Starting phenix.real_space_refine on Thu Mar 13 09:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0p_34413/03_2025/8h0p_34413.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 62 5.16 5 C 5682 2.51 5 N 1531 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8932 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "R" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2305 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 3 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1768 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Time building chain proxies: 6.73, per 1000 atoms: 0.75 Number of scatterers: 8932 At special positions: 0 Unit cell: (124.8, 92.56, 127.92, 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 62 16.00 O 1657 8.00 N 1531 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.619A pdb=" N ALA L 25 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 70 Proline residue: R 47 - end of helix Processing helix chain 'R' and resid 79 through 106 removed outlier: 3.932A pdb=" N VAL R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Proline residue: R 98 - end of helix Processing helix chain 'R' and resid 112 through 147 Proline residue: R 120 - end of helix Processing helix chain 'R' and resid 156 through 174 Processing helix chain 'R' and resid 176 through 181 removed outlier: 4.064A pdb=" N VAL R 180 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE R 181 " --> pdb=" O PRO R 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 176 through 181' Processing helix chain 'R' and resid 206 through 221 removed outlier: 3.954A pdb=" N LYS R 210 " --> pdb=" O GLU R 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL R 214 " --> pdb=" O LYS R 210 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 244 removed outlier: 3.544A pdb=" N ILE R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 292 removed outlier: 3.541A pdb=" N THR R 260 " --> pdb=" O LYS R 256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 3.619A pdb=" N PHE R 291 " --> pdb=" O MET R 287 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN R 292 " --> pdb=" O TYR R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 314 removed outlier: 3.747A pdb=" N LEU R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 328 removed outlier: 3.689A pdb=" N ASN R 320 " --> pdb=" O ASN R 316 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 329 through 342 removed outlier: 3.773A pdb=" N HIS R 334 " --> pdb=" O SER R 330 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU R 339 " --> pdb=" O PHE R 335 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N CYS R 340 " --> pdb=" O ASN R 336 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.541A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.562A pdb=" N CYS A 219 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 221 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.654A pdb=" N ALA A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 removed outlier: 3.597A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.525A pdb=" N PHE A 295 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 296 " --> pdb=" O PRO A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 296' Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.762A pdb=" N ILE A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.813A pdb=" N ILE A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.546A pdb=" N PHE E 31 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.742A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.746A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 183 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 195 removed outlier: 3.684A pdb=" N ALA A 225 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.419A pdb=" N ARG B 51 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.701A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 93 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.926A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.884A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 207 removed outlier: 4.108A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.781A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.004A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.396A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.396A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 186 through 187 423 hydrogen bonds defined for protein. 