Starting phenix.real_space_refine on Fri Aug 22 20:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wcb_37437/08_2025/8wcb_37437.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.189 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 49 5.16 5 C 4953 2.51 5 N 1346 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1686 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 6 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2354 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "R" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1719 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 12, 'TRANS': 235} Chain breaks: 12 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1681 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "Y" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 337 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HAI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.38, per 1000 atoms: 0.18 Number of scatterers: 7784 At special positions: 0 Unit cell: (80.96, 118.68, 121.44, 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 49 16.00 O 1436 8.00 N 1346 7.00 C 4953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 344.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 32.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 4.033A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.575A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.886A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.387A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 4.037A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.229A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 removed outlier: 3.619A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'R' and resid 24 through 46 removed outlier: 4.317A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 71 removed outlier: 3.644A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 83 removed outlier: 3.539A pdb=" N CYS R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 93 No H-bonds generated for 'chain 'R' and resid 91 through 93' Processing helix chain 'R' and resid 94 through 121 Processing helix chain 'R' and resid 135 through 157 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 174 through 179 removed outlier: 4.278A pdb=" N LEU R 178 " --> pdb=" O GLN R 174 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 174 through 179' Processing helix chain 'R' and resid 186 through 194 removed outlier: 3.755A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 220 removed outlier: 3.762A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 268 removed outlier: 3.632A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 279 through 284 Processing helix chain 'R' and resid 291 through 304 Proline residue: R 298 - end of helix removed outlier: 3.509A pdb=" N PHE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 309 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 11 through 24 removed outlier: 3.562A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 36 through 36 No H-bonds generated for 'chain 'Y' and resid 36 through 36' Processing helix chain 'Y' and resid 39 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.548A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.926A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.146A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.434A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.705A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B 170 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.996A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.589A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.686A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (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 58 through 60 removed outlier: 6.437A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'S' and resid 174 through 176 Processing sheet with id=AB4, first strand: chain 'S' and resid 189 through 190 Processing sheet with id=AB5, first strand: chain 'S' and resid 225 through 227 341 hydrogen bonds defined for protein. 969 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: 0.93 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.50: 4776 1.50 - 1.84: 3161 1.84 - 2.19: 0 2.19 - 2.53: 0 2.53 - 2.87: 1 Bond restraints: 7938 Sorted by residual: bond pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 1.331 2.874 -1.543 1.33e-02 5.65e+03 1.35e+04 bond pdb=" C LEU R 286 " pdb=" N TYR R 287 " ideal model delta sigma weight residual 1.329 1.474 -0.145 1.40e-02 5.10e+03 1.07e+02 bond pdb=" CA ILE R 110 " pdb=" C ILE R 110 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.18e-02 7.18e+03 4.48e+01 bond pdb=" C ILE S 189 " pdb=" O ILE S 189 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C THR R 101 " pdb=" O THR R 101 " ideal model delta sigma weight residual 1.237 1.163 0.073 1.16e-02 7.43e+03 3.98e+01 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.07: 