Starting phenix.real_space_refine on Thu Mar 13 15:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6v_25729/03_2025/7t6v_25729.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.048 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 5734 2.51 5 N 1506 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.61 Number of scatterers: 8949 At special positions: 0 Unit cell: (106.029, 106.029, 132.804, 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 1645 8.00 N 1506 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.08 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 87 removed outlier: 4.019A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.584A pdb=" N ASP R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.079A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 3.590A pdb=" N PHE R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 208 removed outlier: 3.535A pdb=" N THR R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.855A pdb=" N LEU R 243 " --> pdb=" O PRO R 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.647A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.755A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.898A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.551A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.005A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.001A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.538A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.978A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.541A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.720A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.561A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.099A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.546A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.698A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.850A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.925A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.748A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.825A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.770A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.677A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.442A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.972A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.345A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.882A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1578 1.32 - 1.45: 2386 1.45 - 1.57: 5081 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9139 Sorted by residual: bond pdb=" CA SER R 84 " pdb=" CB SER R 84 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.56e-02 4.11e+03 1.40e+01 bond pdb=" CA SER R 112 " pdb=" CB SER R 112 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.55e-02 4.16e+03 1.32e+01 bond pdb=" CA SER R 73 " pdb=" CB SER R 73 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" N ILE R 195 " pdb=" CA ILE R 195 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" CA SER R 211 " pdb=" CB SER R 211 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 9134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11575 2.39 - 4.77: 738 4.77 - 7.16: 52 7.16 - 9.55: 5 9.55 - 11.94: 3 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C PRO R 92 " pdb=" CA PRO R 92 " pdb=" CB PRO R 92 " ideal model delta sigma weight residual 112.64 100.70 11.94 1.43e+00 4.89e-01 6.97e+01 angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 120.19 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" C PHE R 161 " pdb=" CA PHE R 161 " pdb=" CB PHE R 161 " ideal model delta sigma weight residual 110.88 101.62 9.26 1.57e+00 4.06e-01 3.48e+01 angle pdb=" C LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta