Starting phenix.real_space_refine on Wed Sep 17 10:07:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.map" model { file = "/net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s2t_19683/09_2025/8s2t_19683.cif" } resolution = 3.3 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= 0.001 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 53 5.16 5 C 5045 2.51 5 N 1400 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7955 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1673 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain breaks: 4 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2269 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.28 Number of scatterers: 7955 At special positions: 0 Unit cell: (82.7105, 100.839, 129.164, 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 53 16.00 O 1457 8.00 N 1400 7.00 C 5045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 216 " distance=2.03 Simple disulfide: pdb=" SG CYS R 209 " - pdb=" SG CYS R 215 " 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: 0.86 Conformation dependent library (CDL) restraints added in 450.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.4% alpha, 21.2% 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 11 through 38 removed outlier: 3.655A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 4.002A pdb=" N ASN A 225 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 317 through 336 Processing helix chain 'A' and resid 354 through 377 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 56 through 86 Processing helix chain 'R' and resid 87 through 90 Processing helix chain 'R' and resid 92 through 111 removed outlier: 3.753A pdb=" N PHE R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 121 removed outlier: 4.130A pdb=" N THR R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE R 118 " --> pdb=" O PHE R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 162 removed outlier: 3.914A pdb=" N CYS R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 171 through 188 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 203 through 209 Processing helix chain 'R' and resid 221 through 233 Processing helix chain 'R' and resid 233 through 263 removed outlier: 4.137A pdb=" N CYS R 261 " --> pdb=" O LYS R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 349 Proline residue: R 339 - end of helix Processing helix chain 'R' and resid 355 through 368 Processing helix chain 'R' and resid 368 through 373 Processing helix chain 'R' and resid 374 through 376 No H-bonds generated for 'chain 'R' and resid 374 through 376' Processing helix chain 'R' and resid 380 through 392 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.207A pdb=" N HIS A 41 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE A 208 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU A 43 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG A 42 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 231 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 44 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 233 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 46 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 273 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HIS A 348 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 275 " --> pdb=" O HIS A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.724A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.795A 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: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.298A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.983A 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 153 removed outlier: 6.396A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.908A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.356A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A 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: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.705A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1203 