Starting phenix.real_space_refine on Thu Jul 2 06:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyx_29599/07_2026/8fyx_29599.map" } resolution = 2.62 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= 0.010 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 4674 2.51 5 N 1240 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7325 Number of models: 1 Model: "" Number of chains: 5 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: 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: "R" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 155 Unusual residues: {'J40': 1, 'Y01': 2, 'YLX': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.47, per 1000 atoms: 0.20 Number of scatterers: 7325 At special positions: 0 Unit cell: (82.82, 97.58, 128.74, 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 1240 7.00 C 4674 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: 0.56 Conformation dependent library (CDL) restraints added in 330.7 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: 1728 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 49.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.569A 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: 4.362A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.737A 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 256 through 260 removed outlier: 4.249A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.040A 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: 3.841A 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 24 removed outlier: 3.529A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 88 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: 3.709A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 Processing helix chain 'R' and resid 177 through 183 removed outlier: 4.310A pdb=" N ARG R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 3.785A 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 Processing helix chain 'R' and resid 325 through 368 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 369 through 371 No H-bonds generated for 'chain 'R' and resid 369 through 371' Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.724A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.055A 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 sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.054A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.723A 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: 6.712A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.187A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.472A 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 151 removed outlier: 4.495A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.512A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A 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: 6.632A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.529A 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: 3.591A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1197 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: 1.20 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1193 1.31 - 1.44: 1954 1.44 - 1.56: 4243 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 7470 Sorted by residual: bond pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.23e-02 6.61e+03 1.50e+01 bond pdb=" O4 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.702 1.629 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N VAL R 70 " pdb=" CA VAL R 70 " ideal model delta sigma weight residual 1.461 1.501 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 bond pdb=" O42 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.548 1.484 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 7465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 10071 3.95 - 7.90: 46 7.90 - 11.84: 1 11.84 - 15.79: 0 15.79 - 19.74: 1 Bond angle restraints: 10119 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 92.86 112.60 -19.74 3.00e+00 1.11e-01 4.33e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 112.72 106.33 6.39 1.14e+00 7.69e-01 3.14e+01 angle pdb=" C ASN R 69 " pdb=" N VAL R 70 " pdb=" CA VAL R 70 " ideal model delta sigma weight residual 120.46 127.68 -7.22 1.37e+00 5.33e-01 2.78e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.97 107.87 5.10 1.06e+00 8.90e-01 2.32e+01 angle pdb=" CA ILE R 47 " pdb=" C ILE R 47 " pdb=" O ILE R 47 " ideal model delta sigma weight residual 120.85 115.81 5.04 1.06e+00 8.90e-01 2.26e+01 ... (remaining 10114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 4360 22.62 - 45.24: 244 45.24 - 67.86: 28 67.86 - 90.49: 8 90.49 - 113.11: 1 Dihedral