Starting phenix.real_space_refine on Tue Mar 3 22:05:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.map" model { file = "/net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uun_20883/03_2026/6uun_20883.cif" } resolution = 3.0 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= 0.004 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 64 5.16 5 C 5693 2.51 5 N 1580 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8980 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 627 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASN:plan1': 4, 'TYR:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 7, 'TRP:plan': 3, 'HIS:plan': 4, 'ASP:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 260 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2565 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 8, 'GLN:plan1': 9, 'TYR:plan': 5, 'GLU:plan': 5, 'ASP:plan': 8, 'TRP:plan': 5, 'PHE:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 232 Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 8980 At special positions: 0 Unit cell: (84.66, 95.45, 160.19, 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 64 16.00 O 1643 8.00 N 1580 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " 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: 0.78 Conformation dependent library (CDL) restraints added in 366.0 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 41.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.668A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.905A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.572A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.542A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.508A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.638A pdb=" N ILE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 155 Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 156 through 167 removed outlier: 3.610A pdb=" N LEU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.593A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 23 through 34 removed outlier: 4.326A pdb=" N GLN P 32 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.708A pdb=" N ASP R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 167 removed outlier: 3.955A pdb=" N ASN R 128 " --> pdb=" O TYR R 124 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS R 132 " --> pdb=" O ASN R 128 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.515A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR R 227 " --> pdb=" O MET R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 Processing helix chain 'R' and resid 263 through 279 removed outlier: 3.570A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 290 through 294 Processing helix chain 'R' and resid 296 through 321 Processing helix chain 'R' and resid 333 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 400 removed outlier: 4.056A pdb=" N ASN R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.110A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.757A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.056A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.517A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.544A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AB4, first strand: chain 'R' and resid 82 through 87 removed outlier: 4.095A pdb=" N THR R 82 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS R 105 " --> pdb=" O THR R 82 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1287 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: 1.39 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2765 1.34 - 1.45: 1409 1.45 - 1.57: 4896 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9154 Sorted by residual: bond pdb=" N VAL R 198 " pdb=" CA VAL R 198 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.67e+00 bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N VAL R 135 " pdb=" CA VAL R 135 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11731 1.53 - 3.06: 621 3.06 - 4.59: 72 4.59 - 6.13: 12 6.13 - 7.66: 3 Bond angle restraints: 12439 Sorted by residual: angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 112.72 105.06 7.66 1.14e+00 7.69e-01 4.51e+01 angle pdb=" C LEU E 156 " pdb=" N ILE E 157 " pdb=" CA ILE E 157 " ideal model delta sigma weight residual 120.33 123.99 -3.66 8.00e-01 1.56e+00 2.09e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.01 