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: 1.36 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1383 1.30 - 1.44: 2383 1.44 - 1.57: 4235 1.57 - 1.70: 47 1.70 - 1.84: 71 Bond restraints: 8119 Sorted by residual: bond pdb=" CB HIS B 225 " pdb=" CG HIS B 225 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.15e+01 bond pdb=" NE ARG C 62 " pdb=" CZ ARG C 62 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.56e+01 bond pdb=" CB ARG A 218 " pdb=" CG ARG A 218 " ideal model delta sigma weight residual 1.520 1.337 0.183 3.00e-02 1.11e+03 3.73e+01 bond pdb=" CB ASP B 205 " pdb=" CG ASP B 205 " ideal model delta sigma weight residual 1.516 1.365 0.151 2.50e-02 1.60e+03 3.63e+01 bond pdb=" CB HIS B 142 " pdb=" CG HIS B 142 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.57e+01 ... (remaining 8114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 9584 2.60 - 5.21: 1228 5.21 - 7.81: 166 7.81 - 10.42: 18 10.42 - 13.02: 3 Bond angle restraints: 10999 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 114.04 101.02 13.02 1.24e+00 6.50e-01 1.10e+02 angle pdb=" C SER R 162 " pdb=" N PRO R 163 " pdb=" CA PRO R 163 " ideal model delta sigma weight residual 119.56 128.23 -8.67 1.01e+00 9.80e-01 7.37e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 109.58 99.00 10.58 1.29e+00 6.01e-01 6.72e+01 angle pdb=" C ASP C 48 " pdb=" N PRO C 49 " pdb=" CA PRO C 49 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.39e+01 angle pdb=" CA HIS A 206 " pdb=" CB HIS A 206 " pdb=" CG HIS A 206 " ideal model delta sigma weight residual 113.80 121.66 -7.86 1.00e+00 1.00e+00 6.17e+01 ... (remaining 10994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4669 17.89 - 35.78: 125 35.78 - 53.67: 27 53.67 - 71.56: 11 71.56 - 89.45: 5 Dihedral angle restraints: 4837 sinusoidal: 1925 harmonic: 2912 Sorted by residual: dihedral pdb=" C TRP B 82 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " ideal model delta harmonic sigma weight residual -122.60 -112.93 -9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS A 206 " pdb=" N HIS A 206 " pdb=" CA HIS A 206 " pdb=" CB HIS A 206 " ideal model delta harmonic sigma weight residual -122.60 -132.24 9.64 0 2.50e+00 1.60e-01 1.49e+01 dihedral pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " pdb=" OD1 ASP N 106 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 4834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 768 0.087 - 0.173: 350 0.173 - 0.259: 83 0.259 - 0.346: 24 0.346 - 0.432: 6 Chirality restraints: 1231 Sorted by residual: chirality pdb=" CA TYR R 244 " pdb=" N TYR R 244 " pdb=" C TYR R 244 " pdb=" CB TYR R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CB VAL A 353 " pdb=" CA VAL A 353 " pdb=" CG1 VAL A 353 " pdb=" CG2 VAL A 353 " both_signs ideal model delta sigma weight residual False -2.63 -3.04 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TRP R 337 " pdb=" N TRP R 337 " pdb=" C TRP R 337 " pdb=" CB TRP R 337 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 1228 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 40 " 0.057 2.00e-02 2.50e+03 3.39e-02 2.29e+01 pdb=" CG TYR C 40 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR C 40 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 40 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 40 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 40 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.061 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP B 99 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " -0.058 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP B 63 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " -0.030 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2854 2.85 - 3.36: 7983 3.36 - 3.87: 14243 3.87 - 4.39: 17710 4.39 - 4.90: 27899 Nonbonded interactions: 70689 Sorted by model distance: nonbonded pdb=" N ASP R 356 " pdb=" OD1 ASP R 356 " model vdw 2.334 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.373 3.120 nonbonded pdb=" N ASP R 204 " pdb=" OD1 ASP