1200 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: 2.89 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2892 1.34 - 1.46: 2132 1.46 - 1.58: 3998 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 9113 Sorted by residual: bond pdb=" C TYR E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 1.334 1.359 -0.026 2.34e-02 1.83e+03 1.19e+00 bond pdb=" CB PRO R 298 " pdb=" CG PRO R 298 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.12e-01 bond pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 1.537 1.540 -0.004 5.00e-03 4.00e+04 4.92e-01 bond pdb=" CA THR B 201 " pdb=" CB THR B 201 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 4.77e-01 bond pdb=" C ILE R 223 " pdb=" N PRO R 224 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.00e-01 ... (remaining 9108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 12093 1.15 - 2.29: 196 2.29 - 3.44: 32 3.44 - 4.59: 7 4.59 - 5.74: 11 Bond angle restraints: 12339 Sorted by residual: angle pdb=" C VAL R 45 " pdb=" N ILE R 46 " pdb=" CA ILE R 46 " ideal model delta sigma weight residual 120.43 122.95 -2.52 9.60e-01 1.09e+00 6.92e+00 angle pdb=" C ILE R 46 " pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 113.70 111.21 2.49 9.50e-01 1.11e+00 6.87e+00 angle pdb=" C ASP B 200 " pdb=" N THR B 201 " pdb=" CA THR B 201 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C HIS L 28 " pdb=" N PHE L 29 " pdb=" CA PHE L 29 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.43e+00 angle pdb=" C TRP R 279 " pdb=" N PHE R 280 " pdb=" CA PHE R 280 " ideal model delta sigma weight residual 120.09 122.37 -2.28 1.25e+00 6.40e-01 3.32e+00 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 5243 15.92 - 31.85: 146 31.85 - 47.77: 25 47.77 - 63.69: 5 63.69 - 79.61: 1 Dihedral angle restraints: 5420 sinusoidal: 2120 harmonic: 3300 Sorted by residual: dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -180.00 -126.84 -53.16 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" N TYR B 64 " pdb=" CA TYR B 64 " pdb=" CB TYR B 64 " pdb=" CG TYR B 64 " ideal model delta sinusoidal sigma weight residual -60.00 -109.61 49.61 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG A 214 " pdb=" CB ARG A 214 " pdb=" CG ARG A 214 " pdb=" CD ARG A 214 " ideal model delta sinusoidal sigma weight residual -60.00 -107.57 47.57 3 1.50e+01 4.44e-03 8.51e+00 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 860 0.026 - 0.052: 338 0.052 - 0.078: 118 0.078 - 0.104: 61 0.104 - 0.130: 28 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE B 237 " pdb=" N ILE B 237 " pdb=" C ILE B 237 " pdb=" CB ILE B 237 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1402 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO E 74 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 208 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO R 209 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 209 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 209 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 280 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO R 281 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 281 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 281 " 0.015 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 809 2.75 - 3.28: 8844 3.28 - 3.82: 15069 3.82 - 4.36: 17608 4.36 - 4.90: 30529 Nonbonded interactions: 72859 Sorted by model distance: nonbonded pdb=" OD1 ASP B 168 " pdb=" OG1 THR B 170 " model vdw 2.208 3.040 nonbonded pdb=" OG SER B 250 " pdb=" OD1 ASP B 252 " model vdw 2.214 3.040 nonbonded pdb=" OG SER E 204 " pdb=" OG1 THR E 215 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR R 201 " pdb=" OH TYR R 286 " model vdw 2.279 3.040 ... (remaining 72854 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.960 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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 : 0.001 0.039 9113 Z= 0.100 Angle : 0.405 5.736 12339 Z= 0.239 Chirality : 0.037 0.130 1405 Planarity : 0.003 0.030 1560 Dihedral : 7.539 79.614 3281 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.49 (0.22), residues: 1108 helix: -0.63 (0.24), residues: 393 sheet: -1.49 (0.29), residues: 273 loop : -2.63 (0.24), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.002 0.000 HIS L 28 PHE 0.008 0.001 PHE B 258 TYR 0.006 0.001 TYR E 235 ARG 0.001 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.976 