10786 9.07 - 18.13: 11 18.13 - 27.20: 0 27.20 - 36.27: 0 36.27 - 45.33: 2 Bond angle restraints: 10799 Sorted by residual: angle pdb=" O ALA B 309 " pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 122.89 81.76 41.13 1.22e+00 6.72e-01 1.14e+03 angle pdb=" C ALA B 309 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 122.36 167.69 -45.33 1.60e+00 3.91e-01 8.03e+02 angle pdb=" CA ALA B 309 " pdb=" C ALA B 309 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 115.88 131.92 -16.04 1.28e+00 6.10e-01 1.57e+02 angle pdb=" N GLN R 52 " pdb=" CA GLN R 52 " pdb=" C GLN R 52 " ideal model delta sigma weight residual 112.89 100.42 12.47 1.24e+00 6.50e-01 1.01e+02 angle pdb=" N LYS R 51 " pdb=" CA LYS R 51 " pdb=" C LYS R 51 " ideal model delta sigma weight residual 114.39 100.50 13.89 1.45e+00 4.76e-01 9.18e+01 ... (remaining 10794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 4119 14.59 - 29.18: 375 29.18 - 43.77: 106 43.77 - 58.36: 17 58.36 - 72.96: 9 Dihedral angle restraints: 4626 sinusoidal: 1531 harmonic: 3095 Sorted by residual: dihedral pdb=" N ASP R 102 " pdb=" C ASP R 102 " pdb=" CA ASP R 102 " pdb=" CB ASP R 102 " ideal model delta harmonic sigma weight residual 122.80 137.53 -14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" C ASP R 102 " pdb=" N ASP R 102 " pdb=" CA ASP R 102 " pdb=" CB ASP R 102 " ideal model delta harmonic sigma weight residual -122.60 -136.61 14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C SER R 48 " pdb=" N SER R 48 " pdb=" CA SER R 48 " pdb=" CB SER R 48 " ideal model delta harmonic sigma weight residual -122.60 -134.77 12.17 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 4623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1200 0.135 - 0.271: 40 0.271 - 0.406: 14 0.406 - 0.541: 2 0.541 - 0.676: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA ASP R 102 " pdb=" N ASP R 102 " pdb=" C ASP R 102 " pdb=" CB ASP R 102 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CA SER R 48 " pdb=" N SER R 48 " pdb=" C SER R 48 " pdb=" CB SER R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 1254 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 309 " 0.155 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C ALA B 309 " -0.338 2.00e-02 2.50e+03 pdb=" O ALA B 309 " 0.128 2.00e-02 2.50e+03 pdb=" N HIS B 311 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 286 " 0.025 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C LEU R 286 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU R 286 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR R 287 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 279 " 0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO R 280 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO R 280 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO R 280 " 0.053 5.00e-02 4.00e+02 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1702 2.78 - 3.31: 7268 3.31 - 3.84: 13051 3.84 - 4.37: 15376 4.37 - 4.90: 26617 Nonbonded interactions: 64014 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.246 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.295 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.296 3.040 nonbonded pdb=" ND2 ASN A 387 " pdb=" O ALA R 123 " model vdw 2.312 3.120 ... (remaining 64009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 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 : 0.019 1.543 7940 Z= 1.393 Angle : 1.204 45.333 10803 Z= 0.799 Chirality : 0.070 0.676 1257 Planarity : 0.009 0.199 1372 Dihedral : 12.909 72.956 2608 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.09 % Allowed : 1.64 % Favored : 97.27 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.27), residues: 1016 helix: 0.04 (0.30), residues: 318 sheet: -0.22 (0.34), residues: 244 loop : -1.16 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 280 TYR 0.029 0.001 TYR R 301 PHE 0.021 0.002 PHE R 184 TRP 0.029 0.003 TRP A 277 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.01867 ( 7938) covalent geometry : angle 1.20432 (10799) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.50898 ( 4) hydrogen bonds : bond 0.16214 ( 341) hydrogen bonds : angle 7.27901 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.7677 (tptt) cc_final: 0.7443 (mmtt) REVERT: R 276 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 8 outliers final: 3 residues processed: 147 average time/residue: 0.0805 time to fit residues: 15.7566 Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 305 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 ASN R 62 HIS R 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157779 restraints weight = 8648.660| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.18 r_work: 0.3758 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7940 Z= 0.176 Angle : 0.610 7.374 10803 Z= 0.322 Chirality : 0.044 0.167 1257 Planarity : 0.005 0.069 1372 Dihedral : 5.541 59.988 1142 