R 204 " model vdw 2.381 3.120 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.386 3.040 ... (remaining 70684 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: 2.360 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.025 0.183 8123 Z= 1.318 Angle : 1.810 13.022 11007 Z= 1.238 Chirality : 0.105 0.432 1231 Planarity : 0.010 0.123 1404 Dihedral : 10.263 89.446 2937 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.26), residues: 982 helix: 0.01 (0.23), residues: 388 sheet: 1.19 (0.34), residues: 198 loop : 0.47 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 27 TYR 0.059 0.008 TYR C 40 PHE 0.037 0.007 PHE R 164 TRP 0.061 0.011 TRP B 99 HIS 0.016 0.004 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.02482 ( 8119) covalent geometry : angle 1.80725 (10999) SS BOND : bond 0.00614 ( 4) SS BOND : angle 4.23785 ( 8) hydrogen bonds : bond 0.14470 ( 428) hydrogen bonds : angle 7.06771 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 324 LYS cc_start: 0.8015 (tttt) cc_final: 0.7691 (ttmm) REVERT: R 355 PRO cc_start: 0.8131 (Cg_exo) cc_final: 0.7918 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1291 time to fit residues: 43.8605 Evaluate side-chains 162 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 206 HIS A 253 GLN A 373 HIS N 120 GLN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107896 restraints weight = 13332.808| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.54 r_work: 0.3384 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8123 Z= 0.203 Angle : 0.703 8.466 11007 Z= 0.384 Chirality : 0.047 0.355 1231 Planarity : 0.005 0.045 1404 Dihedral : 5.979 42.472 1106 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.22 % Allowed : 10.07 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 982 helix: 1.02 (0.25), residues: 397 sheet: 0.48 (0.33), residues: 187 loop : 0.08 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.027 0.002 TYR N 60 PHE 0.027 0.002 PHE N 68 TRP 0.024 0.002 TRP B 99 HIS 0.009 0.002 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8119) covalent geometry : angle 0.70081 (10999) SS BOND : bond 0.00250 ( 4) SS BOND : angle 2.06771 ( 8) hydrogen bonds : bond 0.05250 ( 428) hydrogen bonds : angle 5.44578 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8337 (m-40) cc_final: 0.8134 (m110) REVERT: A 358 ILE cc_start: 0.9174 (tt) cc_final: 0.8873 (tp) REVERT: A 367 ASP cc_start: 0.7917 (m-30) cc_final: 0.7710 (m-30) REVERT: B 13 GLN cc_start: 0.8790 (tt0) cc_final: 0.8418 (pt0) REVERT: B 111 TYR cc_start: 0.8744 (m-80) cc_final: 0.8394 (m-80) REVERT: B 130 GLU cc_start: 0.7184 (pt0) cc_final: 0.6957 (pt0) REVERT: B 134 ARG cc_start: 0.7666 (ptp-170) cc_final: 0.7396 (ptm160) REVERT: B 172 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 291 ASP cc_start: 0.7491 (t70) cc_final: 0.7244 (t70) REVERT: B 339 TRP cc_start: 0.8858 (m100) cc_final: 0.8438 (m-10) REVERT: C 58 GLU cc_start: 0.7985 (mp0) cc_final: 0.7639 (mp0) REVERT: N 95 TYR cc_start: 0.8654 (m-80) cc_final: 0.8222 (m-80) REVERT: N 105 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8153 (mtp-110) REVERT: R 110 LEU cc_start: 0.7901 (mp) cc_final: 0.6917 (tt) REVERT: R 324 LYS cc_start: 0.7276 (tttt) cc_final: 0.6954 (ttmm) REVERT: R 328 ILE cc_start: 0.8626 (mt) cc_final: 0.8352 (tt) REVERT: R 335 LEU cc_start: 0.7939 (tp) cc_final: 0.7421 (mp) outliers start: 19 outliers final: 13 residues processed: 209 average time/residue: 0.1074 time to fit residues: 29.2247 Evaluate side-chains 181 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 80 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: A 19 GLN A 264 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 31 ASN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.126336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106084 restraints weight = 13293.196| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.53 r_work: 0.3365 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8123 Z= 0.185 Angle : 0.629 6.483 11007 Z= 0.337 Chirality : 0.045 0.298 