Fit side-chains REVERT: R 107 ASP cc_start: 0.6990 (t70) cc_final: 0.6711 (t70) REVERT: R 165 MET cc_start: 0.3785 (mmt) cc_final: 0.3467 (mtt) REVERT: A 256 LYS cc_start: 0.8066 (tttt) cc_final: 0.7795 (tttp) REVERT: B 222 MET cc_start: 0.4748 (mmm) cc_final: 0.4535 (ppp) REVERT: E 29 SER cc_start: 0.7431 (t) cc_final: 0.6915 (m) outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.3061 time to fit residues: 85.7111 Evaluate side-chains 151 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 123 GLN R 212 HIS R 257 GLN R 283 HIS R 320 ASN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 195 GLN A 209 GLN B 21 ASN E 34 HIS E 167 HIS E 183 GLN E 194 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.186810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148742 restraints weight = 9238.639| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.63 r_work: 0.3458 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 9113 Z= 0.358 Angle : 0.653 9.238 12339 Z= 0.340 Chirality : 0.047 0.186 1405 Planarity : 0.005 0.037 1560 Dihedral : 4.360 56.034 1230 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.83 % Allowed : 8.15 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.24), residues: 1108 helix: 0.10 (0.25), residues: 396 sheet: -1.28 (0.29), residues: 279 loop : -1.75 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 24 HIS 0.012 0.002 HIS B 96 PHE 0.021 0.002 PHE E 67 TYR 0.014 0.002 TYR A 307 ARG 0.007 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.877 Fit side-chains REVERT: R 165 MET cc_start: 0.5819 (mmt) cc_final: 0.4995 (mtt) REVERT: A 38 ARG cc_start: 0.7216 (mpt180) cc_final: 0.6836 (mtm110) REVERT: A 294 GLU cc_start: 0.7519 (mp0) cc_final: 0.6910 (mm-30) REVERT: E 6 SER cc_start: 0.7007 (p) cc_final: 0.6561 (m) outliers start: 18 outliers final: 10 residues processed: 179 average time/residue: 0.2598 time to fit residues: 60.4680 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 40 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 260 ASN B 225 GLN B 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.189207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.152167 restraints weight = 9353.889| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.62 r_work: 0.3511 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9113 Z= 0.152 Angle : 0.474 5.561 12339 Z= 0.246 Chirality : 0.040 0.165 1405 Planarity : 0.004 0.037 1560 Dihedral : 3.954 56.473 1230 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 10.79 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.25), residues: 1108 helix: 0.77 (0.26), residues: 393 sheet: -1.00 (0.30), residues: 280 loop : -1.38 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 24 HIS 0.007 0.001 HIS E 167 PHE 0.013 0.001 PHE A 194 TYR 0.008 0.001 TYR E 173 ARG 0.005 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.957 Fit side-chains REVERT: R 63 MET cc_start: 0.5873 (mtp) cc_final: 0.5659 (mtp) REVERT: A 38 ARG cc_start: 0.7145 (mpt180) cc_final: 0.6819 (mtm110) REVERT: E 6 SER cc_start: 0.6998 (p) cc_final: 0.6555 (m) REVERT: E 99 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8419 (mt) outliers start: 18 outliers final: 9 residues processed: 159 average time/residue: 0.2333 time to fit residues: 50.2671 Evaluate side-chains 145 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 218 GLN B 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.187147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150774 restraints weight = 9326.127| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.67 r_work: 0.3495 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9113 Z= 0.147 Angle : 0.467 5.915 12339 Z= 0.241 Chirality : 0.040 0.133 1405 Planarity : 0.003 0.037 1560 Dihedral : 3.887 56.954 1230 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.65 % Allowed : 10.49 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.25), residues: 1108 helix: 1.04 (0.27), residues: 392 sheet: -0.80 (0.30), residues: 280 loop : -1.16 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 24 HIS 0.005 0.001 HIS E 167 PHE 0.012 0.001 PHE A 194 TYR 0.008 0.001 TYR E 173 ARG 0.004 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.905 Fit side-chains REVERT: R 63 MET cc_start: 0.6273 (mtp) cc_final: 0.5972 (mtp) REVERT: R 165 MET cc_start: 0.5615 (mmp) cc_final: 0.4087 (mtt) REVERT: A 38 ARG cc_start: 