107.74 5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CA ASN R 281 " pdb=" C ASN R 281 " pdb=" O ASN R 281 " ideal model delta sigma weight residual 121.54 117.06 4.48 1.16e+00 7.43e-01 1.49e+01 angle pdb=" N CYS R 282 " pdb=" CA CYS R 282 " pdb=" C CYS R 282 " ideal model delta sigma weight residual 113.56 108.68 4.88 1.39e+00 5.18e-01 1.23e+01 ... (remaining 12434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5073 17.66 - 35.32: 292 35.32 - 52.97: 51 52.97 - 70.63: 13 70.63 - 88.29: 5 Dihedral angle restraints: 5434 sinusoidal: 1935 harmonic: 3499 Sorted by residual: dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -139.41 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.77 -49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS P 16 " pdb=" SG CYS P 16 " pdb=" SG CYS P 21 " pdb=" CB CYS P 21 " ideal model delta sinusoidal sigma weight residual -86.00 -43.45 -42.55 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 5431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1102 0.055 - 0.111: 258 0.111 - 0.166: 54 0.166 - 0.221: 18 0.221 - 0.277: 6 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1435 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C THR R 196 " -0.025 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO G 55 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG B 52 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1423 2.76 - 3.30: 8778 3.30 - 3.83: 14872 3.83 - 4.37: 18007 4.37 - 4.90: 30630 Nonbonded interactions: 73710 Sorted by model distance: nonbonded pdb=" O ASN R 398 " pdb=" ND2 ASN R 398 " model vdw 2.226 3.120 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.270 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.275 3.120 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.283 3.120 ... (remaining 73705 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: 2.210 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: 0.010 Process input model: 10.210 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:10.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.005 0.039 9163 Z= 0.366 Angle : 0.730 7.657 12457 Z= 0.515 Chirality : 0.055 0.277 1438 Planarity : 0.003 0.036 1597 Dihedral : 11.918 88.291 3135 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.45 % Allowed : 4.20 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -1.59 (0.23), residues: 1176 helix: 0.35 (0.25), residues: 433 sheet: -1.39 (0.32), residues: 223 loop : -2.11 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.009 0.001 TYR P 31 PHE 0.012 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 9154) covalent geometry : angle 0.72871 (12439) SS BOND : bond 0.00162 ( 9) SS BOND : angle 1.25497 ( 18) hydrogen bonds : bond 0.15150 ( 453) hydrogen bonds : angle 6.35703 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7834 (mt0) cc_final: 0.7143 (tp-100) REVERT: A 34 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7979 (ttmm) REVERT: A 274 ASP cc_start: 0.7228 (t0) cc_final: 0.6908 (t70) REVERT: B 111 TYR cc_start: 0.8834 (m-80) cc_final: 0.8547 (m-80) REVERT: B 124 TYR cc_start: 0.8821 (m-80) cc_final: 0.8550 (m-80) REVERT: B 325 MET cc_start: 0.8077 (tpp) cc_final: 0.7689 (tpt) REVERT: E 167 ARG cc_start: 0.4151 (mpt180) cc_final: 0.3350 (mmm-85) REVERT: G 42 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6542 (mm-30) REVERT: N 80 TYR cc_start: 0.8083 (m-80) cc_final: 0.7666 (m-80) REVERT: N 87 LYS cc_start: 0.7990 (mttp) cc_final: 0.7278 (mtpm) REVERT: R 134 LYS cc_start: 0.6307 (ttpt) cc_final: 0.6106 (mmtt) REVERT: R 139 LEU cc_start: 0.6457 (mm) cc_final: 0.6232 (mm) REVERT: R 213 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6256 (mttt) REVERT: R 332 MET cc_start: 0.6557 (mmp) cc_final: 0.6303 (pmm) REVERT: R 381 SER cc_start: 0.7836 (t) cc_final: 0.7489 (m) outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 0.6172 time to fit residues: 120.9078 Evaluate side-chains 135 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 31 GLN A 35 GLN A 262 GLN A 377 ASN A 390 GLN B 6 GLN B 32 GLN B 175 GLN B 340 ASN N 31 ASN N 35 ASN N 74 ASN N 120 GLN P 24 GLN R 172 GLN R 179 ASN R 219 HIS ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122731 restraints weight = 10306.649| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.81 r_work: 0.3285 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9163 Z= 0.120 Angle : 0.518 