sigma weight residual 110.85 120.76 -9.91 1.70e+00 3.46e-01 3.40e+01 angle pdb=" C TYR R 302 " pdb=" N VAL R 303 " pdb=" CA VAL R 303 " ideal model delta sigma weight residual 122.77 116.71 6.06 1.05e+00 9.07e-01 3.33e+01 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 4918 16.49 - 32.99: 396 32.99 - 49.48: 67 49.48 - 65.97: 10 65.97 - 82.46: 8 Dihedral angle restraints: 5399 sinusoidal: 2108 harmonic: 3291 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -163.28 77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 163.97 -70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" C LYS R 99 " pdb=" N LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta harmonic sigma weight residual -122.60 -138.12 15.52 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1078 0.102 - 0.205: 303 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LYS R 99 " pdb=" N LYS R 99 " pdb=" C LYS R 99 " pdb=" CB LYS R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA ASP R 106 " pdb=" N ASP R 106 " pdb=" C ASP R 106 " pdb=" CB ASP R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1409 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 205 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C ARG R 205 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG R 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 299 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO R 299 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO R 299 " -0.023 2.00e-02 2.50e+03 pdb=" N MET R 300 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 183 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP R 183 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 183 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 183 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 183 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 183 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 183 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 183 " 0.000 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 85 2.62 - 3.19: 7877 3.19 - 3.76: 13170 3.76 - 4.33: 18862 4.33 - 4.90: 31124 Nonbonded interactions: 71118 Sorted by model distance: nonbonded pdb=" O ILE L 4 " pdb=" OXT ILE L 5 " model vdw 2.047 3.040 nonbonded pdb=" O THR A 262 " pdb=" NZ LYS A 317 " model vdw 2.268 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.319 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.325 3.040 ... (remaining 71113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.011 0.058 9139 Z= 0.696 Angle : 1.265 11.936 12373 Z= 0.933 Chirality : 0.089 0.512 1412 Planarity : 0.006 0.054 1553 Dihedral : 12.331 82.461 3271 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1123 helix: 2.04 (0.24), residues: 402 sheet: 0.60 (0.30), residues: 278 loop : -0.19 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 183 HIS 0.012 0.002 HIS R 136 PHE 0.033 0.002 PHE B 235 TYR 0.022 0.002 TYR R 302 ARG 0.008 0.001 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: R 77 THR cc_start: 0.8744 (t) cc_final: 0.8414 (p) REVERT: R 103 ILE cc_start: 0.8263 (mm) cc_final: 0.8023 (mt) REVERT: R 161 PHE cc_start: 0.8002 (m-80) cc_final: 0.7785 (m-80) REVERT: R 229 HIS cc_start: 0.7711 (t-90) cc_final: 0.7482 (t-170) REVERT: R 278 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8611 (mmmt) REVERT: R 281 ASP cc_start: 0.7515 (m-30) cc_final: 0.7149 (m-30) REVERT: A 209 LYS cc_start: 0.8085 (mttt) cc_final: 0.7885 (mttt) REVERT: A 271 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7851 (ttpp) REVERT: A 275 GLU cc_start: 0.8400 (tp30) cc_final: 0.8074 (tp30) REVERT: A 309 ASP cc_start: 0.8277 (t70) cc_final: 0.7985 (t70) REVERT: B 45 MET cc_start: 0.8520 (mtt) cc_final: 0.8295 (mtt) REVERT: B 215 GLU cc_start: 0.7986 (mp0) cc_final: 0.7173 (mp0) REVERT: B 233 CYS cc_start: 0.7807 (t) cc_final: 0.7568 (t) REVERT: B 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7333 (t0) REVERT: B 259 GLN cc_start: 0.7507 (tt0) cc_final: 0.7294 (tt0) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.2873 time to fit residues: 98.6807 Evaluate side-chains 239 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 119 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089327 restraints weight = 14720.096| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.43 r_work: 0.3133 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9139 Z= 0.254 Angle : 0.597 9.520 12373 Z= 0.319 Chirality : 0.044 0.188 1412 Planarity : 0.005 0.047 1553 Dihedral : 4.774 54.325 1245 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.85 % Allowed : 10.15 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1123 helix: 1.98 (0.25), residues: 406 sheet: 0.61 (0.30), residues: 267 loop : -0.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 95 HIS 0.005 0.001 HIS B 311 PHE 0.023 0.002 PHE R 161 TYR 0.019 0.001 TYR R 175 ARG 0.005 0.001 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 ARG cc_start: 0.9137 (tpp80) cc_final: 0.8928 (tpp80) REVERT: R 74 PHE cc_start: 0.8196 (t80) cc_final: 0.7889 (t80) REVERT: R 77 THR cc_start: 0.8845 (t) cc_final: 0.8620 (p) REVERT: R 83 VAL cc_start: 0.8684 (t) cc_final: 0.8469 (m) REVERT: R 91 TRP cc_start: 0.9004 (t-100) cc_final: 0.8577 (t-100) REVERT: R 106 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (t0) REVERT: R 189 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7994 (tm-30) REVERT: R 235 LYS cc_start: 0.8589 (pttp) cc_final: 0.8217 (pttp) REVERT: R 241 ARG cc_start: 0.7120 (tmt170) cc_final: 0.6860 (ttp-170) REVERT: R 312 ARG cc_start: 0.8341 (tpp80) cc_final: 0.7988 (tpp80) REVERT: A 197 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8065 (mtpp) REVERT: A 209 LYS cc_start: 0.8687 (mttt) cc_final: 0.8483 (mttt) REVERT: A 275 GLU cc_start: 0.8602 (tp30) cc_final: 0.8326 (tp30) REVERT: A 298 GLU cc_start: 0.7261 (tt0) cc_final: 0.7012 (tt0) REVERT: A 309 ASP cc_start: 0.8430 (t70) cc_final: 0.8050 (t70) REVERT: B 10 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 212 ASP cc_start: 0.8482 (t0) cc_final: 0.7667 (t0) REVERT: B 215 GLU cc_start: 0.8652 (mp0) cc_final: 0.8025 (mp0) REVERT: B 233 CYS cc_start: 0.8748 (t) cc_final: 0.8474 (t) REVERT: B 258 ASP cc_start: 0.8254 (t0) cc_final: 0.7867 (t0) REVERT: B 294 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7936 (t) outliers start: 18 outliers final: 9 residues processed: 265 average time/residue: 0.2752 time to fit residues: 93.1859 Evaluate side-chains 248 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 0.0040 chunk 101 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090170 restraints weight = 14721.795| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.47 r_work: 0.3146 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9139 Z= 0.178 Angle : 0.543 10.419 12373 Z= 0.283 Chirality : 0.042 0.180 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.606 58.815 1243 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.54 % Allowed : 13.95 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1123 helix: 1.96 (0.26), residues: 407 sheet: 0.48 (0.30), residues: 266 loop : -0.24 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 95 HIS 0.004 0.001 HIS A 188 PHE 0.026 0.001 PHE R 180 TYR 0.020 0.001 TYR A 296 ARG 0.009 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8665 (t) cc_final: 0.8435 (m) REVERT: R 87 MET cc_start: 0.8711 (mtt) cc_final: 0.8394 (mtm) REVERT: R 91 TRP cc_start: 0.9003 (t-100) cc_final: 0.8497 (t-100) REVERT: R 