angle restraints: 4641 sinusoidal: 1979 harmonic: 2662 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 65.62 113.11 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 879 0.048 - 0.096: 223 0.096 - 0.144: 50 0.144 - 0.191: 4 0.191 - 0.239: 4 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA VAL R 85 " pdb=" N VAL R 85 " pdb=" C VAL R 85 " pdb=" CB VAL R 85 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA CYS B 271 " pdb=" N CYS B 271 " pdb=" C CYS B 271 " pdb=" CB CYS B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1157 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YLX R 501 " 0.003 2.00e-02 2.50e+03 1.29e-01 2.51e+02 pdb=" C YLX R 501 " -0.002 2.00e-02 2.50e+03 pdb=" O YLX R 501 " -0.164 2.00e-02 2.50e+03 pdb=" C1 YLX R 501 " 0.158 2.00e-02 2.50e+03 pdb=" C8 YLX R 501 " -0.153 2.00e-02 2.50e+03 pdb=" C9 YLX R 501 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 YLX R 501 " -0.041 2.00e-02 2.50e+03 4.53e-02 3.59e+01 pdb=" C16 YLX R 501 " -0.002 2.00e-02 2.50e+03 pdb=" C17 YLX R 501 " 0.056 2.00e-02 2.50e+03 pdb=" C18 YLX R 501 " 0.005 2.00e-02 2.50e+03 pdb=" N2 YLX R 501 " 0.073 2.00e-02 2.50e+03 pdb=" N3 YLX R 501 " -0.042 2.00e-02 2.50e+03 pdb=" N4 YLX R 501 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 185 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C VAL A 185 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL A 185 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 186 " -0.016 2.00e-02 2.50e+03 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 925 2.75 - 3.29: 7226 3.29 - 3.83: 12970 3.83 - 4.36: 15417 4.36 - 4.90: 26644 Nonbonded interactions: 63182 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.215 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.296 3.040 nonbonded pdb=" OD2 ASP R 116 " pdb=" OH TYR R 390 " model vdw 2.301 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.346 3.040 ... (remaining 63177 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: 3.300 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: 0.010 Process input model: 7.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 0.073 7471 Z= 0.299 Angle : 0.755 19.741 10121 Z= 0.440 Chirality : 0.046 0.239 1160 Planarity : 0.006 0.129 1264 Dihedral : 13.796 113.107 2910 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: 0.39 (0.28), residues: 902 helix: 1.58 (0.26), residues: 424 sheet: -0.82 (0.37), residues: 169 loop : -0.90 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.009 0.001 TYR R 195 PHE 0.016 0.002 PHE R 361 TRP 0.013 0.001 TRP R 387 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.30 ( 7470) covalent geometry : angle 0.75456 / 0.44 (10119) SS BOND : bond 0.00164 / 0.09 ( 1) SS BOND : angle 0.64570 / 0.35 ( 2) hydrogen bonds : bond 0.12749 / 8.95 ( 413) hydrogen bonds : angle 6.29267 / 4.54 ( 1197) *********************** 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 97 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.254 Fit side-chains REVERT: A 197 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7413 (mtpp) REVERT: A 209 LYS cc_start: 0.7553 (pttt) cc_final: 0.6957 (pptt) REVERT: B 134 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6297 (ptm160) REVERT: B 217 MET cc_start: 0.7028 (ptt) cc_final: 0.6710 (pmm) REVERT: B 262 MET cc_start: 0.7994 (tpp) cc_final: 0.7358 (tpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.5274 time to fit residues: 54.2299 Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN B 239 ASN R 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.155577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106538 restraints weight = 7593.116| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.39 r_work: 0.2986 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7471 Z= 0.171 Angle : 0.549 8.128 10121 Z= 0.283 Chirality : 0.043 0.186 1160 Planarity : 0.004 0.035 1264 Dihedral : 9.282 88.505 1245 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.90 % Allowed : 7.98 % Favored : 91.12 % 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: 0.76 (0.29), residues: 902 helix: 2.01 (0.25), residues: 425 sheet: -0.79 (0.36), residues: 186 loop : -0.80 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.012 0.001 TYR B 59 PHE 0.016 0.002 PHE R 361 TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 7470) covalent geometry : angle 0.54940 / 0.28 (10119) SS BOND : bond 0.00234 / 0.12 ( 1) SS BOND : angle 0.52331 / 0.28 ( 2) hydrogen bonds : bond 0.04040 / 2.82 ( 413) hydrogen bonds : angle 4.98559 / 3.54 ( 1197) *********************** 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 90 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.276 