Starting phenix.real_space_refine on Wed Sep 17 13:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0p_34413/09_2025/8h0p_34413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0p_34413/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h0p_34413/09_2025/8h0p_34413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0p_34413/09_2025/8h0p_34413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h0p_34413/09_2025/8h0p_34413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0p_34413/09_2025/8h0p_34413.map" } resolution = 3.15 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= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.25, per 1000 atoms: 0.25 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: 0.61 Conformation dependent library (CDL) restraints added in 374.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.32 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: 1.42 Time building geometry restraints manager: 0.83 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: 0.480 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- 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 9114 Z= 0.083 Angle : 0.405 5.736 12341 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 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: -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 ARG 0.001 0.000 ARG B 256 TYR 0.006 0.001 TYR E 235 PHE 0.008 0.001 PHE B 258 TRP 0.010 0.001 TRP B 87 HIS 0.002 0.000 HIS L 28 Details of bonding type rmsd covalent geometry : bond 0.00148 ( 9113) covalent geometry : angle 0.40494 (12339) SS BOND : bond 0.00135 ( 1) SS BOND : angle 0.30910 ( 2) hydrogen bonds : bond 0.11915 ( 419) hydrogen bonds : angle 5.65947 ( 1200) *********************** 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 : 0.261 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: 0.1234 time to fit residues: 34.5612 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 : 0.334 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS R 257 GLN ** R 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 320 ASN A 49 ASN A 58 GLN A 195 GLN A 209 GLN A 357 ASN B 21 ASN B 264 GLN 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 = 0.4197 r_free = 0.4197 target = 0.205345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171323 restraints weight = 9360.903| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.62 r_work: 0.3703 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9114 Z= 0.129 Angle : 0.520 6.759 12341 Z= 0.266 Chirality : 0.042 0.188 1405 Planarity : 0.004 0.035 1560 Dihedral : 3.579 54.564 1230 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.73 % Allowed : 8.04 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.24), residues: 1108 helix: 0.48 (0.26), residues: 398 sheet: -1.11 (0.30), residues: 270 loop : -1.86 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 339 TYR 0.010 0.001 TYR B 150 PHE 0.017 0.002 PHE A 194 TRP 0.017 0.002 TRP L 24 HIS 0.008 0.002 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9113) covalent geometry : angle 0.51937 (12339) SS BOND : bond 0.00247 ( 1) SS BOND : angle 1.15089 ( 2) hydrogen bonds : bond 0.02720 ( 419) hydrogen bonds : angle 4.25507 ( 1200) *********************** 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 187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.259 Fit side-chains REVERT: R 74 MET cc_start: 0.7015 (mmm) cc_final: 0.6744 (mmt) REVERT: R 107 ASP cc_start: 0.7324 (t70) cc_final: 0.6946 (t70) REVERT: R 165 MET cc_start: 0.4911 (mmt) cc_final: 0.4289 (mtt) REVERT: R 258 MET cc_start: 0.7464 (mmt) cc_final: 0.7256 (mmp) REVERT: A 294 GLU cc_start: 0.7267 (mp0) cc_final: 0.6763 (mm-30) REVERT: A 339 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7854 (mtm-85) REVERT: E 29 SER cc_start: 0.8457 (t) cc_final: 0.7944 (m) REVERT: E 141 THR cc_start: 0.7981 (t) cc_final: 0.7335 (p) outliers start: 17 outliers final: 8 residues processed: 181 average time/residue: 0.1176 time to fit residues: 27.9441 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 99 ILE 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 11 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 ASN R 244 HIS R 283 HIS A 49 ASN A 342 ASN B 225 GLN E 34 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.186620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148963 restraints weight = 9263.283| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.63 r_work: 0.3482 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9114 Z= 0.164 Angle : 0.556 7.949 12341 Z= 0.290 Chirality : 0.043 0.191 1405 Planarity : 0.004 0.035 1560 Dihedral : 4.160 56.120 1230 