1231 Planarity : 0.004 0.045 1404 Dihedral : 5.818 48.314 1106 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.93 % Allowed : 12.76 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 982 helix: 1.14 (0.25), residues: 398 sheet: -0.10 (0.33), residues: 198 loop : 0.28 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 27 TYR 0.026 0.002 TYR N 60 PHE 0.024 0.002 PHE N 68 TRP 0.021 0.002 TRP R 199 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8119) covalent geometry : angle 0.62784 (10999) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.77825 ( 8) hydrogen bonds : bond 0.04487 ( 428) hydrogen bonds : angle 5.13491 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8425 (m-40) cc_final: 0.8169 (m110) REVERT: A 358 ILE cc_start: 0.9175 (tt) cc_final: 0.8937 (tp) REVERT: B 6 GLN cc_start: 0.8940 (mt0) cc_final: 0.8470 (mp10) REVERT: B 59 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: B 111 TYR cc_start: 0.8808 (m-80) cc_final: 0.8567 (m-80) REVERT: B 118 ASP cc_start: 0.8068 (m-30) cc_final: 0.7618 (m-30) REVERT: B 134 ARG cc_start: 0.7686 (ptp-170) cc_final: 0.7434 (ptm160) REVERT: B 334 SER cc_start: 0.9142 (m) cc_final: 0.8904 (m) REVERT: C 42 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8115 (mm-30) REVERT: C 58 GLU cc_start: 0.8005 (mp0) cc_final: 0.7727 (mp0) REVERT: N 32 TYR cc_start: 0.8167 (m-80) cc_final: 0.7942 (m-80) REVERT: N 95 TYR cc_start: 0.8655 (m-80) cc_final: 0.8393 (m-80) REVERT: R 110 LEU cc_start: 0.7901 (mp) cc_final: 0.6939 (tt) REVERT: R 320 GLN cc_start: 0.5061 (mt0) cc_final: 0.4830 (pt0) REVERT: R 324 LYS cc_start: 0.7168 (tttt) cc_final: 0.6728 (ttmm) REVERT: R 335 LEU cc_start: 0.8002 (tp) cc_final: 0.7597 (mp) REVERT: R 351 ARG cc_start: 0.7682 (ttt-90) cc_final: 0.7471 (ttm-80) outliers start: 25 outliers final: 18 residues processed: 205 average time/residue: 0.0983 time to fit residues: 26.8850 Evaluate side-chains 188 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 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 = 0.3769 r_free = 0.3769 target = 0.126068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105435 restraints weight = 13446.616| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.63 r_work: 0.3340 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8123 Z= 0.166 Angle : 0.631 9.547 11007 Z= 0.335 Chirality : 0.044 0.250 1231 Planarity : 0.004 0.043 1404 Dihedral : 5.781 54.016 1106 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.98 % Allowed : 13.70 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.27), residues: 982 helix: 1.29 (0.26), residues: 392 sheet: 0.01 (0.33), residues: 200 loop : 0.18 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 98 TYR 0.023 0.002 TYR N 60 PHE 0.017 0.002 PHE N 68 TRP 0.024 0.002 TRP R 199 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8119) covalent geometry : angle 0.62262 (10999) SS BOND : bond 0.00474 ( 4) SS BOND : angle 3.93398 ( 8) hydrogen bonds : bond 0.04185 ( 428) hydrogen bonds : angle 5.05840 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8459 (m-40) cc_final: 0.8162 (m110) REVERT: A 358 ILE cc_start: 0.9175 (tt) cc_final: 0.8918 (tp) REVERT: B 6 GLN cc_start: 0.8970 (mt0) cc_final: 0.8724 (mp10) REVERT: B 9 GLN cc_start: 0.8510 (tp40) cc_final: 0.8005 (tp40) REVERT: B 59 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: B 111 TYR cc_start: 0.8831 (m-80) cc_final: 0.8629 (m-80) REVERT: B 118 ASP cc_start: 0.8120 (m-30) cc_final: 0.7841 (m-30) REVERT: B 130 GLU cc_start: 0.7253 (pt0) cc_final: 0.7038 (pt0) REVERT: B 134 ARG cc_start: 0.7791 (ptp-170) cc_final: 0.7361 (ptm-80) REVERT: B 312 ASP cc_start: 0.7854 (m-30) cc_final: 0.6931 (t0) REVERT: B 334 SER cc_start: 0.9002 (m) cc_final: 0.8790 (m) REVERT: C 25 ILE cc_start: 0.8561 (mt) cc_final: 0.8359 (mt) REVERT: C 42 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8088 (mm-30) REVERT: C 58 GLU cc_start: 0.8029 (mp0) cc_final: 0.7373 (mp0) REVERT: N 32 TYR cc_start: 0.8193 (m-80) cc_final: 0.7990 (m-80) REVERT: R 110 LEU cc_start: 0.7900 (mp) cc_final: 0.6986 (tt) REVERT: R 324 LYS cc_start: 0.7045 (tttt) cc_final: 0.6622 (ttmt) REVERT: R 335 LEU cc_start: 0.7946 (tp) cc_final: 0.7483 (mp) outliers start: 34 outliers final: 22 residues processed: 196 average time/residue: 0.0952 time to fit residues: 24.9107 Evaluate side-chains 189 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.0470 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 0.0010 chunk 94 optimal weight: 0.5980 chunk 59 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 overall best weight: 0.