0.7081 (mpt180) cc_final: 0.6804 (mtm110) REVERT: A 294 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 201 THR cc_start: 0.7466 (m) cc_final: 0.7140 (m) REVERT: B 202 ARG cc_start: 0.7002 (mmp80) cc_final: 0.6441 (mmt-90) REVERT: E 6 SER cc_start: 0.7054 (p) cc_final: 0.6583 (m) REVERT: E 99 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8471 (mt) REVERT: E 158 SER cc_start: 0.7366 (t) cc_final: 0.6857 (p) outliers start: 26 outliers final: 14 residues processed: 158 average time/residue: 0.2368 time to fit residues: 50.1120 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 225 GLN B 235 ASN B 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133229 restraints weight = 9404.062| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.60 r_work: 0.3241 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9113 Z= 0.416 Angle : 0.647 7.027 12339 Z= 0.337 Chirality : 0.045 0.147 1405 Planarity : 0.005 0.040 1560 Dihedral : 4.765 59.856 1230 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.25), residues: 1108 helix: 0.62 (0.27), residues: 394 sheet: -0.95 (0.30), residues: 276 loop : -1.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 24 HIS 0.010 0.002 HIS B 188 PHE 0.019 0.002 PHE B 185 TYR 0.016 0.002 TYR E 173 ARG 0.005 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.935 Fit side-chains REVERT: R 151 MET cc_start: 0.5161 (tpt) cc_final: 0.3863 (mtt) REVERT: R 267 ILE cc_start: 0.8436 (mm) cc_final: 0.8168 (mt) REVERT: A 26 GLU cc_start: 0.8032 (tp30) cc_final: 0.7337 (mt-10) REVERT: A 32 ASP cc_start: 0.7293 (t0) cc_final: 0.6580 (m-30) REVERT: A 38 ARG cc_start: 0.7751 (mpt180) cc_final: 0.7436 (mtm110) REVERT: A 191 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6004 (pm20) REVERT: A 202 HIS cc_start: 0.8592 (m-70) cc_final: 0.8384 (m-70) REVERT: A 253 ASN cc_start: 0.7486 (m110) cc_final: 0.7207 (m-40) REVERT: B 51 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6719 (ttp80) REVERT: B 202 ARG cc_start: 0.7518 (mmp80) cc_final: 0.6949 (mmt-90) REVERT: E 66 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5748 (ttp-110) REVERT: E 99 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8461 (mt) REVERT: E 159 CYS cc_start: 0.7857 (p) cc_final: 0.7366 (m) REVERT: E 193 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7679 (p) outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 0.2401 time to fit residues: 52.0934 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.0040 chunk 79 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 0.0470 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 49 GLN B 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.176894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140428 restraints weight = 9275.310| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.65 r_work: 0.3336 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9113 Z= 0.151 Angle : 0.491 6.687 12339 Z= 0.256 Chirality : 0.040 0.142 1405 Planarity : 0.004 0.038 1560 Dihedral : 4.300 59.748 1230 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.63 % Allowed : 13.24 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1108 helix: 0.98 (0.27), residues: 387 sheet: -0.85 (0.29), residues: 273 loop : -1.06 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 24 HIS 0.005 0.001 HIS L 28 PHE 0.015 0.001 PHE A 194 TYR 0.009 0.001 TYR E 235 ARG 0.003 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.013 Fit side-chains REVERT: R 63 MET cc_start: 0.6682 (mtp) cc_final: 0.6330 (mtp) REVERT: R 106 PHE cc_start: 0.6518 (m-80) cc_final: 0.6273 (m-80) REVERT: R 151 MET cc_start: 0.5101 (tpt) cc_final: 0.3888 (mtt) REVERT: A 32 ASP cc_start: 0.7346 (t0) cc_final: 0.6673 (m-30) REVERT: A 38 ARG cc_start: 0.7533 (mpt180) cc_final: 0.7227 (mtm110) REVERT: A 294 GLU cc_start: 0.7648 (mp0) cc_final: 0.6928 (mm-30) REVERT: B 51 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6644 (ttp80) REVERT: B 106 MET cc_start: 0.9059 (mtp) cc_final: 0.8803 (mtp) REVERT: B 202 ARG cc_start: 0.7414 (mmp80) cc_final: 0.6837 (mmt-90) REVERT: E 66 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5856 (ttp-110) REVERT: E 99 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8389 (mt) REVERT: E 159 CYS cc_start: 0.7682 (p) cc_final: 0.7243 (m) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.2838 time to fit residues: 54.5120 Evaluate side-chains 135 