6.501 12457 Z= 0.277 Chirality : 0.041 0.156 1438 Planarity : 0.003 0.040 1597 Dihedral : 4.433 59.193 1290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.84 % Allowed : 12.05 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.61 (0.24), residues: 1176 helix: 1.32 (0.25), residues: 453 sheet: -1.10 (0.32), residues: 223 loop : -1.70 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.014 0.001 TYR R 277 PHE 0.013 0.001 PHE R 228 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 370 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9154) covalent geometry : angle 0.51723 (12439) SS BOND : bond 0.00177 ( 9) SS BOND : angle 0.82827 ( 18) hydrogen bonds : bond 0.03973 ( 453) hydrogen bonds : angle 4.59555 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8443 (mt0) cc_final: 0.7578 (tp-100) REVERT: A 34 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8306 (ttmt) REVERT: A 36 VAL cc_start: 0.9006 (t) cc_final: 0.8744 (m) REVERT: A 223 ASP cc_start: 0.7722 (p0) cc_final: 0.7516 (t70) REVERT: B 17 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7407 (tt0) REVERT: B 124 TYR cc_start: 0.8979 (m-80) cc_final: 0.8699 (m-80) REVERT: B 127 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8428 (mmtm) REVERT: B 153 ASP cc_start: 0.8323 (p0) cc_final: 0.8119 (p0) REVERT: B 325 MET cc_start: 0.8446 (tpp) cc_final: 0.8024 (tpt) REVERT: E 167 ARG cc_start: 0.4543 (mpt180) cc_final: 0.3640 (mmm-85) REVERT: N 31 ASN cc_start: 0.8239 (m-40) cc_final: 0.7972 (m110) REVERT: N 80 TYR cc_start: 0.8471 (m-80) cc_final: 0.8140 (m-80) REVERT: R 134 LYS cc_start: 0.5984 (ttpt) cc_final: 0.5766 (mmtt) REVERT: R 139 LEU cc_start: 0.6588 (mm) cc_final: 0.6324 (mm) REVERT: R 213 LYS cc_start: 0.6890 (mtmt) cc_final: 0.6494 (mttt) REVERT: R 253 MET cc_start: 0.8084 (ttt) cc_final: 0.7752 (ttp) REVERT: R 269 ILE cc_start: 0.7945 (mm) cc_final: 0.7735 (mp) REVERT: R 332 MET cc_start: 0.6672 (mmp) cc_final: 0.6433 (pmm) REVERT: R 381 SER cc_start: 0.8073 (t) cc_final: 0.7713 (m) outliers start: 25 outliers final: 9 residues processed: 155 average time/residue: 0.6218 time to fit residues: 102.1470 Evaluate side-chains 141 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 overall best weight: 1.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN B 237 ASN R 370 HIS R 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.181009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125772 restraints weight = 10236.511| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.10 r_work: 0.3270 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9163 Z= 0.130 Angle : 0.510 6.266 12457 Z= 0.271 Chirality : 0.042 0.148 1438 Planarity : 0.003 0.039 1597 Dihedral : 4.427 57.483 1290 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 13.86 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.22 (0.24), residues: 1176 helix: 1.62 (0.25), residues: 458 sheet: -1.00 (0.32), residues: 220 loop : -1.43 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.011 0.001 TYR B 105 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9154) covalent geometry : angle 0.50920 (12439) SS BOND : bond 0.00449 ( 9) SS BOND : angle 0.74576 ( 18) hydrogen bonds : bond 0.03548 ( 453) hydrogen bonds : angle 4.32319 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.384 Fit side-chains REVERT: A 31 GLN cc_start: 0.8345 (mt0) cc_final: 0.7512 (tp-100) REVERT: A 34 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8260 (ttmt) REVERT: A 223 ASP cc_start: 0.7929 (p0) cc_final: 0.7706 (t70) REVERT: A 230 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8124 (mt-10) REVERT: A 266 LEU cc_start: 0.8706 (tp) cc_final: 0.8357 (tp) REVERT: B 17 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7498 (tt0) REVERT: B 97 SER cc_start: 0.8132 (p) cc_final: 0.7780 (t) REVERT: B 124 TYR cc_start: 0.9044 (m-80) cc_final: 0.8776 (m-80) REVERT: B 127 LYS cc_start: 0.8731 (mmpt) cc_final: 0.8501 (mmtm) REVERT: B 325 MET cc_start: 0.8415 (tpp) cc_final: 0.7912 (tpt) REVERT: E 167 ARG cc_start: 0.4663 (mpt180) cc_final: 0.3739 (mmm-85) REVERT: N 65 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8179 (ttpt) REVERT: N 73 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7284 (t0) REVERT: N 80 TYR cc_start: 0.8524 (m-80) cc_final: 0.8223 (m-80) REVERT: N 87 LYS cc_start: 0.8130 (mtpm) cc_final: 0.6898 (mttt) REVERT: N 89 GLU cc_start: 0.7662 (pt0) cc_final: 0.6980 (pp20) REVERT: N 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.8121 (m-30) REVERT: N 106 ASP cc_start: 0.8971 (p0) cc_final: 0.8707 (p0) REVERT: R 127 CYS cc_start: 0.4772 (OUTLIER) cc_final: 0.4157 (p) REVERT: R 134 LYS cc_start: 0.6194 (ttpt) cc_final: 0.5949 (mmtt) REVERT: R 182 PHE cc_start: 0.7443 (t80) cc_final: 0.6931 (t80) REVERT: R 213 LYS cc_start: 0.6926 (mtmt) cc_final: 0.6519 (mttt) REVERT: R 216 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.5841 (tt0) REVERT: R 253 MET cc_start: 0.8028 (ttt) cc_final: 0.7703 (ttp) REVERT: R 269 ILE cc_start: 0.8123 (mm) cc_final: 0.7875 (mp) REVERT: R 332 MET cc_start: 0.6792 (mmp) cc_final: 0.6313 (pmm) REVERT: R 370 HIS cc_start: 0.6558 (m-70) cc_final: 0.6217 (m90) REVERT: R 381 SER cc_start: 0.8033 (t) cc_final: 0.7643 (m) outliers start: 26 outliers final: 13 residues processed: 152 average time/residue: 0.6037 time to fit residues: 97.4710 Evaluate side-chains 150 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 284 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** R 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126142 restraints weight = 10392.725| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.04 r_work: 0.3275 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9163 Z= 0.120 Angle : 0.496 6.251 12457 Z= 0.264 Chirality : 0.041 0.183 1438 Planarity : 0.003 0.038 1597 Dihedral : 4.395 56.586 1290 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.18 % Allowed : 15.00 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: -0.04 (0.25), residues: 1176 helix: 1.70 (0.25), residues: 466 sheet: -0.89 (0.32), residues: 218 loop : -1.32 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.010 0.001 TYR R 278 PHE 0.013 0.001 PHE R 228 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9154) covalent geometry : angle 0.49600 (12439) SS BOND : bond 0.00267 ( 9) SS BOND : angle 0.76120 ( 18) hydrogen bonds : bond 0.03338 ( 453) hydrogen bonds : angle 4.18652 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7377 (mmmm) REVERT: A 21 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 31 GLN cc_start: 0.8404 (mt0) cc_final: 0.7571 (tp-100) REVERT: A 34 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8243 (ttmt) REVERT: A 230 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 266 LEU cc_start: 0.8728 (tp) cc_final: 0.8394 (tp) REVERT: B 17 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7512 (tt0) REVERT: B 97 SER cc_start: 0.8135 (p) cc_final: 0.7677 (t) REVERT: B 124 TYR cc_start: 0.9025 (m-80) cc_final: 0.8738 (m-80) REVERT: B 127 LYS cc_start: 0.8768 (mmpt) cc_final: 0.8513 (mmtm) REVERT: B 325 MET cc_start: 0.8402 (tpp) cc_final: 0.7921 (tpt) REVERT: E 167 ARG cc_start: 0.4690 (mpt180) cc_final: 0.3800 (mmm-85) REVERT: N 65 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8105 (ttpt) REVERT: N 73 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7244 (t0) REVERT: N 80 TYR cc_start: 0.8498 (m-80) cc_final: 0.8237 (m-80) REVERT: N 87 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7400 (mtpp) REVERT: N 89 GLU cc_start: 0.7603 (pt0) cc_final: 0.7057 (pp20) REVERT: N 90 ASP cc_start: 0.8358 (m-30) cc_final: 0.8103 (m-30) REVERT: N 105 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7572 (ttp-110) REVERT: R 127 CYS cc_start: 0.4619 (OUTLIER) cc_final: 0.4069 (p) REVERT: R 134 LYS cc_start: 0.6262 (ttpt) cc_final: 0.6043 (mmtt) REVERT: R 182 PHE cc_start: 0.7461 (t80) cc_final: 0.6922 (t80) REVERT: R 213 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6502 (mttt) REVERT: R 251 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.7091 (t-170) REVERT: R 253 MET cc_start: 0.8004 (ttt) cc_final: 0.7558 (ttp) REVERT: R 332 MET cc_start: 0.6763 (mmp) cc_final: 0.6321 (pmm) REVERT: R 370 HIS cc_start: 0.6610 (m-70) cc_final: 0.6204 (m90) REVERT: R 381 SER cc_start: 0.8028 (t) cc_final: 0.7655 (m) outliers start: 28 outliers final: 14 residues processed: 154 average time/residue: 0.5818 time to fit residues: 95.3867 Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.180928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138499 restraints weight = 10366.662| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.24 r_work: 0.3265 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.117 Angle : 0.492 6.354 12457 Z= 0.262 Chirality : 0.041 0.149 