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.83 % Allowed : 9.88 % Favored : 88.29 % 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: -0.69 (0.25), residues: 1108 helix: 0.93 (0.27), residues: 394 sheet: -0.89 (0.30), residues: 278 loop : -1.39 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 263 TYR 0.018 0.002 TYR E 190 PHE 0.014 0.002 PHE B 185 TRP 0.017 0.002 TRP L 24 HIS 0.009 0.002 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9113) covalent geometry : angle 0.55593 (12339) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.21767 ( 2) hydrogen bonds : bond 0.03056 ( 419) hydrogen bonds : angle 4.29316 ( 1200) *********************** 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 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.376 Fit side-chains REVERT: R 74 MET cc_start: 0.7504 (mmm) cc_final: 0.7295 (mmt) REVERT: A 38 ARG cc_start: 0.7232 (mpt180) cc_final: 0.6901 (mtm110) REVERT: B 51 ARG cc_start: 0.7007 (ttp80) cc_final: 0.6792 (ttp80) REVERT: B 168 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (p0) REVERT: B 202 ARG cc_start: 0.7220 (mmp80) cc_final: 0.6426 (mmt-90) REVERT: B 224 ARG cc_start: 0.7231 (mtp180) cc_final: 0.7000 (mmt180) REVERT: E 6 SER cc_start: 0.7002 (p) cc_final: 0.6540 (m) REVERT: E 99 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8398 (mt) REVERT: E 158 SER cc_start: 0.7473 (t) cc_final: 0.7063 (p) outliers start: 18 outliers final: 11 residues processed: 159 average time/residue: 0.1185 time to fit residues: 25.0089 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 168 ASP 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 56 THR 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 49 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 123 GLN A 218 GLN B 225 GLN B 235 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.187510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151493 restraints weight = 9487.368| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.66 r_work: 0.3475 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9114 Z= 0.104 Angle : 0.477 6.177 12341 Z= 0.246 Chirality : 0.040 0.139 1405 Planarity : 0.003 0.037 1560 Dihedral : 3.931 56.065 1230 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.14 % Allowed : 11.20 % Favored : 86.66 % 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: -0.40 (0.26), residues: 1108 helix: 1.11 (0.27), residues: 392 sheet: -0.77 (0.30), residues: 280 loop : -1.11 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 191 TYR 0.011 0.001 TYR E 173 PHE 0.015 0.001 PHE A 194 TRP 0.026 0.001 TRP L 24 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9113) covalent geometry : angle 0.47670 (12339) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.35773 ( 2) hydrogen bonds : bond 0.02618 ( 419) hydrogen bonds : angle 4.11668 ( 1200) *********************** 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 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.259 Fit side-chains REVERT: R 63 MET cc_start: 0.5764 (mtp) cc_final: 0.5411 (mtp) REVERT: R 165 MET cc_start: 0.5533 (mmp) cc_final: 0.4016 (mtt) REVERT: A 38 ARG cc_start: 0.7259 (mpt180) cc_final: 0.6854 (mtm110) REVERT: B 51 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6479 (ttp80) REVERT: B 224 ARG cc_start: 0.7296 (mtp180) cc_final: 0.6973 (mmt180) REVERT: E 6 SER cc_start: 0.7047 (p) cc_final: 0.6600 (m) REVERT: E 66 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5223 (ttp-110) REVERT: E 99 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8421 (mt) REVERT: E 158 SER cc_start: 0.7509 (t) cc_final: 0.7117 (p) outliers start: 21 outliers final: 12 residues processed: 156 average time/residue: 0.1074 time to fit residues: 22.3475 Evaluate side-chains 155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 235 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 225 GLN B 235 ASN B 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.177524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140061 restraints weight = 9430.972| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.68 r_work: 0.3306 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9114 Z= 0.192 Angle : 0.571 6.514 12341 Z= 0.298 Chirality : 0.043 0.146 1405 Planarity : 0.004 0.037 1560 Dihedral : 4.501 57.444 1230 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.55 % Allowed : 11.61 % Favored : 85.85 % 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: -0.52 (0.25), residues: 1108 helix: 0.98 (0.27), residues: 388 sheet: -0.87 (0.30), residues: 278 loop : -1.08 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 191 TYR 0.018 0.002 TYR E 190 PHE 0.017 0.002 