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 31 ASN R 94 ASN ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.129667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.109349 restraints weight = 13271.190| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.65 r_work: 0.3410 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8123 Z= 0.122 Angle : 0.590 8.943 11007 Z= 0.312 Chirality : 0.044 0.315 1231 Planarity : 0.004 0.046 1404 Dihedral : 5.479 46.924 1106 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 15.11 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.27), residues: 982 helix: 1.52 (0.26), residues: 389 sheet: -0.04 (0.33), residues: 205 loop : 0.16 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 88 TYR 0.022 0.001 TYR N 60 PHE 0.021 0.002 PHE N 108 TRP 0.027 0.002 TRP R 199 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8119) covalent geometry : angle 0.58473 (10999) SS BOND : bond 0.00629 ( 4) SS BOND : angle 2.97666 ( 8) hydrogen bonds : bond 0.03883 ( 428) hydrogen bonds : angle 4.89750 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8400 (m-40) cc_final: 0.8109 (m110) REVERT: A 358 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8955 (tp) REVERT: B 6 GLN cc_start: 0.8919 (mt0) cc_final: 0.8695 (mp10) REVERT: B 9 GLN cc_start: 0.8620 (tp40) cc_final: 0.8350 (tp40) REVERT: B 59 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: B 130 GLU cc_start: 0.7165 (pt0) cc_final: 0.6964 (pt0) REVERT: B 134 ARG cc_start: 0.7684 (ptp-170) cc_final: 0.7313 (ptm-80) REVERT: B 234 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: C 22 GLU cc_start: 0.8160 (tp30) cc_final: 0.7847 (tp30) REVERT: C 58 GLU cc_start: 0.8038 (mp0) cc_final: 0.7427 (mp0) REVERT: N 13 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8354 (mm-40) REVERT: N 46 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7794 (pt0) REVERT: N 117 TYR cc_start: 0.8465 (m-80) cc_final: 0.7842 (m-80) REVERT: R 110 LEU cc_start: 0.7821 (mp) cc_final: 0.6858 (tt) REVERT: R 324 LYS cc_start: 0.6887 (tttt) cc_final: 0.6355 (ttmm) REVERT: R 335 LEU cc_start: 0.7790 (tp) cc_final: 0.7392 (mp) outliers start: 25 outliers final: 14 residues processed: 192 average time/residue: 0.0974 time to fit residues: 25.0290 Evaluate side-chains 190 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 85 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 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 = 0.3765 r_free = 0.3765 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105933 restraints weight = 13255.175| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.57 r_work: 0.3367 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8123 Z= 0.155 Angle : 0.595 7.409 11007 Z= 0.315 Chirality : 0.044 0.288 1231 Planarity : 0.004 0.044 1404 Dihedral : 5.421 44.352 1106 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.98 % Allowed : 15.57 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.27), residues: 982 helix: 1.63 (0.26), residues: 383 sheet: -0.22 (0.34), residues: 209 loop : 0.16 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.018 0.002 TYR N 60 PHE 0.018 0.002 PHE N 108 TRP 0.020 0.002 TRP R 364 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8119) covalent geometry : angle 0.58941 (10999) SS BOND : bond 0.00579 ( 4) SS BOND : angle 3.03636 ( 8) hydrogen bonds : bond 0.03819 ( 428) hydrogen bonds : angle 4.85830 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8464 (m-40) cc_final: 