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.342 55.549 1290 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.52 % Allowed : 15.34 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.13 (0.25), residues: 1176 helix: 1.81 (0.25), residues: 466 sheet: -0.91 (0.32), residues: 220 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.011 0.001 TYR R 278 PHE 0.013 0.001 PHE A 212 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9154) covalent geometry : angle 0.49184 (12439) SS BOND : bond 0.00177 ( 9) SS BOND : angle 0.65432 ( 18) hydrogen bonds : bond 0.03201 ( 453) hydrogen bonds : angle 4.10221 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.351 Fit side-chains REVERT: A 21 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: A 31 GLN cc_start: 0.8436 (mt0) cc_final: 0.7633 (tp-100) REVERT: A 266 LEU cc_start: 0.8727 (tp) cc_final: 0.8398 (tp) REVERT: A 333 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.3508 (ttt180) REVERT: B 97 SER cc_start: 0.8192 (p) cc_final: 0.7733 (t) REVERT: B 127 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8540 (mmtm) REVERT: B 325 MET cc_start: 0.8429 (tpp) cc_final: 0.7959 (tpt) REVERT: E 167 ARG cc_start: 0.4740 (mpt180) cc_final: 0.3790 (mmm-85) REVERT: N 5 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7212 (tp40) REVERT: N 65 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: N 73 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7260 (t0) REVERT: N 80 TYR cc_start: 0.8536 (m-80) cc_final: 0.8294 (m-80) REVERT: N 87 LYS cc_start: 0.8011 (mtpm) cc_final: 0.7326 (mtpp) REVERT: N 89 GLU cc_start: 0.7722 (pt0) cc_final: 0.7195 (pp20) REVERT: N 90 ASP cc_start: 0.8359 (m-30) cc_final: 0.8150 (m-30) REVERT: N 105 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7593 (ttp-110) REVERT: R 127 CYS cc_start: 0.4358 (OUTLIER) cc_final: 0.3891 (p) REVERT: R 134 LYS cc_start: 0.6313 (ttpt) cc_final: 0.6025 (mmtt) REVERT: R 182 PHE cc_start: 0.7548 (t80) cc_final: 0.7036 (t80) REVERT: R 213 LYS cc_start: 0.7115 (mtmt) cc_final: 0.6608 (mttt) REVERT: R 253 MET cc_start: 0.8043 (ttt) cc_final: 0.7716 (ttp) REVERT: R 332 MET cc_start: 0.6787 (mmp) cc_final: 0.6316 (pmm) REVERT: R 370 HIS cc_start: 0.6616 (m-70) cc_final: 0.6203 (m90) REVERT: R 381 SER cc_start: 0.8114 (t) cc_final: 0.7746 (m) outliers start: 31 outliers final: 16 residues processed: 147 average time/residue: 0.6065 time to fit residues: 94.7258 Evaluate side-chains 149 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN R 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122970 restraints weight = 10307.873| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.89 r_work: 0.3259 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9163 Z= 0.154 Angle : 0.529 7.189 12457 Z= 0.280 Chirality : 0.042 0.169 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.460 54.583 1290 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 16.14 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.13 (0.25), residues: 1176 helix: 1.79 (0.25), residues: 467 sheet: -1.03 (0.31), residues: 223 loop : -1.03 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.014 0.001 TYR B 105 PHE 0.014 0.001 PHE A 212 TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9154) covalent geometry : angle 0.52862 (12439) SS BOND : bond 0.00184 ( 9) SS BOND : angle 0.68390 ( 18) hydrogen bonds : bond 0.03412 ( 453) hydrogen bonds : angle 4.16066 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7635 (mmmm) cc_final: 0.7303 (mmmm) REVERT: A 21 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 31 GLN cc_start: 0.8307 (mt0) cc_final: 0.7508 (tp-100) REVERT: A 266 LEU cc_start: 0.8728 (tp) cc_final: 0.8396 (tp) REVERT: A 333 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.3505 (ttt180) REVERT: B 97 SER cc_start: 0.8171 (p) cc_final: 0.7729 (t) REVERT: B 127 LYS cc_start: 0.8759 (mmpt) cc_final: 0.8529 (mmtm) REVERT: B 325 MET cc_start: 0.8409 (tpp) cc_final: 0.7924 (tpt) REVERT: E 151 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5141 (mt) REVERT: E 167 ARG cc_start: 0.4855 (mpt180) cc_final: 0.3843 (mmm-85) REVERT: N 5 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7260 (tp40) REVERT: N 65 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: N 73 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7162 (t0) REVERT: N 80 TYR cc_start: 0.8556 (m-80) cc_final: 0.8266 (m-80) REVERT: N 87 LYS