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.971 Fit side-chains REVERT: D 24 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7836 (ttp-110) REVERT: D 52 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6522 (mt0) REVERT: D 53 MET cc_start: 0.6476 (mtp) cc_final: 0.6146 (mtp) REVERT: D 248 LYS cc_start: 0.8089 (tppt) cc_final: 0.7291 (mtpm) REVERT: D 270 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (mtmp) REVERT: S 60 TYR cc_start: 0.8405 (m-80) cc_final: 0.8172 (m-80) REVERT: S 78 THR cc_start: 0.7692 (t) cc_final: 0.7435 (m) REVERT: E 25 PHE cc_start: 0.7894 (t80) cc_final: 0.7660 (t80) REVERT: E 104 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8548 (mp) REVERT: E 269 TYR cc_start: 0.7882 (m-80) cc_final: 0.7659 (m-80) outliers start: 35 outliers final: 17 residues processed: 145 average time/residue: 1.1657 time to fit residues: 181.2014 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 : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP 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 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 104 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.141171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102254 restraints weight = 14144.990| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.51 r_work: 0.3254 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9247 Z= 0.294 Angle : 0.647 8.048 12513 Z= 0.336 Chirality : 0.045 0.223 1407 Planarity : 0.004 0.058 1578 Dihedral : 5.655 75.584 1304 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.45 % Allowed : 18.56 % Favored : 77.99 % 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: -0.72 (0.25), residues: 1130 helix: 0.69 (0.30), residues: 342 sheet: 0.13 (0.31), residues: 272 loop : -1.65 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.002 PHE E 255 TYR 0.023 0.002 TYR B 105 ARG 0.009 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 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.044 Fit side-chains REVERT: D 24 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7822 (ttp-110) REVERT: D 52 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6472 (mt0) REVERT: D 53 MET cc_start: 0.6443 (mtp) cc_final: 0.6148 (mtp) REVERT: D 248 LYS cc_start: 0.8034 (tppt) cc_final: 0.7253 (mtpm) REVERT: D 270 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (mtmp) REVERT: S 78 THR cc_start: 0.7671 (t) cc_final: 0.7436 (m) REVERT: S 93 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: E 104 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8553 (mp) REVERT: E 269 TYR cc_start: 0.7844 (m-80) cc_final: 0.7608 (m-80) outliers start: 34 outliers final: 19 residues processed: 138 average time/residue: 1.1644 time to fit residues: 172.4544 Evaluate side-chains 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 128 THR 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 S residue 93 MET Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 231 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: 3.9990 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 96 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.144422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105722 restraints weight = 14333.160| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.56 r_work: 0.3319 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2931 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= 0.143 Angle : 0.568 8.509 12513 Z= 0.294 Chirality : 0.042 0.205 1407 Planarity : 0.003 0.037 1578 Dihedral : 5.271 72.589 1304 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.33 % Allowed : 19.68 % Favored : 77.99 % 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: 342 sheet: 0.19 (0.31), residues: 278 loop : -1.55 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 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 141 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.970 Fit side-chains REVERT: D 24 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7770 (ttp-110) REVERT: D 53 MET cc_start: 0.6552 (mtp) cc_final: 0.6271 (mtp) REVERT: D 195 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7083 (t70) REVERT: D 248 LYS cc_start: 0.7897 (tppt) cc_final: 0.7171 (mtpm) REVERT: D 270 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8143 (mtmp) REVERT: S 60 TYR cc_start: 0.8122 (m-80) cc_final: 0.7901 (m-80) REVERT: S 78 THR cc_start: 0.7586 (t) cc_final: 0.7324 (m) REVERT: E 52 PHE cc_start: 0.6274 (m-10) cc_final: 0.6042 (OUTLIER) REVERT: E 269 TYR cc_start: 0.7698 (m-80) cc_final: 0.7488 (m-80) outliers start: 23 outliers final: 14 residues processed: 133 average time/residue: 1.2235 time to fit residues: 174.3057 Evaluate side-chains 129 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS 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 159 THR 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 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.143872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105309 restraints weight = 13949.592| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.50 r_work: 0.3315 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9247 Z= 0.175 Angle : 0.577 8.930 12513 Z= 0.299 Chirality : 0.043 0.205 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.192 68.901 1304 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.93 % Allowed : 20.39 % 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 (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: -0.45 (0.25), residues: 1130 helix: 0.97 (0.30), residues: 343 sheet: 0.22 (0.31), residues: 279 loop : -1.50 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.032 0.001 PHE E 38 TYR 0.012 0.001 TYR S 190 ARG 0.006 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: 19 poor density : 119 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: D 24 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7831 (ttp-110) REVERT: D 52 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6442 (mt0) REVERT: D 53 MET cc_start: 0.6478 (mtp) cc_final: 0.6241 (mtp) REVERT: D 195 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7144 (t70) REVERT: D 270 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8300 (mtmp) REVERT: S 60 TYR cc_start: 0.8285 (m-80) cc_final: 0.8061 (m-80) REVERT: S 78 THR cc_start: 0.7631 (t) cc_final: 0.7402 (m) REVERT: E 220 MET cc_start: 0.8185 (tpp) cc_final: 0.7710 (tpp) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 1.2008 time to fit residues: 171.1351 Evaluate side-chains 133 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 195 HIS 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 239 VAL 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: 0.7980 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.0570 chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105601 restraints weight = 14095.929| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.55 r_work: 0.3312 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3073 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= 0.168 Angle : 0.584 9.050 12513 Z= 0.301 Chirality : 0.043 0.202 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.147 68.271 1304 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.72 % Allowed : 21.20 % Favored : 77.08 % 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: -0.41 (0.25), residues: 1130 helix: 1.00 (0.30), residues: 343 sheet: 0.25 (0.31), residues: 279 loop : -1.48 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 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 134 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: D 24 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7829 (ttp-110) REVERT: D 52 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6377 (mt0) REVERT: D 53 MET cc_start: 0.6468 (mtp) cc_final: 0.6235 (mtp) REVERT: D 195 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7133 (t70) REVERT: D 248 LYS cc_start: 0.7890 (tppt) cc_final: 0.7134 (mtpm) REVERT: D 270 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8248 (mtmp) REVERT: S 60 TYR cc_start: 0.8299 (m-80) cc_final: 0.8089 (m-80) REVERT: S 78 THR cc_start: 0.7552 (t) cc_final: 0.7311 (m) REVERT: E 220 MET cc_start: 0.8185 (tpp) cc_final: 0.7719 (tpp) outliers start: 17 outliers final: 15 residues processed: 128 average time/residue: 1.2571 time to fit residues: 172.0915 Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 195 HIS 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 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: 0.9980 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.144021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105108 restraints weight = 13986.962| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.52 r_work: 0.3309 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3111 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= 0.187 Angle : 0.595 9.057 12513 Z= 0.307 Chirality : 0.043 0.201 1407 Planarity : 0.003 0.039 1578 Dihedral : 5.135 64.824 1304 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.93 % Allowed : 20.99 % Favored : 77.08 % 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: -0.36 (0.25), residues: 1130 helix: 1.01 (0.30), residues: 345 sheet: 0.31 (0.31), residues: 272 loop : -1.44 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7712.95 seconds wall clock time: 136 minutes 27.20 seconds (8187.20 seconds total)