PHE B 185 TRP 0.014 0.002 TRP L 24 HIS 0.008 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9113) covalent geometry : angle 0.57100 (12339) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.26115 ( 2) hydrogen bonds : bond 0.03125 ( 419) hydrogen bonds : angle 4.46411 ( 1200) *********************** 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 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.343 Fit side-chains REVERT: R 63 MET cc_start: 0.6236 (mtp) cc_final: 0.5916 (mtp) REVERT: R 151 MET cc_start: 0.5362 (tpt) cc_final: 0.4019 (mtt) REVERT: A 32 ASP cc_start: 0.7348 (t0) cc_final: 0.6578 (m-30) REVERT: A 38 ARG cc_start: 0.7353 (mpt180) cc_final: 0.7066 (mtm110) REVERT: B 51 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6660 (ttp80) REVERT: B 201 THR cc_start: 0.7587 (m) cc_final: 0.7230 (m) REVERT: B 202 ARG cc_start: 0.7404 (mmp80) cc_final: 0.6800 (mmt-90) REVERT: E 99 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8476 (mt) REVERT: E 159 CYS cc_start: 0.7787 (p) cc_final: 0.7189 (m) REVERT: E 192 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6624 (mmm) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 0.1206 time to fit residues: 25.5432 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 300 THR 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 115 THR Chi-restraints excluded: chain E residue 192 MET 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 86 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 260 ASN B 49 GLN B 225 GLN B 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.171900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135067 restraints weight = 9417.716| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.66 r_work: 0.3255 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9114 Z= 0.205 Angle : 0.586 6.860 12341 Z= 0.305 Chirality : 0.044 0.199 1405 Planarity : 0.004 0.038 1560 Dihedral : 4.640 59.287 1230 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.34 % Allowed : 12.93 % Favored : 84.73 % 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: -0.56 (0.25), residues: 1108 helix: 0.81 (0.27), residues: 387 sheet: -0.71 (0.30), residues: 267 loop : -1.11 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 73 TYR 0.016 0.002 TYR E 173 PHE 0.016 0.002 PHE B 156 TRP 0.014 0.002 TRP A 263 HIS 0.008 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9113) covalent geometry : angle 0.58586 (12339) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.23742 ( 2) hydrogen bonds : bond 0.03211 ( 419) hydrogen bonds : angle 4.57848 ( 1200) *********************** 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 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6562 (mtp) cc_final: 0.6106 (mtp) REVERT: R 106 PHE cc_start: 0.6588 (m-80) cc_final: 0.6264 (m-80) REVERT: R 151 MET cc_start: 0.5237 (tpt) cc_final: 0.3986 (mtt) REVERT: A 32 ASP cc_start: 0.7203 (t0) cc_final: 0.6607 (m-30) REVERT: A 38 ARG cc_start: 0.7690 (mpt180) cc_final: 0.7338 (mtm110) REVERT: B 51 ARG cc_start: 0.7202 (ttp80) cc_final: 0.6698 (ttp80) REVERT: B 202 ARG cc_start: 0.7488 (mmp80) cc_final: 0.6898 (mmt-90) REVERT: E 99 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8475 (mt) REVERT: E 159 CYS cc_start: 0.7756 (p) cc_final: 0.7334 (m) outliers start: 23 outliers final: 16 residues processed: 144 average time/residue: 0.1205 time to fit residues: 22.6783 Evaluate side-chains 142 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 283 VAL 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 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU 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 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 260 ASN B 49 GLN B 264 GLN E 167 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.178116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141444 restraints weight = 9306.242| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.59 r_work: 0.3346 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9114 Z= 0.115 Angle : 0.517 6.753 12341 Z= 0.267 Chirality : 0.041 0.187 1405 Planarity : 0.004 0.037 1560 Dihedral : 4.366 59.292 1230 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.73 % Allowed : 13.95 % 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 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: -0.34 (0.25), residues: 1108 helix: 1.00 (0.27), residues: 386 sheet: -0.61 (0.31), residues: 260 loop : -0.97 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 24 TYR 0.012 0.001 TYR E 190 PHE 0.018 0.001 PHE A 194 TRP 0.012 0.001 TRP A 263 HIS 0.010 0.001 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9113) covalent