cc_start: 0.8113 (mtpm) cc_final: 0.7003 (mttt) REVERT: N 89 GLU cc_start: 0.7641 (pt0) cc_final: 0.7127 (pp20) REVERT: N 90 ASP cc_start: 0.8298 (m-30) cc_final: 0.8074 (m-30) REVERT: R 127 CYS cc_start: 0.4259 (OUTLIER) cc_final: 0.3799 (p) REVERT: R 134 LYS cc_start: 0.6310 (ttpt) cc_final: 0.6048 (mmtt) REVERT: R 213 LYS cc_start: 0.7121 (mtmt) cc_final: 0.6627 (mttt) REVERT: R 253 MET cc_start: 0.8013 (ttt) cc_final: 0.7694 (ttp) REVERT: R 332 MET cc_start: 0.6842 (mmp) cc_final: 0.6371 (pmm) REVERT: R 370 HIS cc_start: 0.6602 (m-70) cc_final: 0.6194 (m90) REVERT: R 381 SER cc_start: 0.8131 (t) cc_final: 0.7726 (m) outliers start: 35 outliers final: 18 residues processed: 152 average time/residue: 0.5826 time to fit residues: 94.3671 Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.181103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.139275 restraints weight = 10414.026| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.03 r_work: 0.3290 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9163 Z= 0.106 Angle : 0.490 6.433 12457 Z= 0.260 Chirality : 0.041 0.147 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.285 54.100 1290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.41 % Allowed : 17.27 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.34 (0.25), residues: 1176 helix: 1.91 (0.25), residues: 465 sheet: -0.76 (0.32), residues: 215 loop : -0.92 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.022 0.001 TYR P 31 PHE 0.014 0.001 PHE R 228 TRP 0.016 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9154) covalent geometry : angle 0.49013 (12439) SS BOND : bond 0.00161 ( 9) SS BOND : angle 0.60631 ( 18) hydrogen bonds : bond 0.03068 ( 453) hydrogen bonds : angle 4.04971 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.247 Fit side-chains REVERT: A 17 LYS cc_start: 0.7653 (mmmm) cc_final: 0.7413 (mmmm) REVERT: A 21 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 31 GLN cc_start: 0.8331 (mt0) cc_final: 0.7567 (tp-100) REVERT: A 333 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.3549 (ttt180) REVERT: B 97 SER cc_start: 0.8199 (p) cc_final: 0.7816 (t) REVERT: B 127 LYS cc_start: 0.8785 (mmpt) cc_final: 0.8571 (mmtm) REVERT: B 325 MET cc_start: 0.8408 (tpp) cc_final: 0.7847 (tpt) REVERT: E 151 ILE cc_start: 0.5362 (OUTLIER) cc_final: 0.5075 (mt) REVERT: E 167 ARG cc_start: 0.4730 (mpt180) cc_final: 0.3821 (mmm-85) REVERT: N 65 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8104 (ttpt) REVERT: N 73 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7208 (t0) REVERT: N 80 TYR cc_start: 0.8527 (m-80) cc_final: 0.8277 (m-80) REVERT: N 87 LYS cc_start: 0.8016 (mtpm) cc_final: 0.7347 (mtpp) REVERT: N 89 GLU cc_start: 0.7667 (pt0) cc_final: 0.7243 (pp20) REVERT: N 90 ASP cc_start: 0.8289 (m-30) cc_final: 0.8071 (m-30) REVERT: R 127 CYS cc_start: 0.4053 (OUTLIER) cc_final: 0.3601 (p) REVERT: R 134 LYS cc_start: 0.6350 (ttpt) cc_final: 0.6015 (mmtt) REVERT: R 182 PHE cc_start: 0.7622 (t80) cc_final: 0.7130 (t80) REVERT: R 213 LYS cc_start: 0.7157 (mtmt) cc_final: 0.6668 (mttt) REVERT: R 253 MET cc_start: 0.8017 (ttt) cc_final: 0.7701 (ttp) REVERT: R 332 MET cc_start: 0.6830 (mmp) cc_final: 0.6386 (pmm) REVERT: R 370 HIS cc_start: 0.6593 (m-70) cc_final: 0.6227 (m90) REVERT: R 373 MET cc_start: 0.7281 (ttp) cc_final: 0.6905 (ttp) REVERT: R 381 SER cc_start: 0.8130 (t) cc_final: 0.7745 (m) outliers start: 30 outliers final: 16 residues processed: 152 average time/residue: 0.5673 time to fit residues: 91.7038 Evaluate side-chains 150 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN G 59 ASN N 39 GLN R 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.176449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119274 restraints weight = 10291.412| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.89 r_work: 0.3223 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9163 Z= 0.227 Angle : 0.596 6.717 12457 Z= 0.316 Chirality : 0.045 0.161 1438 Planarity : 0.004 0.037 1597 Dihedral : 4.728 55.763 1290 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.52 % Allowed : 17.95 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.12 (0.25), residues: 1176 helix: 1.70 (0.25), residues: 467 sheet: -0.98 (0.32), residues: 216 loop : -0.97 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.019 0.002 TYR B 105 PHE 0.014 0.002 PHE A 212 TRP 0.017 0.002 TRP