Starting phenix.real_space_refine on Thu Jul 2 06:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyt_29597/07_2026/8fyt_29597.map" } resolution = 2.64 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= 0.049 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 4673 2.51 5 N 1237 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7321 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1891 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 232} Chain breaks: 1 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: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 151 Unusual residues: {'7LD': 1, 'J40': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.44, per 1000 atoms: 0.20 Number of scatterers: 7321 At special positions: 0 Unit cell: (76.176, 100.51, 129.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 2 15.00 O 1355 8.00 N 1237 7.00 C 4673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 0.57 Conformation dependent library (CDL) restraints added in 316.0 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.718A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 178 through 183 removed outlier: 4.307A pdb=" N ASP R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 removed outlier: 3.571A pdb=" N LYS R 228 " --> pdb=" O PHE R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 368 Proline residue: R 360 - end of helix removed outlier: 3.604A pdb=" N VAL R 364 " --> pdb=" O PRO R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 401 removed outlier: 4.161A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.597A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.579A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.742A 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 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.980A 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 329 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.156A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.553A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.167A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.536A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.430A 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: 6.725A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.527A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.701A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.449A 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: 6.273A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.677A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1152 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: 0.72 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1223 1.32 - 1.44: 1928 1.44 - 1.57: 4236 1.57 - 1.69: 3 1.69 - 1.82: 76 Bond restraints: 7466 Sorted by residual: bond pdb=" O4 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.702 1.626 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N LEU R 368 " pdb=" CA LEU R 368 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" N VAL R 70 " pdb=" CA VAL R 70 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N ILE R 75 " pdb=" CA ILE R 75 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" N ILE R 385 " pdb=" CA ILE R 385 " ideal model delta sigma weight residual 1.459 1.500 -0.040 1.30e-02 5.92e+03 9.69e+00 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10077 3.84 - 7.67: 34 7.67 - 11.51: 3 11.51 - 15.35: 0 15.35 - 19.18: 1 Bond angle restraints: 10115 Sorted by residual: angle pdb=" O1 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O13 J40 R 502 " ideal model delta sigma weight residual 92.86 112.04 -19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" N ASP B 247 " pdb=" CA ASP B 247 " pdb=" C ASP B 247 " ideal model delta sigma weight residual 113.19 108.49 4.70 1.19e+00 7.06e-01 1.56e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.41 107.43 4.98 1.30e+00 5.92e-01 1.47e+01 angle pdb=" CA VAL R 70 " pdb=" C VAL R 70 " pdb=" O VAL R 70 " ideal model delta sigma weight residual 121.05 117.23 3.82 1.04e+00 9.25e-01 1.35e+01 angle pdb=" CA ASP B 258 " pdb=" C ASP B 258 " pdb=" O ASP B 258 " ideal model delta sigma weight residual 121.54 117.47 