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.77 % Allowed : 9.28 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.27), residues: 1018 helix: 1.05 (0.31), residues: 296 sheet: -0.02 (0.32), residues: 256 loop : -1.04 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.014 0.002 TYR S 50 PHE 0.020 0.002 PHE R 184 TRP 0.019 0.002 TRP B 332 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7938) covalent geometry : angle 0.60947 (10799) SS BOND : bond 0.00154 ( 2) SS BOND : angle 0.75619 ( 4) hydrogen bonds : bond 0.03658 ( 341) hydrogen bonds : angle 5.42455 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.288 Fit side-chains REVERT: B 101 MET cc_start: 0.8426 (mtp) cc_final: 0.8174 (mtp) REVERT: R 276 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6546 (m-80) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.0742 time to fit residues: 13.6912 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 259 GLN S 179 GLN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.161344 restraints weight = 8587.560| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.14 r_work: 0.3799 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7940 Z= 0.120 Angle : 0.532 6.069 10803 Z= 0.283 Chirality : 0.041 0.158 1257 Planarity : 0.004 0.053 1372 Dihedral : 4.901 58.017 1139 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.91 % Allowed : 11.73 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.27), residues: 1018 helix: 1.58 (0.31), residues: 294 sheet: 0.06 (0.33), residues: 252 loop : -0.98 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.009 0.001 TYR S 95 PHE 0.016 0.001 PHE R 184 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7938) covalent geometry : angle 0.53160 (10799) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.62047 ( 4) hydrogen bonds : bond 0.03111 ( 341) hydrogen bonds : angle 4.94003 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.201 Fit side-chains REVERT: A 280 ARG cc_start: 0.6785 (tpt90) cc_final: 0.6558 (ttt-90) REVERT: B 52 ARG cc_start: 0.8506 (ptp-110) cc_final: 0.8299 (ptp-110) REVERT: R 276 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6594 (m-80) outliers start: 14 outliers final: 8 residues processed: 122 average time/residue: 0.0855 time to fit residues: 14.3173 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 78 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160439 restraints weight = 8701.039| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.13 r_work: 0.3836 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7940 Z= 0.119 Angle : 0.517 5.935 10803 Z= 0.275 Chirality : 0.042 0.179 1257 Planarity : 0.004 0.046 1372 Dihedral : 4.730 55.204 1139 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.32 % Allowed : 13.23 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.27), residues: 1018 helix: 1.78 (0.31), residues: 295 sheet: 0.05 (0.33), residues: 252 loop : -0.91 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.009 0.001 TYR S 95 PHE 0.013 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7938) covalent geometry : angle 0.51725 (10799) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.69430 ( 4) hydrogen bonds : bond 0.02909 ( 341) hydrogen bonds : angle 4.78332 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.205 Fit side-chains REVERT: A 280 ARG cc_start: 0.6960 (tpt90) cc_final: 0.6720 (ttt-90) REVERT: B 78 LYS cc_start: 0.8061 (tptt) cc_final: 0.7771 (mmtt) REVERT: B 105 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 239 ASN cc_start: 0.7261 (m-40) cc_final: 0.7014 (m-40) REVERT: B 262 MET cc_start: 0.4445 (pmm) cc_final: 0.4228 (pmm) REVERT: R 276 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6604 (m-80) outliers start: 17 outliers final: 11 residues processed: 132 average time/residue: 0.0807 time to fit residues: 14.5560 Evaluate side-chains 127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 293 ASN Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 294 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161589 restraints weight = 8641.130| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.15 r_work: 0.3848 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7940 Z= 0.108 Angle : 0.506 6.715 10803 Z= 0.266 Chirality : 0.041 0.149 1257 Planarity : 0.003 0.040 1372 Dihedral : 4.579 52.801 1139 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 14.19 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.27), residues: 1018 helix: 1.91 (0.31), residues: 297 sheet: -0.01 (0.33), residues: 255 loop : -0.87 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.008 0.001 TYR S 95 PHE 0.013 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7938) covalent geometry : angle 0.50572 (10799) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.59296 ( 4) hydrogen bonds : bond 0.02786 ( 341) hydrogen bonds : angle 4.61827 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.203 Fit side-chains REVERT: A 280 