B 99 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9154) covalent geometry : angle 0.59596 (12439) SS BOND : bond 0.00208 ( 9) SS BOND : angle 0.84848 ( 18) hydrogen bonds : bond 0.03798 ( 453) hydrogen bonds : angle 4.27699 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.353 Fit side-chains REVERT: A 17 LYS cc_start: 0.7522 (mmmm) cc_final: 0.7307 (mmmm) REVERT: A 21 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 31 GLN cc_start: 0.8308 (mt0) cc_final: 0.7505 (tp-100) REVERT: A 266 LEU cc_start: 0.8669 (tp) cc_final: 0.8325 (tp) REVERT: A 333 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.3461 (ttt180) REVERT: B 127 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8524 (mmtm) REVERT: B 325 MET cc_start: 0.8409 (tpp) cc_final: 0.7962 (tpt) REVERT: E 151 ILE cc_start: 0.5364 (OUTLIER) cc_final: 0.5104 (mt) REVERT: E 167 ARG cc_start: 0.4802 (mpt180) cc_final: 0.3761 (mmm-85) REVERT: G 47 GLU cc_start: 0.8356 (pt0) cc_final: 0.8058 (pt0) REVERT: N 5 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7375 (tp40) REVERT: N 65 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: N 80 TYR cc_start: 0.8593 (m-80) cc_final: 0.8324 (m-80) REVERT: N 87 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7425 (mtpp) REVERT: N 89 GLU cc_start: 0.7543 (pt0) cc_final: 0.7124 (pp20) REVERT: N 105 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7603 (ttp-110) REVERT: R 127 CYS cc_start: 0.3968 (OUTLIER) cc_final: 0.3690 (p) REVERT: R 134 LYS cc_start: 0.6351 (ttpt) cc_final: 0.6032 (mmtt) REVERT: R 165 TYR cc_start: 0.6426 (t80) cc_final: 0.6099 (t80) REVERT: R 253 MET cc_start: 0.8010 (ttt) cc_final: 0.7786 (ttt) REVERT: R 332 MET cc_start: 0.6990 (mmp) cc_final: 0.6253 (pmm) REVERT: R 370 HIS cc_start: 0.6600 (m-70) cc_final: 0.6204 (m90) REVERT: R 381 SER cc_start: 0.8199 (t) cc_final: 0.7772 (m) outliers start: 31 outliers final: 19 residues processed: 148 average time/residue: 0.6157 time to fit residues: 96.5838 Evaluate side-chains 147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 175 GLN G 59 ASN R 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.178687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121904 restraints weight = 10339.111| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.96 r_work: 0.3254 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.141 Angle : 0.535 6.954 12457 Z= 0.283 Chirality : 0.042 0.145 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.524 54.537 1290 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.18 % Allowed : 18.98 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.26 (0.25), residues: 1176 helix: 1.80 (0.25), residues: 465 sheet: -0.91 (0.32), residues: 217 loop : -0.86 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.015 0.001 TYR P 31 PHE 0.014 0.001 PHE A 212 TRP 0.017 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9154) covalent geometry : angle 0.53500 (12439) SS BOND : bond 0.00185 ( 9) SS BOND : angle 0.68968 ( 18) hydrogen bonds : bond 0.03369 ( 453) hydrogen bonds : angle 4.17914 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7454 (mmmm) cc_final: 0.7210 (mmmm) REVERT: A 21 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: A 31 GLN cc_start: 0.8310 (mt0) cc_final: 0.7486 (tp-100) REVERT: A 266 LEU cc_start: 0.8672 (tp) cc_final: 0.8313 (tp) REVERT: A 333 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.3540 (ttt180) REVERT: B 127 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8510 (mmtm) REVERT: B 325 MET cc_start: 0.8379 (tpp) cc_final: 0.7831 (tpt) REVERT: E 151 ILE cc_start: 0.5406 (OUTLIER) cc_final: 0.5122 (mt) REVERT: E 167 ARG cc_start: 0.4685 (mpt180) cc_final: 0.3681 (mmm-85) REVERT: G 47 GLU cc_start: 0.8294 (pt0) cc_final: 0.8012 (pt0) REVERT: N 5 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7236 (tp40) REVERT: N 80 TYR cc_start: 0.8611 (m-80) cc_final: 0.8346 (m-80) REVERT: N 87 LYS cc_start: 0.7975 (mtpm) cc_final: 0.7237 (mttt) REVERT: N 89 GLU cc_start: 0.7438 (pt0) cc_final: 0.7054 (pp20) REVERT: N 105 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7493 (ttp-110) REVERT: R 127 CYS cc_start: 0.3961 (OUTLIER) cc_final: 0.3682 (p) REVERT: R 134 LYS cc_start: 0.6329 (ttpt) cc_final: 0.6015 (mmtt) REVERT: R 165 TYR cc_start: 0.6353 (t80) cc_final: 0.6076 (t80) REVERT: R 202 GLN cc_start: 0.6228 (mm110) cc_final: 0.5997 (mm-40) REVERT: R 