4.07 1.16e+00 7.43e-01 1.23e+01 ... (remaining 10110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 4355 23.24 - 46.48: 225 46.48 - 69.72: 33 69.72 - 92.97: 6 92.97 - 116.21: 1 Dihedral angle restraints: 4620 sinusoidal: 1960 harmonic: 2660 Sorted by residual: dihedral pdb=" C40 J40 R 502 " pdb=" C41 J40 R 502 " pdb=" C42 J40 R 502 " pdb=" C43 J40 R 502 " ideal model delta sinusoidal sigma weight residual 178.73 62.52 116.21 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" CA PHE R 204 " pdb=" C PHE R 204 " pdb=" N TYR R 205 " pdb=" CA TYR R 205 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 341 " pdb=" CB ASP A 341 " pdb=" CG ASP A 341 " pdb=" OD1 ASP A 341 " ideal model delta sinusoidal sigma weight residual -30.00 -89.04 59.04 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 4617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 788 0.039 - 0.079: 244 0.079 - 0.118: 102 0.118 - 0.157: 19 0.157 - 0.197: 8 Chirality restraints: 1161 Sorted by residual: chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CA VAL R 89 " pdb=" N VAL R 89 " pdb=" C VAL R 89 " pdb=" CB VAL R 89 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA LEU B 69 " pdb=" N LEU B 69 " pdb=" C LEU B 69 " pdb=" CB LEU B 69 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1158 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 7LD R 501 " -0.894 2.00e-02 2.50e+03 6.47e-01 6.27e+03 pdb=" C16 7LD R 501 " 0.072 2.00e-02 2.50e+03 pdb=" C17 7LD R 501 " 0.646 2.00e-02 2.50e+03 pdb=" C19 7LD R 501 " -0.710 2.00e-02 2.50e+03 pdb=" N3 7LD R 501 " 0.001 2.00e-02 2.50e+03 pdb=" O1 7LD R 501 " 0.884 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 159 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR B 159 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 159 " 0.021 2.00e-02 2.50e+03 pdb=" N SER B 160 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 125 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C TRP R 125 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP R 125 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS R 126 " -0.014 2.00e-02 2.50e+03 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 683 2.75 - 3.28: 7173 3.28 - 3.82: 12624 3.82 - 4.36: 14913 4.36 - 4.90: 26076 Nonbonded interactions: 61469 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" O LEU R 166 " pdb=" OH TYR R 198 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.296 3.040 ... (remaining 61464 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7467 Z= 0.318 Angle : 0.743 19.183 10117 Z= 0.441 Chirality : 0.048 0.197 1161 Planarity : 0.019 0.647 1263 Dihedral : 13.752 116.208 2891 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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 are not related in a simple way. whole: 1.18 (0.28), residues: 902 helix: 1.95 (0.26), residues: 411 sheet: 0.55 (0.39), residues: 175 loop : -0.62 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 65 TYR 0.012 0.001 TYR R 195 PHE 0.011 0.002 PHE B 199 TRP 0.027 0.002 TRP R 125 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.32 ( 7466) covalent geometry : angle 0.74300 / 0.44 (10115) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.08454 / 0.05 ( 2) hydrogen bonds : bond 0.13365 / 9.19 ( 398) hydrogen bonds : angle 5.99148 / 4.45 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7716 (mtpp) REVERT: A 32 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7531 (mtt90) REVERT: A 193 ASP cc_start: 0.7706 (m-30) cc_final: 0.7436 (m-30) REVERT: A 240 MET cc_start: 0.3831 (tpt) cc_final: 0.1989 (ttm) REVERT: B 42 ARG cc_start: 0.7476 (tmt170) cc_final: 0.7223 (tpt90) REVERT: B 267 ASP cc_start: 0.7664 (m-30) cc_final: 0.7410 (m-30) REVERT: G 21 MET cc_start: 0.7449 (tmm) cc_final: 0.7169 (tmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3575 time to fit residues: 42.0676 Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 237 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113598 restraints weight = 8121.147| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.28 r_work: 0.3269 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7467 Z= 0.167 Angle : 0.541 9.511 10117 Z= 0.283 Chirality : 0.043 0.279 1161 Planarity : 0.004 0.047 1263 Dihedral : 9.183 79.764 1225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.54 % Allowed : 6.18 % Favored : 92.28 % 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 are not related in a simple way. whole: 1.21 (0.28), residues: 902 helix: 2.17 (0.26), residues: 411 sheet: 0.13 (0.38), residues: 190 loop : -0.65 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.012 0.001 TYR R 195 PHE 0.012 0.002 PHE B 199 TRP 0.030 0.002 TRP B 169 HIS 0.008 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7466) covalent geometry : angle 0.54154 / 0.28 (10115) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.17577 / 0.10 ( 2) hydrogen bonds : bond 0.04176 / 2.98 ( 398) hydrogen bonds : angle 4.57554 / 3.43 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7455 (mtpp) REVERT: R 356 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7330 (mm) REVERT: A 51 LYS cc_start: 0.6260 (ttmt) cc_final: 0.5973 (mttp) REVERT: A 193 ASP cc_start: 0.8191 (m-30) cc_final: 0.7885 (m-30) REVERT: B 46 ARG cc_start: 0.6912 (mtp-110) cc_final: 0.5921 (mtp85) REVERT: B 156 GLN cc_start: 0.8020 (mt0) cc_final: 0.7801 (mt0) REVERT: B 267 ASP cc_start: 0.7757 (m-30) cc_final: 0.7460 (m-30) REVERT: B 336 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7919 (mp) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.3995 time to fit residues: 43.1029 Evaluate side-chains 98 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113313 restraints weight = 8013.384| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.25 r_work: 0.3268 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7467 Z= 0.157 Angle : 0.513 9.386 10117 Z= 0.270 Chirality : 0.042 0.261 1161 Planarity : 0.004 0.045 1263 Dihedral : 8.838 76.953 1225 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.67 % Allowed : 10.30 % Favored : 88.03 % 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 are not related in a simple way. whole: 1.20 (0.28), residues: 902 helix: 2.24 (0.26), residues: 411 sheet: 0.16 (0.39), residues: 177 loop : -0.77 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.011 0.001 TYR R 195 PHE 0.012 0.002 PHE B 199 TRP 0.021 0.002 TRP B 169 HIS 0.007 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7466) covalent geometry : angle 0.51292 / 0.27 (10115) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.08615 / 0.05 ( 2) hydrogen bonds : bond 0.03915 / 2.79 ( 398) hydrogen bonds : angle 4.44942 / 3.32 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7443 (mtpp) REVERT: R 356 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 51 LYS cc_start: 0.6312 (ttmt) cc_final: 0.5639 (mtmt) REVERT: A 193 ASP cc_start: 0.8192 (m-30) cc_final: 0.7912 (m-30) REVERT: A 240 MET cc_start: 0.3538 (tpt) cc_final: 0.1516 (ttp) REVERT: B 46 ARG cc_start: 0.6976 (mtp-110) cc_final: 0.5968 (mtp85) REVERT: B 153 ASP cc_start: 0.6961 (t0) cc_final: 0.6653 (t0) REVERT: B 156 GLN cc_start: 0.8009 (mt0) cc_final: 0.7717 (mt0) REVERT: B 267 ASP cc_start: 0.7764 (m-30) cc_final: 0.7465 (m-30) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.4041 time to fit residues: 40.0545 Evaluate side-chains 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113506 restraints weight = 8175.150| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.28 r_work: 0.3262 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7467 Z= 0.143 Angle : 0.494 8.758 10117 Z= 0.260 Chirality : 0.042 0.231 1161 Planarity : 0.003 0.039 1263 Dihedral : 8.742 81.425 1225 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.80 % Allowed : 11.58 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.28), residues: 902 helix: 2.34 (0.26), residues: 409 sheet: 0.17 (0.38), residues: 177 loop : -0.80 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.011 0.001 TYR R 195 PHE 0.011 0.001 PHE B 199 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7466) covalent geometry : angle 0.49387 / 0.26 (10115) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.06322 / 0.04 ( 2) hydrogen bonds : bond 0.03699 / 2.64 ( 398) hydrogen bonds : angle 4.34033 / 3.24 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.255 Fit side-chains REVERT: R 191 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7469 (mtpp) REVERT: R 356 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7397 (mm) REVERT: A 51 LYS cc_start: 0.6281 (ttmt) cc_final: 0.5594 (mtmt) REVERT: A 193 ASP cc_start: 0.8293 (m-30) cc_final: 0.8042 (m-30) REVERT: A 240 MET cc_start: 0.3567 (tpt) cc_final: 0.1516 (ttp) REVERT: B 46 ARG cc_start: 0.7049 (mtp-110) cc_final: 0.6068 (mtp85) REVERT: B 153 ASP cc_start: 0.7115 (t0) cc_final: 0.6847 (t0) REVERT: B 156 GLN cc_start: 0.8076 (mt0) cc_final: 0.7793 (mt0) REVERT: B 267 ASP cc_start: 0.7782 (m-30) cc_final: 0.7485 (m-30) REVERT: G 58 GLU cc_start: 0.6692 (pm20) cc_final: 0.6490 (pm20) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.3486 time to fit residues: 37.7820 Evaluate side-chains 100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113617 restraints weight = 8091.702| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.27 r_work: 0.3271 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.137 Angle : 0.493 8.126 10117 Z= 0.260 Chirality : 0.042 0.202 1161 Planarity : 0.003 0.038 1263 Dihedral : 8.778 86.372 1225 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.19 % Allowed : 12.61 % Favored : 85.20 % 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 are not related in a simple way. whole: 1.31 (0.29), residues: 902 helix: 2.40 (0.26), residues: 409 sheet: 0.18 (0.38), residues: 184 loop : -0.80 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.011 0.001 TYR R 195 PHE 0.011 0.001 PHE R 204 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7466) covalent geometry : angle 0.49345 / 0.26 (10115) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 0.04212 / 0.02 ( 2) hydrogen bonds : bond 0.03623 / 2.59 ( 398) hydrogen bonds : angle 4.30190 / 3.21 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.189 Fit side-chains REVERT: R 191 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7515 (mtpp) REVERT: R 356 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 51 LYS cc_start: 0.6241 (ttmt) cc_final: 0.5579 (mtpt) REVERT: A 193 ASP cc_start: 0.8279 (m-30) cc_final: 0.8021 (m-30) REVERT: A 240 MET cc_start: 0.3568 (tpt) cc_final: 0.1490 (ttp) REVERT: B 46 ARG cc_start: 0.7014 (mtp-110) cc_final: 0.6030 (mtp85) REVERT: B 153 ASP cc_start: 0.7164 (t0) cc_final: 0.6920 (t0) REVERT: B 155 ASN cc_start: 0.8234 (t0) cc_final: 0.7884 (t0) REVERT: B 156 GLN cc_start: 0.8132 (mt0) cc_final: 0.7854 (mt0) REVERT: B 267 ASP cc_start: 0.7764 (m-30) cc_final: 0.7470 (m-30) REVERT: G 58 GLU cc_start: 0.6704 (pm20) cc_final: 0.6463 (pm20) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.3401 time to fit residues: 36.5810 Evaluate side-chains 101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113909 restraints weight = 8100.332| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.28 r_work: 0.3277 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.131 Angle : 0.486 7.536 10117 Z= 0.257 Chirality : 0.041 0.175 1161 Planarity : 0.003 0.040 1263 Dihedral : 8.744 88.964 1225 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.45 % Allowed : 12.74 % Favored : 84.81 % 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 are not related in a simple way. whole: 1.32 (0.29), residues: 902 helix: 2.35 (0.26), residues: 415 sheet: 0.13 (0.37), residues: 189 loop : -0.74 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7466) covalent geometry : angle 0.48636 / 0.26 (10115) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.05744 / 0.03 ( 2) hydrogen bonds : bond 0.03524 / 2.51 ( 398) hydrogen bonds : angle 4.25473 / 3.18 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.186 Fit side-chains REVERT: R 191 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7485 (mtpp) REVERT: R 356 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7351 (mm) REVERT: A 51 LYS cc_start: 0.6267 (ttmt) cc_final: 0.5602 (mtpt) REVERT: A 193 ASP cc_start: 0.8296 (m-30) cc_final: 0.8066 (m-30) REVERT: B 46 ARG cc_start: 0.7031 (mtp-110) cc_final: 0.6091 (mtp85) REVERT: B 153 ASP cc_start: 0.7345 (t0) cc_final: 0.7104 (t0) REVERT: B 155 ASN cc_start: 0.8277 (t0) cc_final: 0.7907 (t0) REVERT: B 267 ASP cc_start: 0.7767 (m-30) cc_final: 0.7480 (m-30) REVERT: G 58 GLU cc_start: 0.6685 (pm20) cc_final: 0.6423 (pm20) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.3371 time to fit residues: 37.8458 Evaluate side-chains 100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113651 restraints weight = 8053.397| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.28 r_work: 0.3278 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.134 Angle : 0.499 7.563 10117 Z= 0.261 Chirality : 0.041 0.174 1161 Planarity : 0.004 0.045 1263 Dihedral : 8.601 88.455 1225 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.57 % Allowed : 13.77 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.29), residues: 902 helix: 2.34 (0.26), residues: 420 sheet: 0.16 (0.38), residues: 184 loop : -0.78 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.010 0.001 TYR R 195 PHE 0.012 0.001 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7466) covalent geometry : angle 0.49911 / 0.26 (10115) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.03945 / 0.02 ( 2) hydrogen bonds : bond 0.03525 / 2.51 ( 398) hydrogen bonds : angle 4.24383 / 3.17 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7512 (mtpp) REVERT: R 356 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7399 (mm) REVERT: A 51 LYS cc_start: 0.6300 (ttmt) cc_final: 0.5632 (mtpt) REVERT: A 193 ASP cc_start: 0.8297 (m-30) cc_final: 0.8066 (m-30) REVERT: A 197 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7716 (mttm) REVERT: B 46 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6125 (mtp85) REVERT: B 153 ASP cc_start: 0.7687 (t0) cc_final: 0.7370 (t0) REVERT: B 155 ASN cc_start: 0.8297 (t0) cc_final: 0.7935 (t0) REVERT: B 267 ASP cc_start: 0.7818 (m-30) cc_final: 0.7544 (m-30) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 0.3313 time to fit residues: 36.3355 Evaluate side-chains 101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113835 restraints weight = 8141.642| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.29 r_work: 0.3279 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7467 Z= 0.124 Angle : 0.489 7.463 10117 Z= 0.256 Chirality : 0.041 0.169 1161 Planarity : 0.004 0.047 1263 Dihedral : 8.366 88.701 1225 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 14.67 % Favored : 83.27 % 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 are not related in a simple way. whole: 1.36 (0.29), residues: 902 helix: 2.38 (0.26), residues: 420 sheet: 0.10 (0.37), residues: 189 loop : -0.73 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.010 0.001 TYR R 195 PHE 0.012 0.001 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 7466) covalent geometry : angle 0.48912 / 0.26 (10115) SS BOND : bond 0.00080 / 0.04 ( 1) SS BOND : angle 0.05869 / 0.03 ( 2) hydrogen bonds : bond 0.03438 / 2.45 ( 398) hydrogen bonds : angle 4.20291 / 3.14 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7520 (mtpp) REVERT: R 356 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7362 (mm) REVERT: A 51 LYS cc_start: 0.6300 (ttmt) cc_final: 0.5631 (mtpt) REVERT: A 193 ASP cc_start: 0.8308 (m-30) cc_final: 0.8076 (m-30) REVERT: A 197 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7698 (mttm) REVERT: B 46 ARG cc_start: 0.7043 (mtp-110) cc_final: 0.6140 (mtp85) REVERT: B 153 ASP cc_start: 0.7744 (t0) cc_final: 0.7475 (t0) REVERT: B 155 ASN cc_start: 0.8316 (t0) cc_final: 0.7953 (t0) REVERT: B 170 ASP cc_start: 0.7570 (t70) cc_final: 0.7003 (t0) REVERT: B 267 ASP cc_start: 0.7807 (m-30) cc_final: 0.7534 (m-30) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.3355 time to fit residues: 35.6958 Evaluate side-chains 100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113418 restraints weight = 7990.143| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.29 r_work: 0.3262 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.120 Angle : 0.487 7.355 10117 Z= 0.255 Chirality : 0.041 0.165 1161 Planarity : 0.004 0.048 1263 Dihedral : 8.117 89.450 1225 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.57 % Allowed : 14.29 % Favored : 83.14 % 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 are not related in a simple way. whole: 1.38 (0.29), residues: 902 