geometry : angle 0.51669 (12339) SS BOND : bond 0.00188 ( 1) SS BOND : angle 0.41840 ( 2) hydrogen bonds : bond 0.02719 ( 419) hydrogen bonds : angle 4.35630 ( 1200) *********************** 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 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.359 Fit side-chains REVERT: R 63 MET cc_start: 0.6708 (mtp) cc_final: 0.6250 (mtp) REVERT: R 106 PHE cc_start: 0.6648 (m-80) cc_final: 0.6275 (m-80) REVERT: R 151 MET cc_start: 0.5943 (tpt) cc_final: 0.4508 (mtt) REVERT: A 32 ASP cc_start: 0.7202 (t0) cc_final: 0.6631 (m-30) REVERT: A 38 ARG cc_start: 0.7499 (mpt180) cc_final: 0.7194 (mtm110) REVERT: B 51 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6613 (ttp80) REVERT: B 185 PHE cc_start: 0.8071 (m-80) cc_final: 0.7754 (m-80) REVERT: E 99 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8385 (mt) REVERT: E 159 CYS cc_start: 0.7663 (p) cc_final: 0.7241 (m) REVERT: E 192 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6556 (mmm) outliers start: 17 outliers final: 12 residues processed: 141 average time/residue: 0.1415 time to fit residues: 25.4838 Evaluate side-chains 137 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 315 ASP 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 90 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.0570 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 49 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 = 0.3930 r_free = 0.3930 target = 0.178755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142561 restraints weight = 9356.563| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.66 r_work: 0.3390 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9114 Z= 0.105 Angle : 0.506 6.965 12341 Z= 0.262 Chirality : 0.041 0.188 1405 Planarity : 0.004 0.036 1560 Dihedral : 4.247 59.524 1230 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.83 % Allowed : 14.46 % Favored : 83.71 % 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: -0.12 (0.26), residues: 1108 helix: 1.20 (0.27), residues: 386 sheet: -0.49 (0.31), residues: 260 loop : -0.85 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.010 0.001 TYR E 235 PHE 0.018 0.001 PHE A 194 TRP 0.012 0.001 TRP A 263 HIS 0.009 0.001 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9113) covalent geometry : angle 0.50553 (12339) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.50863 ( 2) hydrogen bonds : bond 0.02582 ( 419) hydrogen bonds : angle 4.21962 ( 1200) *********************** 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 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.404 Fit side-chains REVERT: R 63 MET cc_start: 0.6658 (mtp) cc_final: 0.6187 (mtp) REVERT: R 106 PHE cc_start: 0.6568 (m-80) cc_final: 0.6156 (m-80) REVERT: R 151 MET cc_start: 0.5694 (tpt) cc_final: 0.4306 (mtt) REVERT: A 32 ASP cc_start: 0.7208 (t0) cc_final: 0.6673 (m-30) REVERT: A 38 ARG cc_start: 0.7388 (mpt180) cc_final: 0.7086 (mtm110) REVERT: B 24 ARG cc_start: 0.6029 (ttp-110) cc_final: 0.4934 (ptm-80) REVERT: B 51 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6734 (ttp80) REVERT: B 272 ASP cc_start: 0.7308 (m-30) cc_final: 0.7054 (m-30) REVERT: E 158 SER cc_start: 0.7705 (t) cc_final: 0.7330 (p) REVERT: E 159 CYS cc_start: 0.7652 (p) cc_final: 0.7256 (m) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.1369 time to fit residues: 24.6651 Evaluate side-chains 143 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain A residue 235 TYR 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 90 THR Chi-restraints excluded: chain E residue 192 MET 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 18 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.176584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140074 restraints weight = 9391.994| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.65 r_work: 0.3336 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9114 Z= 0.127 Angle : 0.522 7.280 12341 Z= 0.269 Chirality : 0.042 0.182 1405 Planarity : 0.004 0.079 1560 Dihedral : 4.327 59.628 1230 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.73 % Allowed : 14.36 % Favored : 83.91 % 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: -0.12 (0.26), residues: 1108 helix: 1.19 (0.27), residues: 386 sheet: -0.48 (0.31), residues: 260 loop : -0.85 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 24 TYR 0.012 0.001 TYR E 190 PHE 0.018 0.001 PHE A 194 TRP 0.009 0.001 TRP R 279 HIS 0.008 0.001 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9113) covalent geometry : angle 0.52208 (12339) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.38477 ( 2) hydrogen bonds : bond 0.02724 ( 419) hydrogen bonds : angle 4.23850 ( 1200) *********************** 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 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.338 Fit side-chains REVERT: R 63 MET cc_start: 0.6602 (mtp) cc_final: 0.6123 (mtp) REVERT: R 106 PHE cc_start: 0.6608 (m-80) cc_final: 0.6202 (m-80) REVERT: R 151 MET cc_start: 0.5773 (tpt) cc_final: 0.4348 (mtt) REVERT: A 32 ASP cc_start: 0.7219 (t0) cc_final: 0.6637 (m-30) REVERT: A 38 ARG cc_start: 0.7502 (mpt180) cc_final: 0.7158 (mtm110) REVERT: B 24 ARG cc_start: 0.5838 (ttp-110) cc_final: 0.4810 (ptm-80) REVERT: B 51 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6708 (ttp80) REVERT: B 272 ASP cc_start: 0.7405 (m-30) cc_final: 0.7121 (m-30) REVERT: E 158 SER cc_start: 0.7723 (t) cc_final: 0.7357 (p) REVERT: E 159 CYS cc_start: 0.7691 (p) cc_final: 0.7279 (m) REVERT: G 20 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6653 (ttp) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.1212 time to fit residues: 21.6098 Evaluate side-chains 138 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 93 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 219 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.178205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.141922 restraints weight = 9379.659| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.64 r_work: 0.3356 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9114 Z= 0.108 Angle : 0.511 8.746 12341 Z= 0.262 Chirality : 0.041 0.193 1405 Planarity : 0.004 0.052 1560 Dihedral : 4.275 59.436 1230 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 14.15 % Favored : 83.71 % 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: -0.04 (0.26), residues: 1108 helix: 1.27 (0.27), residues: 386 sheet: -0.47 (0.31), residues: 260 loop : -0.81 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.015 0.001 TYR E 190 PHE 0.019 0.001 PHE A 194 TRP 0.009 0.001 TRP B 337 HIS 0.007 0.001 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9113) covalent geometry : angle 0.51121 (12339) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.42102 ( 2) hydrogen bonds : bond 0.02632 ( 419) hydrogen bonds : angle 4.17591 ( 1200) ********************** 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 146 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.365 Fit side-chains REVERT: R 63 MET cc_start: 0.6560 (mtp) cc_final: 0.6085 (mtp) REVERT: R 106 PHE cc_start: 0.6559 (m-80) cc_final: 0.6233 (m-80) REVERT: R 151 MET cc_start: 0.5795 (tpt) cc_final: 0.4363 (mtt) REVERT: A 32 ASP cc_start: 0.7224 (t0) cc_final: 0.6617 (m-30) REVERT: A 38 ARG cc_start: 0.7452 (mpt180) cc_final: 0.7105 (mtm110) REVERT: B 24 ARG cc_start: 0.5911 (ttp-110) cc_final: 0.4992 (ptm-80) REVERT: B 51 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6757 (ttp80) REVERT: B 272 ASP cc_start: 0.7413 (m-30) cc_final: 0.7144 (m-30) REVERT: E 158 SER cc_start: 0.7673 (t) cc_final: 0.7320 (p) REVERT: E 159 CYS cc_start: 0.7623 (p) cc_final: 0.7232 (m) REVERT: G 20 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6630 (ttp) outliers start: 21 outliers final: 17 residues processed: 139 average time/residue: 0.1264 time to fit residues: 22.9887 Evaluate side-chains 141 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 215 LEU 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 266 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 107 optimal weight: 0.0000 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.178731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143280 restraints weight = 9271.419| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.61 r_work: 0.3359 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9114 Z= 0.114 Angle : 0.521 7.690 12341 Z= 0.265 Chirality : 0.042 0.196 1405 Planarity : 0.004 0.051 1560 Dihedral : 4.262 59.385 1230 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.24 % Allowed : 14.05 % Favored : 83.71 % 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: -0.01 (0.26), residues: 1108 helix: 1.30 (0.27), residues: 387 sheet: -0.42 (0.31), residues: 257 loop : -0.81 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 24 TYR 0.015 0.001 TYR E 190 PHE 0.020 0.001 PHE A 194 TRP 0.049 0.002 TRP L 24 HIS 0.006 0.001 HIS R 244 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9113) covalent geometry : angle 0.52057 (12339) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.39482 ( 2) hydrogen bonds : bond 0.02631 ( 419) hydrogen bonds : angle 4.16920 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2739.28 seconds wall clock time: 47 minutes 41.06 seconds (2861.06 seconds total)