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 ASN A 218 GLN B 49 GLN B 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.171666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135374 restraints weight = 9442.849| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.60 r_work: 0.3248 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9113 Z= 0.315 Angle : 0.584 6.981 12339 Z= 0.305 Chirality : 0.043 0.147 1405 Planarity : 0.004 0.039 1560 Dihedral : 4.609 59.965 1230 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.24 % Allowed : 13.14 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.25), residues: 1108 helix: 0.88 (0.27), residues: 387 sheet: -0.85 (0.30), residues: 268 loop : -1.14 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 24 HIS 0.008 0.002 HIS B 188 PHE 0.016 0.002 PHE L 29 TYR 0.015 0.002 TYR E 102 ARG 0.007 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.988 Fit side-chains REVERT: R 63 MET cc_start: 0.6870 (mtp) cc_final: 0.6663 (mtp) REVERT: R 106 PHE cc_start: 0.6662 (m-80) cc_final: 0.6292 (m-80) REVERT: R 151 MET cc_start: 0.5612 (tpt) cc_final: 0.4326 (mtt) REVERT: A 26 GLU cc_start: 0.8003 (tp30) cc_final: 0.7325 (mt-10) REVERT: A 32 ASP cc_start: 0.7221 (t0) cc_final: 0.6608 (m-30) REVERT: A 38 ARG cc_start: 0.7767 (mpt180) cc_final: 0.7434 (mtm110) REVERT: A 202 HIS cc_start: 0.8642 (m-70) cc_final: 0.8232 (m-70) REVERT: A 294 GLU cc_start: 0.7630 (mp0) cc_final: 0.7300 (mp0) REVERT: B 51 ARG cc_start: 0.7049 (ttp80) cc_final: 0.6716 (ttp80) REVERT: E 66 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.6016 (ttp-110) REVERT: E 99 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8457 (mt) REVERT: E 159 CYS cc_start: 0.7754 (p) cc_final: 0.7326 (m) REVERT: E 160 ARG cc_start: 0.7371 (ttp80) cc_final: 0.7087 (ttp80) outliers start: 22 outliers final: 14 residues processed: 144 average time/residue: 0.2677 time to fit residues: 50.2957 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.175835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139786 restraints weight = 9508.617| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.67 r_work: 0.3327 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9113 Z= 0.150 Angle : 0.494 7.530 12339 Z= 0.257 Chirality : 0.041 0.137 1405 Planarity : 0.004 0.037 1560 Dihedral : 4.289 59.860 1230 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.83 % Allowed : 13.85 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1108 helix: 1.08 (0.27), residues: 386 sheet: -0.74 (0.30), residues: 264 loop : -0.97 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 24 HIS 0.005 0.001 HIS L 28 PHE 0.015 0.001 PHE A 194 TYR 0.009 0.001 TYR E 235 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.991 Fit side-chains REVERT: R 106 PHE cc_start: 0.6619 (m-80) cc_final: 0.6240 (m-80) REVERT: R 151 MET cc_start: 0.5362 (tpt) cc_final: 0.4099 (mtt) REVERT: A 32 ASP cc_start: 0.7253 (t0) cc_final: 0.6642 (m-30) REVERT: A 38 ARG cc_start: 0.7555 (mpt180) cc_final: 0.7205 (mtm110) REVERT: A 202 HIS cc_start: 0.8614 (m-70) cc_final: 0.8177 (m-70) REVERT: A 253 ASN cc_start: 0.7699 (m110) cc_final: 0.7462 (m-40) REVERT: A 294 GLU cc_start: 0.7716 (mp0) cc_final: 0.7372 (mp0) REVERT: B 51 ARG cc_start: 0.7079 (ttp80) cc_final: 0.6722 (ttp80) REVERT: B 106 MET cc_start: 0.9058 (mtp) cc_final: 0.8815 (mtp) REVERT: B 185 PHE cc_start: 0.8138 (m-80) cc_final: 0.7828 (m-80) REVERT: B 272 ASP cc_start: 0.7399 (m-30) cc_final: 0.7154 (m-30) REVERT: E 66 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5942 (ttp-110) REVERT: E 99 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8354 (mt) REVERT: E 159 CYS cc_start: 0.7680 (p) cc_final: 0.7218 (m) REVERT: E 160 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6990 (ttp80) outliers start: 18 outliers final: 13 residues processed: 146 average time/residue: 0.2881 time to fit residues: 54.7475 Evaluate side-chains 143 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.175279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139668 restraints weight = 9473.227| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.62 r_work: 0.3330 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9113 Z= 0.170 Angle : 0.505 7.736 12339 Z= 0.262 Chirality : 0.041 0.136 1405 Planarity : 0.004 0.042 1560 Dihedral : 4.268 59.966 1230 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 13.44 