helix: 2.43 (0.26), residues: 415 sheet: 0.13 (0.37), residues: 186 loop : -0.74 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.001 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7466) covalent geometry : angle 0.48665 / 0.26 (10115) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.03334 / 0.02 ( 2) hydrogen bonds : bond 0.03377 / 2.41 ( 398) hydrogen bonds : angle 4.16768 / 3.11 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7575 (mtpp) REVERT: R 356 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 51 LYS cc_start: 0.6136 (ttmt) cc_final: 0.5490 (mtpt) REVERT: A 193 ASP cc_start: 0.8308 (m-30) cc_final: 0.8075 (m-30) REVERT: A 197 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7624 (mttm) REVERT: B 46 ARG cc_start: 0.6991 (mtp-110) cc_final: 0.6034 (mtp85) REVERT: B 155 ASN cc_start: 0.8288 (t0) cc_final: 0.7995 (t0) REVERT: B 170 ASP cc_start: 0.7556 (t70) cc_final: 0.7011 (t0) REVERT: B 267 ASP cc_start: 0.7819 (m-30) cc_final: 0.7551 (m-30) REVERT: G 58 GLU cc_start: 0.6632 (pm20) cc_final: 0.6319 (pm20) outliers start: 20 outliers final: 14 residues processed: 105 average time/residue: 0.3356 time to fit residues: 37.9831 Evaluate side-chains 103 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 175 TRP Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112398 restraints weight = 8043.027| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.29 r_work: 0.3249 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7467 Z= 0.142 Angle : 0.507 7.353 10117 Z= 0.267 Chirality : 0.042 0.165 1161 Planarity : 0.004 0.053 1263 Dihedral : 8.079 88.907 1225 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.19 % Allowed : 14.67 % Favored : 83.14 % 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 are not related in a simple way. whole: 1.35 (0.29), residues: 902 helix: 2.35 (0.26), residues: 422 sheet: 0.12 (0.37), residues: 188 loop : -0.73 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.010 0.001 TYR R 195 PHE 0.012 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7466) covalent geometry : angle 0.50727 / 0.27 (10115) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.06542 / 0.04 ( 2) hydrogen bonds : bond 0.03540 / 2.52 ( 398) hydrogen bonds : angle 4.23081 / 3.16 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: R 191 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7578 (mtpp) REVERT: R 356 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7369 (mm) REVERT: A 51 LYS cc_start: 0.6106 (ttmt) cc_final: 0.5465 (mtpt) REVERT: A 193 ASP cc_start: 0.8306 (m-30) cc_final: 0.8078 (m-30) REVERT: A 197 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7634 (mttm) REVERT: B 46 ARG cc_start: 0.6996 (mtp-110) cc_final: 0.6023 (mtp85) REVERT: B 156 GLN cc_start: 0.8301 (mt0) cc_final: 0.8009 (mt0) REVERT: B 170 ASP cc_start: 0.7556 (t70) cc_final: 0.7077 (t0) REVERT: B 267 ASP cc_start: 0.7837 (m-30) cc_final: 0.7563 (m-30) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.3549 time to fit residues: 37.8055 Evaluate side-chains 103 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114248 restraints weight = 7997.243| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.28 r_work: 0.3268 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7467 Z= 0.114 Angle : 0.482 7.279 10117 Z= 0.256 Chirality : 0.041 0.164 1161 Planarity : 0.004 0.055 1263 Dihedral : 7.975 89.307 1225 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.06 % Allowed : 15.06 % Favored : 82.88 % 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 are not related in a simple way. whole: 1.41 (0.29), residues: 902 helix: 2.44 (0.26), residues: 420 sheet: 0.11 (0.37), residues: 186 loop : -0.73 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.009 0.001 TYR R 195 PHE 0.011 0.001 PHE R 204 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7466) covalent geometry : angle 0.48168 / 0.26 (10115) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.02525 / 0.01 ( 2) hydrogen bonds : bond 0.03335 / 2.37 ( 398) hydrogen bonds : angle 4.14422 / 3.09 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.35 seconds wall clock time: 38 minutes 0.60 seconds (2280.60 seconds total)