ARG cc_start: 0.7005 (tpt90) cc_final: 0.6742 (ttt-90) REVERT: B 78 LYS cc_start: 0.8065 (tptt) cc_final: 0.7770 (mmtt) REVERT: B 239 ASN cc_start: 0.7292 (m-40) cc_final: 0.7032 (m-40) REVERT: B 262 MET cc_start: 0.4534 (pmm) cc_final: 0.4137 (pmm) REVERT: B 311 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7008 (m-70) REVERT: B 332 TRP cc_start: 0.8357 (m-10) cc_final: 0.7751 (m-10) REVERT: R 104 MET cc_start: 0.7352 (ttt) cc_final: 0.7015 (tpp) REVERT: R 276 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6638 (m-80) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.0744 time to fit residues: 13.0123 Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain R residue 293 ASN Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.197790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158829 restraints weight = 8651.221| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.16 r_work: 0.3822 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7940 Z= 0.120 Angle : 0.517 6.126 10803 Z= 0.272 Chirality : 0.042 0.199 1257 Planarity : 0.003 0.037 1372 Dihedral : 4.563 51.148 1139 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.59 % Allowed : 14.73 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 1018 helix: 1.93 (0.31), residues: 297 sheet: 0.01 (0.33), residues: 255 loop : -0.84 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.008 0.001 TYR S 95 PHE 0.011 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7938) covalent geometry : angle 0.51715 (10799) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.57686 ( 4) hydrogen bonds : bond 0.02828 ( 341) hydrogen bonds : angle 4.66137 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.188 Fit side-chains REVERT: A 280 ARG cc_start: 0.7001 (tpt90) cc_final: 0.6687 (ttt-90) REVERT: B 78 LYS cc_start: 0.8053 (tptt) cc_final: 0.7765 (mmtt) REVERT: B 239 ASN cc_start: 0.7404 (m-40) cc_final: 0.7139 (m-40) REVERT: B 262 MET cc_start: 0.4553 (OUTLIER) cc_final: 0.4135 (pmm) REVERT: B 311 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7154 (m-70) REVERT: B 332 TRP cc_start: 0.8390 (m-10) cc_final: 0.7750 (m-10) REVERT: R 104 MET cc_start: 0.7472 (ttt) cc_final: 0.7131 (tpp) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.0781 time to fit residues: 14.0702 Evaluate side-chains 130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.1980 chunk 4 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.199535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160603 restraints weight = 8678.337| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.18 r_work: 0.3844 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7940 Z= 0.106 Angle : 0.500 6.002 10803 Z= 0.266 Chirality : 0.041 0.145 1257 Planarity : 0.003 0.034 1372 Dihedral : 4.233 51.979 1137 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 16.10 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.27), residues: 1018 helix: 2.00 (0.31), residues: 299 sheet: 0.08 (0.33), residues: 254 loop : -0.84 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.007 0.001 TYR S 103 PHE 0.014 0.001 PHE R 257 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 7938) covalent geometry : angle 0.50040 (10799) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.56402 ( 4) hydrogen bonds : bond 0.02714 ( 341) hydrogen bonds : angle 4.52294 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.407 Fit side-chains REVERT: A 36 VAL cc_start: 0.8316 (t) cc_final: 0.8093 (t) REVERT: A 280 ARG cc_start: 0.6698 (tpt90) cc_final: 0.6201 (ttp-110) REVERT: A 381 ASP cc_start: 0.7478 (t0) cc_final: 0.7214 (t0) REVERT: B 78 LYS cc_start: 0.7971 (tptt) cc_final: 0.7720 (mmtt) REVERT: B 239 ASN cc_start: 0.7219 (m-40) cc_final: 0.6951 (m-40) REVERT: B 262 MET cc_start: 0.4487 (pmm) cc_final: 0.4131 (pmm) REVERT: B 311 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7057 (m-70) REVERT: B 332 TRP cc_start: 0.8300 (m-10) cc_final: 0.7587 (m-10) REVERT: R 104 MET cc_start: 0.7390 (ttt) cc_final: 0.7094 (tpp) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.0980 time to fit residues: 18.0303 Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 0.0770 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN B 88 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152163 restraints weight = 8784.325| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.14 r_work: 0.3760 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7940 Z= 0.180 Angle : 0.574 6.393 10803 Z= 0.302 Chirality : 0.044 0.161 1257 Planarity : 0.004 0.034 1372 Dihedral : 4.610 49.685 1137 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.18 % Allowed : 16.64 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.27), residues: 1018 helix: 1.76 (0.31), residues: 298 sheet: -0.17 (0.31), residues: 276 loop : -0.73 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.013 0.002 TYR S 50 PHE 0.015 0.002 PHE A 376 TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7938) covalent