0.8181 (m110) REVERT: A 358 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8955 (tp) REVERT: B 6 GLN cc_start: 0.8917 (mt0) cc_final: 0.8680 (mp10) REVERT: B 9 GLN cc_start: 0.8597 (tp40) cc_final: 0.8290 (tp40) REVERT: B 59 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: B 130 GLU cc_start: 0.7161 (pt0) cc_final: 0.6903 (pt0) REVERT: B 134 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7355 (ptm-80) REVERT: B 234 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: C 11 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7901 (pt0) REVERT: C 22 GLU cc_start: 0.8337 (tp30) cc_final: 0.8018 (tp30) REVERT: C 58 GLU cc_start: 0.8057 (mp0) cc_final: 0.7462 (mp0) REVERT: N 13 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8390 (mm-40) REVERT: N 46 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: N 117 TYR cc_start: 0.8642 (m-80) cc_final: 0.8062 (m-80) REVERT: R 104 ASP cc_start: 0.8405 (m-30) cc_final: 0.8091 (t0) REVERT: R 110 LEU cc_start: 0.7884 (mp) cc_final: 0.6946 (tt) REVERT: R 324 LYS cc_start: 0.6887 (tttt) cc_final: 0.6377 (ttmm) REVERT: R 335 LEU cc_start: 0.7869 (tp) cc_final: 0.7466 (mp) outliers start: 34 outliers final: 18 residues processed: 194 average time/residue: 0.1005 time to fit residues: 26.2431 Evaluate side-chains 189 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 121 TRP Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 373 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 = 0.3788 r_free = 0.3788 target = 0.127204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.106783 restraints weight = 13315.349| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.62 r_work: 0.3369 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8123 Z= 0.145 Angle : 0.592 6.772 11007 Z= 0.311 Chirality : 0.043 0.272 1231 Planarity : 0.004 0.048 1404 Dihedral : 5.375 42.834 1106 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.33 % Allowed : 15.46 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.27), residues: 982 helix: 1.70 (0.26), residues: 383 sheet: -0.17 (0.33), residues: 217 loop : -0.00 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.017 0.001 TYR N 60 PHE 0.020 0.002 PHE N 29 TRP 0.022 0.002 TRP R 364 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8119) covalent geometry : angle 0.58757 (10999) SS BOND : bond 0.00572 ( 4) SS BOND : angle 2.86474 ( 8) hydrogen bonds : bond 0.03730 ( 428) hydrogen bonds : angle 4.80985 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8484 (m-40) cc_final: 0.8195 (m110) REVERT: A 358 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8944 (tp) REVERT: B 6 GLN cc_start: 0.8926 (mt0) cc_final: 0.8691 (mp10) REVERT: B 9 GLN cc_start: 0.8610 (tp40) cc_final: 0.8290 (tp40) REVERT: B 59 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: B 130 GLU cc_start: 0.7184 (pt0) cc_final: 0.6928 (pt0) REVERT: B 134 ARG cc_start: 0.7670 (ptp-170) cc_final: 0.7249 (ptm-80) REVERT: B 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: C 11 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7821 (pt0) REVERT: C 58 GLU cc_start: 0.8096 (mp0) cc_final: 0.7561 (mp0) REVERT: N 13 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8416 (mm-40) REVERT: N 31 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (t0) REVERT: N 46 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: N 117 TYR cc_start: 0.8576 (m-80) cc_final: 0.7986 (m-80) REVERT: R 104 ASP cc_start: 0.8400 (m-30) cc_final: 0.8080 (t0) REVERT: R 110 LEU cc_start: 0.7951 (mp) cc_final: 0.6947 (tt) REVERT: R 324 LYS cc_start: 0.6819 (tttt) cc_final: 0.6310 (ttmm) REVERT: R 335 LEU cc_start: 0.7892 (tp) cc_final: 0.7472 (mp) outliers start: 37 outliers final: 22 residues processed: 196 average time/residue: 0.1021 time to fit residues: 26.7880 Evaluate side-chains 194 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 373 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 = 0.3765 r_free = 0.3765 target = 0.125193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104796 restraints