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.25), residues: 1108 helix: 1.17 (0.27), residues: 387 sheet: -0.71 (0.30), residues: 264 loop : -0.89 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 24 HIS 0.008 0.001 HIS A 327 PHE 0.016 0.001 PHE A 194 TYR 0.010 0.001 TYR E 235 ARG 0.015 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.919 Fit side-chains REVERT: R 63 MET cc_start: 0.6488 (mtp) cc_final: 0.6109 (mtp) REVERT: R 151 MET cc_start: 0.5972 (tpt) cc_final: 0.4470 (mtt) REVERT: A 32 ASP cc_start: 0.7234 (t0) cc_final: 0.6634 (m-30) REVERT: A 38 ARG cc_start: 0.7527 (mpt180) cc_final: 0.7176 (mtm110) REVERT: A 59 MET cc_start: 0.7034 (ptp) cc_final: 0.6814 (ptp) REVERT: A 202 HIS cc_start: 0.8605 (m-70) cc_final: 0.8188 (m-70) REVERT: A 253 ASN cc_start: 0.7663 (m110) cc_final: 0.7409 (m-40) REVERT: A 294 GLU cc_start: 0.7696 (mp0) cc_final: 0.7331 (mp0) REVERT: A 343 ASP cc_start: 0.7850 (m-30) cc_final: 0.7624 (m-30) REVERT: B 24 ARG cc_start: 0.6024 (ttp-110) cc_final: 0.4914 (ptm-80) REVERT: B 51 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6732 (ttp80) REVERT: B 106 MET cc_start: 0.9063 (mtp) cc_final: 0.8824 (mtp) REVERT: B 185 PHE cc_start: 0.8123 (m-80) cc_final: 0.7792 (m-80) REVERT: B 202 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7206 (mmt-90) REVERT: B 219 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6640 (mmp80) REVERT: B 272 ASP cc_start: 0.7360 (m-30) cc_final: 0.7137 (m-30) REVERT: E 66 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5967 (ttp-110) REVERT: E 159 CYS cc_start: 0.7702 (p) cc_final: 0.7210 (m) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.2769 time to fit residues: 50.8519 Evaluate side-chains 141 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.168013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131577 restraints weight = 9473.645| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.62 r_work: 0.3229 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9113 Z= 0.343 Angle : 0.617 10.038 12339 Z= 0.318 Chirality : 0.045 0.151 1405 Planarity : 0.005 0.062 1560 Dihedral : 4.772 59.715 1230 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.04 % Allowed : 13.75 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.25), residues: 1108 helix: 0.93 (0.27), residues: 388 sheet: -0.83 (0.30), residues: 259 loop : -0.97 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 87 HIS 0.010 0.002 HIS B 188 PHE 0.017 0.002 PHE A 194 TYR 0.015 0.002 TYR B 269 ARG 0.014 0.001 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.990 Fit side-chains REVERT: R 151 MET cc_start: 0.5846 (tpt) cc_final: 0.4735 (mtt) REVERT: A 26 GLU cc_start: 0.8007 (tp30) cc_final: 0.7267 (mt-10) REVERT: A 32 ASP cc_start: 0.7205 (t0) cc_final: 0.6609 (m-30) REVERT: A 38 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7370 (mtm110) REVERT: A 202 HIS cc_start: 0.8650 (m-70) cc_final: 0.8238 (m-70) REVERT: A 253 ASN cc_start: 0.7690 (m110) cc_final: 0.7355 (m-40) REVERT: A 294 GLU cc_start: 0.7680 (mp0) cc_final: 0.7181 (mp0) REVERT: B 51 ARG cc_start: 0.7100 (ttp80) cc_final: 0.6754 (ttp80) REVERT: E 17 ARG cc_start: 0.6769 (tpt170) cc_final: 0.6552 (tpt170) REVERT: E 66 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.6015 (ttp-110) REVERT: E 159 CYS cc_start: 0.7763 (p) cc_final: 0.7374 (m) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.2920 time to fit residues: 50.9747 Evaluate side-chains 136 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.0030 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.174900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139287 restraints weight = 9414.169| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.64 r_work: 0.3349 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9113 Z= 0.162 Angle : 0.524 8.960 12339 Z= 0.270 Chirality : 0.041 0.162 1405 Planarity : 0.004 0.055 1560 Dihedral : 4.374 59.720 1230 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.53 % Allowed : 13.54 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.25), residues: 1108 helix: 1.12 (0.27), residues: 388 sheet: -0.77 (0.30), residues: 262 loop : -0.86 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 24 HIS 0.006 0.001 HIS A 327 PHE 0.017 0.001 PHE R 68 TYR 0.009 0.001 TYR E 235 ARG 0.014 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.56 seconds wall clock time: 101 minutes 31.01 seconds (6091.01 seconds total)