189 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7976 (tm-30) REVERT: R 231 LYS cc_start: 0.8867 (mttm) cc_final: 0.8572 (ttmm) REVERT: R 241 ARG cc_start: 0.7029 (tmt170) cc_final: 0.6738 (ttp-170) REVERT: R 310 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8303 (mtm110) REVERT: R 312 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8145 (tpp80) REVERT: A 197 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8134 (mtpp) REVERT: A 209 LYS cc_start: 0.8559 (mttt) cc_final: 0.8354 (mttt) REVERT: A 275 GLU cc_start: 0.8668 (tp30) cc_final: 0.8327 (tp30) REVERT: A 298 GLU cc_start: 0.7335 (tt0) cc_final: 0.7064 (tt0) REVERT: A 309 ASP cc_start: 0.8374 (t70) cc_final: 0.7967 (t70) REVERT: B 13 GLN cc_start: 0.8615 (tt0) cc_final: 0.8072 (tm-30) REVERT: B 212 ASP cc_start: 0.8464 (t0) cc_final: 0.7541 (t0) REVERT: B 215 GLU cc_start: 0.8634 (mp0) cc_final: 0.7942 (mp0) REVERT: B 233 CYS cc_start: 0.8727 (t) cc_final: 0.8436 (t) REVERT: B 258 ASP cc_start: 0.8258 (t0) cc_final: 0.7834 (t0) REVERT: B 294 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7911 (t) REVERT: E 67 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7773 (ptt-90) outliers start: 15 outliers final: 8 residues processed: 265 average time/residue: 0.2791 time to fit residues: 94.6785 Evaluate side-chains 253 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.090287 restraints weight = 14574.769| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.43 r_work: 0.3148 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9139 Z= 0.175 Angle : 0.524 8.653 12373 Z= 0.273 Chirality : 0.042 0.183 1412 Planarity : 0.004 0.040 1553 Dihedral : 4.382 50.728 1243 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.64 % Allowed : 14.77 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1123 helix: 1.98 (0.26), residues: 409 sheet: 0.41 (0.30), residues: 266 loop : -0.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 95 HIS 0.003 0.001 HIS A 188 PHE 0.020 0.001 PHE R 161 TYR 0.021 0.001 TYR A 296 ARG 0.010 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8622 (t) cc_final: 0.8380 (m) REVERT: R 87 MET cc_start: 0.8744 (mtt) cc_final: 0.8431 (mtm) REVERT: R 91 TRP cc_start: 0.8989 (t-100) cc_final: 0.8786 (t-100) REVERT: R 189 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7981 (tm-30) REVERT: R 235 LYS cc_start: 0.8585 (pttp) cc_final: 0.8216 (pttp) REVERT: R 241 ARG cc_start: 0.7069 (tmt170) cc_final: 0.6736 (ttp-170) REVERT: R 310 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8253 (mtm110) REVERT: A 189 PHE cc_start: 0.8686 (p90) cc_final: 0.8305 (p90) REVERT: A 197 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8133 (mtpp) REVERT: A 275 GLU cc_start: 0.8672 (tp30) cc_final: 0.8346 (tp30) REVERT: A 298 GLU cc_start: 0.7341 (tt0) cc_final: 0.7050 (tt0) REVERT: A 309 ASP cc_start: 0.8371 (t70) cc_final: 0.7855 (t70) REVERT: B 212 ASP cc_start: 0.8475 (t0) cc_final: 0.7501 (t0) REVERT: B 215 GLU cc_start: 0.8692 (mp0) cc_final: 0.7944 (mp0) REVERT: B 233 CYS cc_start: 0.8711 (t) cc_final: 0.8400 (t) REVERT: B 258 ASP cc_start: 0.8263 (t0) cc_final: 0.7857 (t0) REVERT: B 294 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7915 (t) REVERT: B 336 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8366 (mp) REVERT: E 234 GLU cc_start: 0.7751 (pm20) cc_final: 0.6893 (pm20) outliers start: 16 outliers final: 10 residues processed: 267 average time/residue: 0.2785 time to fit residues: 95.0658 Evaluate side-chains 252 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090577 restraints weight = 14555.412| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.44 r_work: 0.3155 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.170 Angle : 0.530 8.735 12373 