weight = 13358.689| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.59 r_work: 0.3345 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8123 Z= 0.169 Angle : 0.609 7.439 11007 Z= 0.319 Chirality : 0.044 0.258 1231 Planarity : 0.004 0.046 1404 Dihedral : 5.395 42.040 1106 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.04 % Allowed : 14.64 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.28), residues: 982 helix: 1.57 (0.26), residues: 389 sheet: -0.42 (0.33), residues: 231 loop : 0.14 (0.36), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.018 0.002 TYR B 264 PHE 0.018 0.002 PHE N 29 TRP 0.030 0.002 TRP R 364 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8119) covalent geometry : angle 0.60375 (10999) SS BOND : bond 0.00545 ( 4) SS BOND : angle 2.95721 ( 8) hydrogen bonds : bond 0.03807 ( 428) hydrogen bonds : angle 4.86618 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 208 PHE cc_start: 0.8037 (m-80) cc_final: 0.7566 (m-10) REVERT: A 257 ASN cc_start: 0.8495 (m-40) cc_final: 0.8198 (m110) REVERT: A 358 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 6 GLN cc_start: 0.8939 (mt0) cc_final: 0.8688 (mp10) REVERT: B 9 GLN cc_start: 0.8603 (tp40) cc_final: 0.8287 (tp40) REVERT: B 59 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: B 130 GLU cc_start: 0.7184 (pt0) cc_final: 0.6917 (pt0) REVERT: B 134 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7267 (ptm-80) REVERT: B 234 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: C 11 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7739 (pt0) REVERT: C 58 GLU cc_start: 0.8155 (mp0) cc_final: 0.7616 (mp0) REVERT: N 13 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8444 (mm-40) REVERT: N 31 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.8002 (t0) REVERT: N 46 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: N 87 LYS cc_start: 0.8595 (mttm) cc_final: 0.8336 (mtmm) REVERT: R 104 ASP cc_start: 0.8375 (m-30) cc_final: 0.8088 (t0) REVERT: R 110 LEU cc_start: 0.7955 (mp) cc_final: 0.6959 (tt) REVERT: R 324 LYS cc_start: 0.6823 (tttt) cc_final: 0.6329 (ttmm) REVERT: R 335 LEU cc_start: 0.7954 (tp) cc_final: 0.7510 (mp) outliers start: 43 outliers final: 28 residues processed: 193 average time/residue: 0.0992 time to fit residues: 25.7123 Evaluate side-chains 191 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 373 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 = 0.3775 r_free = 0.3775 target = 0.126033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105750 restraints weight = 13349.680| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.60 r_work: 0.3354 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8123 Z= 0.151 Angle : 0.604 7.877 11007 Z= 0.318 Chirality : 0.044 0.249 1231 Planarity : 0.004 0.049 1404 Dihedral : 5.358 41.667 1106 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.33 % Allowed : 15.81 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.28), residues: 982 helix: 1.55 (0.26), residues: 389 sheet: -0.27 (0.34), residues: 220 loop : -0.04 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.015 0.002 TYR B 264 PHE 0.017 0.002 PHE N 108 TRP 0.029 0.002 TRP R 364 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8119) covalent geometry : angle 0.59901 (10999) SS BOND : bond 0.00504 ( 4) SS BOND : angle 2.80597 ( 8) hydrogen bonds : bond 0.03775 ( 428) hydrogen bonds : angle 4.87241 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 257 ASN cc_start: 0.8493 (m-40) cc_final: 0.8201 (m110) REVERT: A 358 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8929 (tp) REVERT: B 9 GLN cc_start: 0.8590 (tp40) cc_final: 0.8274 (tp40) REVERT: B 59 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 130 GLU cc_start: 0.7249 (pt0) cc_final: 0.6989 (pt0) REVERT: B 134 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7236 (ptm-80) REVERT: B 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: C 11 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7802 (pt0) REVERT: C 58 GLU cc_start: 0.8203 (mp0) cc_final: 