geometry : angle 0.57395 (10799) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.73428 ( 4) hydrogen bonds : bond 0.03231 ( 341) hydrogen bonds : angle 4.99592 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.287 Fit side-chains REVERT: B 105 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 205 ASP cc_start: 0.7459 (t0) cc_final: 0.7252 (t0) REVERT: B 311 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7143 (m-70) REVERT: R 104 MET cc_start: 0.7626 (ttt) cc_final: 0.7251 (tpp) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.0891 time to fit residues: 15.3610 Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 chunk 5 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 220 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.196976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157233 restraints weight = 8696.728| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.21 r_work: 0.3815 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7940 Z= 0.116 Angle : 0.528 7.413 10803 Z= 0.278 Chirality : 0.042 0.146 1257 Planarity : 0.003 0.032 1372 Dihedral : 4.396 52.028 1137 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.91 % Allowed : 17.60 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.27), residues: 1018 helix: 1.85 (0.32), residues: 298 sheet: -0.07 (0.33), residues: 257 loop : -0.77 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.007 0.001 TYR R 209 PHE 0.016 0.001 PHE R 273 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7938) covalent geometry : angle 0.52839 (10799) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.63004 ( 4) hydrogen bonds : bond 0.02835 ( 341) hydrogen bonds : angle 4.67257 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.6622 (mp0) cc_final: 0.6352 (mp0) REVERT: B 197 ARG cc_start: 0.6738 (mmm160) cc_final: 0.6420 (mtp85) REVERT: B 262 MET cc_start: 0.4526 (pmm) cc_final: 0.4275 (pmm) REVERT: B 311 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.7070 (m-70) REVERT: R 104 MET cc_start: 0.7449 (ttt) cc_final: 0.7203 (tpp) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.0856 time to fit residues: 13.9306 Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 94 optimal weight: 0.0970 chunk 24 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 239 ASN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.194908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154993 restraints weight = 8662.783| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.18 r_work: 0.3789 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7940 Z= 0.142 Angle : 0.546 6.476 10803 Z= 0.289 Chirality : 0.042 0.151 1257 Planarity : 0.003 0.032 1372 Dihedral : 4.475 51.022 1137 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.32 % Allowed : 17.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.27), residues: 1018 helix: 1.82 (0.31), residues: 299 sheet: -0.14 (0.32), residues: 267 loop : -0.77 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.011 0.001 TYR B 85 PHE 0.017 0.002 PHE R 273 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7938) covalent geometry : angle 0.54584 (10799) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.63824 ( 4) hydrogen bonds : bond 0.02930 ( 341) hydrogen bonds : angle 4.77504 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.319 Fit side-chains REVERT: B 262 MET cc_start: 0.4587 (pmm) cc_final: 0.4271 (pmm) REVERT: B 311 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7177 (m-70) REVERT: S 219 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7557 (mp) outliers start: 17 outliers final: 13 residues processed: 120 average time/residue: 0.0918 time to fit residues: 15.3662 Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 136 ILE Chi-restraints excluded: chain R residue 253 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 85 optimal weight: 0.0870 chunk 60 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159368 restraints weight = 8616.177| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.19 r_work: 0.3833 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7940 Z= 0.110 Angle : 0.528 7.591 10803 Z= 0.280 Chirality : 0.041 0.148 1257 Planarity : 0.003 0.032 1372 Dihedral : 4.304 52.309 1137 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.91 % Allowed : 18.28 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.27), residues: 1018 helix: 1.87 (0.31), residues: 305 sheet: -0.03 (0.33), residues: 257 loop : -0.79 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.010 0.001 TYR S 103 PHE 0.016 0.001 PHE R 273 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7938) covalent geometry : angle 0.52757 (10799) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.54784 ( 4) hydrogen bonds : bond 0.02705 ( 341) hydrogen bonds : angle 4.55705 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.80 seconds wall clock time: 41 minutes 30.91 seconds (2490.91 seconds total)