Z= 0.273 Chirality : 0.041 0.185 1412 Planarity : 0.004 0.044 1553 Dihedral : 4.303 48.918 1243 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.54 % Allowed : 16.72 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1123 helix: 2.01 (0.26), residues: 409 sheet: 0.37 (0.29), residues: 275 loop : -0.19 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE R 180 TYR 0.020 0.001 TYR A 296 ARG 0.010 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8626 (t) cc_final: 0.8379 (m) REVERT: R 87 MET cc_start: 0.8704 (mtt) cc_final: 0.8387 (mtm) REVERT: R 189 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7920 (tm-30) REVERT: R 203 ILE cc_start: 0.8856 (tt) cc_final: 0.8468 (mm) REVERT: R 235 LYS cc_start: 0.8589 (pttp) cc_final: 0.8216 (pttp) REVERT: R 241 ARG cc_start: 0.7089 (tmt170) cc_final: 0.6863 (ttt180) REVERT: R 310 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8305 (mtm110) REVERT: A 189 PHE cc_start: 0.8677 (p90) cc_final: 0.8252 (p90) REVERT: A 197 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8079 (mtpp) REVERT: A 232 LEU cc_start: 0.8810 (mt) cc_final: 0.8566 (mp) REVERT: A 275 GLU cc_start: 0.8643 (tp30) cc_final: 0.8316 (tp30) REVERT: A 298 GLU cc_start: 0.7335 (tt0) cc_final: 0.7036 (tt0) REVERT: A 309 ASP cc_start: 0.8430 (t70) cc_final: 0.8011 (t0) REVERT: B 212 ASP cc_start: 0.8501 (t0) cc_final: 0.7556 (t0) REVERT: B 215 GLU cc_start: 0.8674 (mp0) cc_final: 0.7910 (mp0) REVERT: B 233 CYS cc_start: 0.8713 (t) cc_final: 0.8407 (t) REVERT: B 258 ASP cc_start: 0.8283 (t0) cc_final: 0.7898 (t0) REVERT: B 294 CYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 336 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8378 (mp) REVERT: E 128 MET cc_start: 0.9188 (mmm) cc_final: 0.8211 (mmm) REVERT: E 132 THR cc_start: 0.8432 (m) cc_final: 0.8111 (t) REVERT: E 234 GLU cc_start: 0.7801 (pm20) cc_final: 0.7006 (pm20) outliers start: 15 outliers final: 12 residues processed: 252 average time/residue: 0.2768 time to fit residues: 90.7046 Evaluate side-chains 253 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090301 restraints weight = 14585.068| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.42 r_work: 0.3148 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9139 Z= 0.178 Angle : 0.526 8.666 12373 Z= 0.272 Chirality : 0.041 0.191 1412 Planarity : 0.004 0.048 1553 Dihedral : 4.238 46.741 1243 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.05 % Allowed : 17.03 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1123 helix: 2.02 (0.26), residues: 409 sheet: 0.32 (0.29), residues: 286 loop : -0.15 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.027 0.001 PHE R 163 TYR 0.021 0.001 TYR A 296 ARG 0.011 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: R 54 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7838 (mmm160) REVERT: R 83 VAL cc_start: 0.8646 (t) cc_final: 0.8382 (m) REVERT: R 87 MET cc_start: 0.8711 (mtt) cc_final: 0.8401 (mtm) REVERT: R 189 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7914 (tm-30) REVERT: R 203 ILE cc_start: 0.8859 (tt) cc_final: 0.8518 (mm) REVERT: R 235 LYS cc_start: 0.8571 (pttp) cc_final: 0.8202 (pttp) REVERT: R 310 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8494 (mtm-85) REVERT: A 189 PHE cc_start: 0.8666 (p90) cc_final: 0.8259 (p90) REVERT: A 197 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7988 (mttm) REVERT: A 232 LEU cc_start: 0.8804 (mt) cc_final: 0.8595 (mp) REVERT: A 275 GLU cc_start: 0.8621 (tp30) cc_final: 0.8284 (tp30) REVERT: A 298 GLU cc_start: 0.7331 (tt0) cc_final: 0.7023 (tt0) REVERT: A 309 ASP cc_start: 0.8378 (t70) cc_final: 0.7965 (t0) REVERT: B 161 SER cc_start: 0.8732 (p) cc_final: 0.8345 (p) REVERT: B 163 ASP cc_start: 0.7551 (p0) cc_final: 0.7106 (p0) REVERT: B 212 ASP cc_start: 0.8494 (t0) cc_final: 0.7559 (t0) REVERT: B 215 GLU cc_start: 0.8638 (mp0) cc_final: 0.7900 (mp0) REVERT: B 233 CYS cc_start: 0.8693 (t) cc_final: 0.8390 (t) REVERT: B 258 ASP cc_start: 0.8265 (t0) cc_final: 0.7901 (t0) REVERT: B 294 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7915 (t) REVERT: B 336 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8391 (mp) REVERT: E 132 THR cc_start: 0.8379 (m) cc_final: 0.8049 (t) REVERT: E 234 GLU cc_start: 0.7797 (pm20) cc_final: 0.7031 (pm20) outliers start: 20 outliers final: 15 residues processed: 258 average time/residue: 0.3139 time to fit residues: 105.6010 Evaluate side-chains 263 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0170 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090608 restraints weight = 14760.636| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.45 r_work: 0.3151 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9139 Z= 0.165 Angle : 0.530 8.879 12373 Z= 0.272 Chirality : 0.041 0.195 1412 Planarity : 0.004 0.051 1553 Dihedral : 4.191 44.719 1243 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.15 % Allowed : 17.64 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1123 helix: 2.02 (0.26), residues: 410 sheet: 0.25 (0.29), residues: 291 loop : -0.12 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE R 180 TYR 0.020 0.001 TYR A 296 ARG 0.012 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: R 54 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7837 (mmm160) REVERT: R 83 VAL cc_start: 0.8653 (t) cc_final: 0.8396 (m) REVERT: R 170 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: R 189 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7911 (tm-30) REVERT: R 203 ILE cc_start: 0.8874 (tt) cc_final: 0.8560 (mm) REVERT: R 229 HIS cc_start: 0.8110 (t70) cc_final: 0.7863 (t70) REVERT: R 235 LYS cc_start: 0.8604 (pttp) cc_final: 0.8255 (pttp) REVERT: R 252 ILE cc_start: 0.8740 (mm) cc_final: 0.8513 (mt) REVERT: R 310 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8503 (mtm-85) REVERT: A 197 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8010 (mttm) REVERT: A 232 LEU cc_start: 0.8796 (mt) cc_final: 0.8572 (mp) REVERT: A 298 GLU cc_start: 0.7351 (tt0) cc_final: 0.7049 (tt0) REVERT: B 161 SER cc_start: 0.8744 (p) cc_final: 0.8416 (p) REVERT: B 163 ASP cc_start: 0.7482 (p0) cc_final: 0.6993 (p0) REVERT: B 212 ASP cc_start: 0.8516 (t0) cc_final: 0.7745 (t0) REVERT: B 215 GLU cc_start: 0.8705 (mp0) cc_final: 0.8087 (mp0) REVERT: B 233 CYS cc_start: 0.8691 (t) cc_final: 0.8390 (t) REVERT: B 258 ASP cc_start: 0.8262 (t0) cc_final: 0.7847 (t0) REVERT: B 259 GLN cc_start: 0.8342 (tt0) cc_final: 0.7872 (mt0) REVERT: B 294 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7884 (t) REVERT: B 336 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (mp) REVERT: E 128 MET cc_start: 0.9209 (mmm) cc_final: 0.8282 (mmm) REVERT: E 132 THR cc_start: 0.8355 (m) cc_final: 0.8045 (t) REVERT: E 234 GLU cc_start: 0.7832 (pm20) cc_final: 0.7103 (pm20) outliers start: 21 outliers final: 14 residues processed: 260 average time/residue: 0.2559 time to fit residues: 86.3176 Evaluate side-chains 258 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090299 restraints weight = 14825.976| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.47 r_work: 0.3145 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9139 Z= 0.182 Angle : 0.545 9.333 12373 Z= 0.281 Chirality : 0.042 0.198 1412 Planarity : 0.004 0.040 1553 Dihedral : 4.226 43.190 1243 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.85 % Allowed : 18.05 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1123 helix: 2.03 (0.26), residues: 411 sheet: 0.24 (0.29), residues: 291 loop : -0.14 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 91 HIS 0.004 0.001 HIS A 188 PHE 0.016 0.001 PHE R 180 TYR 0.020 0.001 TYR A 296 ARG 0.008 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 VAL cc_start: 0.8827 (t) cc_final: 0.8617 (p) REVERT: R 54 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7778 (mmm160) REVERT: R 83 VAL cc_start: 0.8677 (t) cc_final: 0.8397 (m) REVERT: R 87 MET cc_start: 0.8681 (mtt) cc_final: 0.8410 (mtm) REVERT: R 189 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7920 (tm-30) REVERT: R 203 ILE cc_start: 0.8833 (tt) cc_final: 0.8545 (mm) REVERT: R 229 HIS cc_start: 0.8106 (t70) cc_final: 0.7885 (t70) REVERT: R 310 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8513 (mtm-85) REVERT: R 312 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8192 (tpp80) REVERT: A 197 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7985 (tttp) REVERT: A 232 LEU cc_start: 0.8786 (mt) cc_final: 0.8555 (mp) REVERT: A 298 GLU cc_start: 0.7388 (tt0) cc_final: 0.7073 (tt0) REVERT: B 161 SER cc_start: 0.8752 (p) cc_final: 0.8457 (p) REVERT: B 163 ASP cc_start: 0.7479 (p0) cc_final: 0.7069 (p0) REVERT: B 212 ASP cc_start: 0.8500 (t0) cc_final: 0.7676 (t0) REVERT: B 215 GLU cc_start: 0.8716 (mp0) cc_final: 0.7956 (mp0) REVERT: B 233 CYS cc_start: 0.8693 (t) cc_final: 0.8371 (t) REVERT: B 254 ASP cc_start: 0.8161 (t0) cc_final: 0.7569 (t0) REVERT: B 258 ASP cc_start: 0.8263 (t0) cc_final: 0.7864 (t0) REVERT: B 259 GLN cc_start: 0.8380 (tt0) cc_final: 0.7992 (mt0) REVERT: B 336 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E 128 MET cc_start: 0.9215 (mmm) cc_final: 0.8362 (mmm) REVERT: E 132 THR cc_start: 0.8359 (m) cc_final: 0.8063 (t) REVERT: E 234 GLU cc_start: 0.7831 (pm20) cc_final: 0.7094 (pm20) outliers start: 18 outliers final: 15 residues processed: 255 average time/residue: 0.2596 time to fit residues: 85.8839 Evaluate side-chains 257 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090582 restraints weight = 14782.481| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.46 r_work: 0.3152 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9139 Z= 0.172 Angle : 0.559 9.727 12373 Z= 0.287 Chirality : 0.041 0.193 1412 Planarity : 0.004 0.060 1553 Dihedral : 4.219 40.636 1243 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 19.38 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1123 helix: 2.06 (0.26), residues: 411 sheet: 0.23 (0.29), residues: 296 loop : -0.07 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE R 180 TYR 0.019 0.001 TYR A 296 ARG 0.014 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 VAL cc_start: 0.8823 (t) cc_final: 0.8596 (p) REVERT: R 54 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7723 (mmm160) REVERT: R 83 VAL cc_start: 0.8672 (t) cc_final: 0.8392 (m) REVERT: R 87 MET cc_start: 0.8690 (mtt) cc_final: 0.8419 (mtp) REVERT: R 91 TRP cc_start: 0.9006 (t-100) cc_final: 0.8766 (t-100) REVERT: R 189 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7938 (tm-30) REVERT: R 203 ILE cc_start: 0.8826 (tt) cc_final: 0.8536 (mm) REVERT: R 310 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8515 (mtm-85) REVERT: R 312 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8129 (tpp80) REVERT: A 298 GLU cc_start: 0.7373 (tt0) cc_final: 0.7065 (tt0) REVERT: A 309 ASP cc_start: 0.8400 (t0) cc_final: 0.8104 (t70) REVERT: B 161 SER cc_start: 0.8754 (p) cc_final: 0.8434 (p) REVERT: B 163 ASP cc_start: 0.7440 (p0) cc_final: 0.6980 (p0) REVERT: B 212 ASP cc_start: 0.8498 (t0) cc_final: 0.7821 (t0) REVERT: B 215 GLU cc_start: 0.8715 (mp0) cc_final: 0.8101 (mp0) REVERT: B 233 CYS cc_start: 0.8694 (t) cc_final: 0.8376 (t) REVERT: B 254 ASP cc_start: 0.8154 (t0) cc_final: 0.7600 (t0) REVERT: B 258 ASP cc_start: 0.8243 (t0) cc_final: 0.7829 (t0) REVERT: B 259 GLN cc_start: 0.8357 (tt0) cc_final: 0.7988 (mt0) REVERT: E 128 MET cc_start: 0.9204 (mmm) cc_final: 0.8377 (mmm) REVERT: E 132 THR cc_start: 0.8306 (m) cc_final: 0.8011 (t) REVERT: E 234 GLU cc_start: 0.7842 (pm20) cc_final: 0.7125 (pm20) outliers start: 14 outliers final: 14 residues processed: 250 average time/residue: 0.2509 time to fit residues: 81.6735 Evaluate side-chains 252 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088113 restraints weight = 14862.630| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.44 r_work: 0.3111 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9139 Z= 0.273 Angle : 0.598 9.648 12373 Z= 0.311 Chirality : 0.043 0.208 1412 Planarity : 0.004 0.044 1553 Dihedral : 4.432 40.413 1243 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 19.69 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1123 helix: 1.95 (0.26), residues: 409 sheet: 0.11 (0.29), residues: 297 loop : -0.12 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 91 HIS 0.004 0.001 HIS A 188 PHE 0.020 0.002 PHE R 161 TYR 0.020 0.001 TYR A 296 ARG 0.008 0.001 ARG C 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 VAL cc_start: 0.8825 (t) cc_final: 0.8605 (p) REVERT: R 83 VAL cc_start: 0.8704 (t) cc_final: 0.8429 (m) REVERT: R 91 TRP cc_start: 0.9055 (t-100) cc_final: 0.8851 (t-100) REVERT: R 189 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7916 (tm-30) REVERT: R 203 ILE cc_start: 0.8853 (tt) cc_final: 0.8632 (mm) REVERT: R 310 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8544 (mtm-85) REVERT: R 312 ARG cc_start: 0.8606 (tpp80) cc_final: 0.8318 (tpp80) REVERT: A 232 LEU cc_start: 0.8864 (mt) cc_final: 0.8637 (mp) REVERT: A 298 GLU cc_start: 0.7403 (tt0) cc_final: 0.7083 (tt0) REVERT: B 161 SER cc_start: 0.8753 (p) cc_final: 0.8462 (p) REVERT: B 163 ASP cc_start: 0.7496 (p0) cc_final: 0.7031 (p0) REVERT: B 212 ASP cc_start: 0.8564 (t0) cc_final: 0.7878 (t0) REVERT: B 215 GLU cc_start: 0.8733 (mp0) cc_final: 0.7950 (mp0) REVERT: B 233 CYS cc_start: 0.8714 (t) cc_final: 0.8409 (t) REVERT: B 254 ASP cc_start: 0.8230 (t0) cc_final: 0.7737 (t0) REVERT: B 258 ASP cc_start: 0.8246 (t0) cc_final: 0.7832 (t0) REVERT: B 259 GLN cc_start: 0.8392 (tt0) cc_final: 0.8016 (mt0) REVERT: B 289 TYR cc_start: 0.8776 (m-80) cc_final: 0.8271 (m-80) REVERT: B 336 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8389 (mp) REVERT: E 128 MET cc_start: 0.9164 (mmm) cc_final: 0.8343 (mmm) REVERT: E 132 THR cc_start: 0.8402 (m) cc_final: 0.8070 (t) REVERT: E 172 SER cc_start: 0.8853 (p) cc_final: 0.8647 (p) REVERT: E 234 GLU cc_start: 0.7834 (pm20) cc_final: 0.7131 (pm20) outliers start: 16 outliers final: 13 residues processed: 261 average time/residue: 0.2499 time to fit residues: 85.0613 Evaluate side-chains 257 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.104179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.089907 restraints weight = 14733.929| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.42 r_work: 0.3144 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9139 Z= 0.183 Angle : 0.577 9.443 12373 Z= 0.296 Chirality : 0.042 0.206 1412 Planarity : 0.004 0.062 1553 Dihedral : 4.295 36.461 1243 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.64 % Allowed : 20.10 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1123 helix: 2.00 (0.26), residues: 411 sheet: 0.14 (0.29), residues: 297 loop : -0.07 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.001 PHE R 180 TYR 0.014 0.001 TYR E 102 ARG 0.015 0.001 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.55 seconds wall clock time: 93 minutes 26.77 seconds (5606.77 seconds total)