0.7668 (mp0) REVERT: N 13 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8428 (mm-40) REVERT: N 46 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: N 87 LYS cc_start: 0.8636 (mttm) cc_final: 0.8400 (mtmm) REVERT: N 117 TYR cc_start: 0.8605 (m-80) cc_final: 0.7965 (m-80) REVERT: R 208 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8184 (tmm-80) REVERT: R 324 LYS cc_start: 0.6880 (tttt) cc_final: 0.6330 (ttmm) REVERT: R 335 LEU cc_start: 0.7954 (tp) cc_final: 0.7505 (mp) outliers start: 37 outliers final: 25 residues processed: 183 average time/residue: 0.0969 time to fit residues: 24.1011 Evaluate side-chains 187 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Chi-restraints excluded: chain R residue 365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 92 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.128710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.108559 restraints weight = 13280.740| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.61 r_work: 0.3398 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8123 Z= 0.129 Angle : 0.592 8.349 11007 Z= 0.310 Chirality : 0.044 0.238 1231 Planarity : 0.004 0.047 1404 Dihedral : 5.274 41.381 1106 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.40 % Allowed : 16.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 982 helix: 1.57 (0.26), residues: 389 sheet: -0.30 (0.34), residues: 219 loop : -0.17 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.015 0.002 TYR N 60 PHE 0.018 0.002 PHE N 108 TRP 0.041 0.002 TRP R 364 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8119) covalent geometry : angle 0.58792 (10999) SS BOND : bond 0.00465 ( 4) SS BOND : angle 2.48888 ( 8) hydrogen bonds : bond 0.03693 ( 428) hydrogen bonds : angle 4.87826 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.342 Fit side-chains REVERT: A 257 ASN cc_start: 0.8484 (m-40) cc_final: 0.8193 (m110) REVERT: B 59 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: B 126 LEU cc_start: 0.8935 (mt) cc_final: 0.8734 (mt) REVERT: B 134 ARG cc_start: 0.7623 (ptp-170) cc_final: 0.7146 (ptm-80) REVERT: B 234 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: C 58 GLU cc_start: 0.8211 (mp0) cc_final: 0.7671 (mp0) REVERT: N 13 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8401 (mm-40) REVERT: N 46 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: N 117 TYR cc_start: 0.8623 (m-80) cc_final: 0.8022 (m-80) REVERT: R 208 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8179 (tmm-80) REVERT: R 324 LYS cc_start: 0.6721 (tttt) cc_final: 0.6195 (ttmm) REVERT: R 335 LEU cc_start: 0.7842 (tp) cc_final: 0.7409 (mp) outliers start: 29 outliers final: 21 residues processed: 181 average time/residue: 0.0997 time to fit residues: 24.4941 Evaluate side-chains 180 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 88 ARG Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 232 SER Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.126352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106137 restraints weight = 13401.394| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.62 r_work: 0.3364 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8123 Z= 0.159 Angle : 0.619 8.262 11007 Z= 0.323 Chirality : 0.045 0.272 1231 Planarity : 0.004 0.050 1404 Dihedral : 5.306 41.168 1106 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.63 % Allowed : 16.16 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.28), residues: 982 helix: 1.60 (0.26), residues: 389 sheet: -0.32 (0.34), residues: 222 loop : -0.15 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.017 0.002 TYR B 264 PHE 0.017 0.002 PHE N 103 TRP 0.034 0.002 TRP R 364 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8119) covalent geometry : angle 0.61440 (10999) SS BOND : bond 0.00552 ( 4) SS BOND : angle 2.78736 ( 8) hydrogen bonds : bond 0.03750 ( 428) hydrogen bonds : angle 4.92284 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.54 seconds wall clock time: 33 minutes 41.21 seconds (2021.21 seconds total)