213 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6470 (mttt) REVERT: R 215 SER cc_start: 0.6397 (OUTLIER) cc_final: 0.5877 (p) REVERT: R 253 MET cc_start: 0.7961 (ttt) cc_final: 0.7742 (ttt) REVERT: R 332 MET cc_start: 0.6995 (mmp) cc_final: 0.6219 (pmm) REVERT: R 370 HIS cc_start: 0.6557 (m-70) cc_final: 0.6189 (m90) REVERT: R 381 SER cc_start: 0.8140 (t) cc_final: 0.7701 (m) outliers start: 28 outliers final: 19 residues processed: 143 average time/residue: 0.5646 time to fit residues: 85.9330 Evaluate side-chains 146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN R 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122765 restraints weight = 10354.744| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.00 r_work: 0.3269 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9163 Z= 0.128 Angle : 0.523 7.392 12457 Z= 0.277 Chirality : 0.042 0.143 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.435 53.842 1290 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.95 % Allowed : 19.20 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.35 (0.25), residues: 1176 helix: 1.88 (0.25), residues: 465 sheet: -0.84 (0.32), residues: 215 loop : -0.84 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.013 0.001 TYR P 31 PHE 0.038 0.001 PHE A 222 TRP 0.019 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9154) covalent geometry : angle 0.52327 (12439) SS BOND : bond 0.00175 ( 9) SS BOND : angle 0.64975 ( 18) hydrogen bonds : bond 0.03210 ( 453) hydrogen bonds : angle 4.10818 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7412 (mmmm) cc_final: 0.7189 (mmmm) REVERT: A 21 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 31 GLN cc_start: 0.8285 (mt0) cc_final: 0.7484 (tp-100) REVERT: A 333 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.3534 (ttt180) REVERT: B 127 LYS cc_start: 0.8726 (mmpt) cc_final: 0.8510 (mmtm) REVERT: B 325 MET cc_start: 0.8405 (tpp) cc_final: 0.7823 (tpt) REVERT: E 151 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5203 (mt) REVERT: E 167 ARG cc_start: 0.4536 (mpt180) cc_final: 0.3691 (mmm-85) REVERT: G 47 GLU cc_start: 0.8266 (pt0) cc_final: 0.8038 (pt0) REVERT: N 5 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7232 (tp40) REVERT: N 73 ASP cc_start: 0.7624 (t70) cc_final: 0.7232 (t0) REVERT: N 80 TYR cc_start: 0.8618 (m-80) cc_final: 0.8404 (m-80) REVERT: N 87 LYS cc_start: 0.7987 (mtpm) cc_final: 0.7635 (mttt) REVERT: N 89 GLU cc_start: 0.7453 (pt0) cc_final: 0.6974 (pp20) REVERT: R 127 CYS cc_start: 0.3908 (OUTLIER) cc_final: 0.3606 (p) REVERT: R 134 LYS cc_start: 0.6385 (ttpt) cc_final: 0.6057 (mmtt) REVERT: R 165 TYR cc_start: 0.6374 (t80) cc_final: 0.6070 (t80) REVERT: R 202 GLN cc_start: 0.6214 (mm110) cc_final: 0.5935 (mm-40) REVERT: R 213 LYS cc_start: 0.7006 (mtpt) cc_final: 0.6485 (mttt) REVERT: R 215 SER cc_start: 0.6377 (OUTLIER) cc_final: 0.5859 (p) REVERT: R 253 MET cc_start: 0.7912 (ttt) cc_final: 0.7688 (ttt) REVERT: R 332 MET cc_start: 0.7003 (mmp) cc_final: 0.6265 (pmm) REVERT: R 370 HIS cc_start: 0.6541 (m-70) cc_final: 0.6168 (m90) REVERT: R 381 SER cc_start: 0.8119 (t) cc_final: 0.7678 (m) outliers start: 26 outliers final: 20 residues processed: 149 average time/residue: 0.5800 time to fit residues: 92.0936 Evaluate side-chains 155 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 281 ASN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124632 restraints weight = 10220.137| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.73 r_work: 0.3313 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9163 Z= 0.107 Angle : 0.506 6.684 12457 Z= 0.268 Chirality : 0.041 0.148 1438 Planarity : 0.003 0.036 1597 Dihedral : 4.340 53.255 1290 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.84 % Allowed : 19.55 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 0.52 (0.25), residues: 1176 helix: 2.04 (0.25), residues: 459 sheet: -0.67 (0.32), residues: 214 loop : -0.77 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.013 0.001 TYR P 31 PHE 0.023 0.001 PHE A 222 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9154) covalent geometry : angle 0.50577 (12439) SS BOND : bond 0.00139 ( 9) SS BOND : angle 0.62838 ( 18) hydrogen bonds : bond 0.03058 ( 453) hydrogen bonds : angle 4.04707 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.88 seconds wall clock time: 64 minutes 23.68 seconds (3863.68 seconds total)