Fit side-chains REVERT: A 24 ARG cc_start: 0.5752 (mtm-85) cc_final: 0.5250 (mtm110) REVERT: A 197 LYS cc_start: 0.7118 (mtpp) cc_final: 0.6771 (mtpp) REVERT: A 209 LYS cc_start: 0.6952 (pttt) cc_final: 0.6356 (pptt) REVERT: B 134 ARG cc_start: 0.5994 (ptp-110) cc_final: 0.5707 (ptm160) REVERT: B 156 GLN cc_start: 0.7046 (mt0) cc_final: 0.6783 (mt0) REVERT: B 197 ARG cc_start: 0.6462 (mtp85) cc_final: 0.6229 (mtp85) REVERT: B 217 MET cc_start: 0.7413 (ptt) cc_final: 0.6532 (pmm) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 0.4275 time to fit residues: 40.0841 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0570 chunk 62 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104611 restraints weight = 7478.303| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.35 r_work: 0.3247 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7471 Z= 0.126 Angle : 0.497 7.849 10121 Z= 0.257 Chirality : 0.041 0.193 1160 Planarity : 0.003 0.033 1264 Dihedral : 8.926 89.252 1245 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.42 % Allowed : 10.42 % Favored : 88.16 % 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: 0.92 (0.29), residues: 902 helix: 2.22 (0.26), residues: 425 sheet: -0.77 (0.35), residues: 187 loop : -0.84 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.009 0.001 TYR R 195 PHE 0.014 0.001 PHE R 361 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7470) covalent geometry : angle 0.49668 / 0.26 (10119) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 0.44523 / 0.23 ( 2) hydrogen bonds : bond 0.03629 / 2.54 ( 413) hydrogen bonds : angle 4.71652 / 3.34 ( 1197) *********************** 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 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.231 Fit side-chains REVERT: A 24 ARG cc_start: 0.6206 (mtm-85) cc_final: 0.5540 (mtm110) REVERT: A 197 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7259 (mtmt) REVERT: A 209 LYS cc_start: 0.7359 (pttt) cc_final: 0.6736 (pptt) REVERT: B 134 ARG cc_start: 0.6455 (ptp-110) cc_final: 0.6144 (ptm160) REVERT: B 197 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6756 (mtp85) REVERT: B 217 MET cc_start: 0.7813 (ptt) cc_final: 0.7097 (pmm) REVERT: R 386 ASN cc_start: 0.7017 (m-40) cc_final: 0.6734 (m-40) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 0.3861 time to fit residues: 33.9545 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.149372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099548 restraints weight = 7595.337| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.40 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7471 Z= 0.188 Angle : 0.541 7.894 10121 Z= 0.279 Chirality : 0.043 0.206 1160 Planarity : 0.003 0.035 1264 Dihedral : 8.994 87.596 1245 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.90 % Allowed : 12.74 % Favored : 86.36 % 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: 0.75 (0.28), residues: 902 helix: 2.10 (0.25), residues: 426 sheet: -0.87 (0.35), residues: 192 loop : -0.94 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.012 0.001 TYR R 195 PHE 0.020 0.002 PHE R 361 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 7470) covalent geometry : angle 0.54068 / 0.28 (10119) SS BOND : bond 0.00298 / 0.16 ( 1) SS BOND : angle 0.57321 / 0.29 ( 2) hydrogen bonds : bond 0.03916 / 2.73 ( 413) hydrogen bonds : angle 4.82939 / 3.42 ( 1197) *********************** 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 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.314 Fit side-chains REVERT: A 24 ARG cc_start: 0.6169 (mtm-85) cc_final: 0.5527 (mtm110) REVERT: A 197 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7115 (mtpp) REVERT: A 209 LYS cc_start: 0.7340 (pttt) cc_final: 0.6649 (pptt) REVERT: A 257 LYS cc_start: 0.7142 (ptmm) cc_final: 0.6913 (pttm) REVERT: B 134 ARG cc_start: 0.6411 (ptp-110) cc_final: 0.6090 (ptm160) REVERT: B 217 MET cc_start: 0.7955 (ptt) cc_final: 0.7138 (pmm) REVERT: B 219 ARG cc_start: 0.7131 (tpp80) cc_final: 0.6650 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.4091 time to fit residues: 34.9242 Evaluate side-chains 76 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.0030 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN R 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103095 restraints weight = 7529.135| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.38 r_work: 0.3222 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7471 Z= 0.127 Angle : 0.488 7.709 10121 Z= 0.253 Chirality : 0.041 0.187 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.794 89.848 1245 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.51 % Allowed : 13.64 % Favored : 85.84 % 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: 0.89 (0.29), residues: 902 helix: 2.24 (0.25), residues: 425 sheet: -0.80 (0.35), residues: 191 loop : -0.90 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.009 0.001 TYR R 195 PHE 0.014 0.001 PHE R 361 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7470) covalent geometry : angle 0.48760 / 0.25 (10119) SS BOND : bond 0.00101 / 0.05 ( 1) SS BOND : angle 0.55731 / 0.29 ( 2) hydrogen bonds : bond 0.03524 / 2.47 ( 413) hydrogen bonds : angle 4.63633 / 3.29 ( 1197) *********************** 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 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6116 (mtm-85) cc_final: 0.5481 (mtm110) REVERT: A 197 LYS cc_start: 0.7467 (mtpp) cc_final: 0.7180 (mtpp) REVERT: A 209 LYS cc_start: 0.7322 (pttt) cc_final: 0.6631 (pptt) REVERT: A 257 LYS cc_start: 0.7151 (ptmm) cc_final: 0.6928 (pttm) REVERT: A 318 GLU cc_start: 0.7936 (tt0) cc_final: 0.7666 (tt0) REVERT: B 134 ARG cc_start: 0.6350 (ptp-110) cc_final: 0.6024 (ptm160) REVERT: B 217 MET cc_start: 0.7914 (ptt) cc_final: 0.7226 (pmt) REVERT: B 323 ASP cc_start: 0.7592 (p0) cc_final: 0.7358 (p0) REVERT: R 172 MET cc_start: 0.5613 (mtm) cc_final: 0.4519 (mmp) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 0.4347 time to fit residues: 37.6571 Evaluate side-chains 79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103054 restraints weight = 7539.689| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.37 r_work: 0.3221 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7471 Z= 0.130 Angle : 0.496 7.710 10121 Z= 0.257 Chirality : 0.041 0.194 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.646 88.571 1245 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.51 % Allowed : 14.41 % Favored : 85.07 % 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: 0.94 (0.29), residues: 902 helix: 2.30 (0.25), residues: 425 sheet: -0.80 (0.35), residues: 191 loop : -0.89 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.010 0.001 TYR R 195 PHE 0.015 0.001 PHE R 361 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7470) covalent geometry : angle 0.49637 / 0.26 (10119) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.52880 / 0.28 ( 2) hydrogen bonds : bond 0.03501 / 2.45 ( 413) hydrogen bonds : angle 4.59097 / 3.26 ( 1197) *********************** 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 82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6109 (mtm-85) cc_final: 0.5481 (mtm110) REVERT: A 197 LYS cc_start: 0.7475 (mtpp) cc_final: 0.7205 (mtpp) REVERT: A 209 LYS cc_start: 0.7294 (pttt) cc_final: 0.6663 (pptt) REVERT: A 257 LYS cc_start: 0.7155 (ptmm) cc_final: 0.6919 (pttm) REVERT: A 318 GLU cc_start: 0.7853 (tt0) cc_final: 0.7569 (tt0) REVERT: B 134 ARG cc_start: 0.6320 (ptp-110) cc_final: 0.5989 (ptm160) REVERT: B 156 GLN cc_start: 0.7723 (mt0) cc_final: 0.7510 (pt0) REVERT: B 217 MET cc_start: 0.7880 (ptt) cc_final: 0.7188 (pmt) REVERT: B 323 ASP cc_start: 0.7565 (p0) cc_final: 0.7358 (p0) REVERT: R 172 MET cc_start: 0.5649 (mtm) cc_final: 0.4554 (mmp) outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 0.4843 time to fit residues: 41.4140 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN R 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102770 restraints weight = 7578.486| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.38 r_work: 0.3216 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7471 Z= 0.132 Angle : 0.489 7.693 10121 Z= 0.254 Chirality : 0.041 0.193 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.584 88.839 1245 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.90 % Allowed : 14.29 % 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: 0.94 (0.29), residues: 902 helix: 2.29 (0.25), residues: 425 sheet: -0.79 (0.35), residues: 190 loop : -0.88 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.010 0.001 TYR R 195 PHE 0.014 0.001 PHE R 361 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7470) covalent geometry : angle 0.48876 / 0.25 (10119) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.51136 / 0.27 ( 2) hydrogen bonds : bond 0.03492 / 2.44 ( 413) hydrogen bonds : angle 4.57050 / 3.25 ( 1197) *********************** 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 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6120 (mtm-85) cc_final: 0.5493 (mtm110) REVERT: A 197 LYS cc_start: 0.7459 (mtpp) cc_final: 0.7223 (mtpp) REVERT: A 209 LYS cc_start: 0.7322 (pttt) cc_final: 0.6629 (pptt) REVERT: A 257 LYS cc_start: 0.7161 (ptmm) cc_final: 0.6924 (pttm) REVERT: A 318 GLU cc_start: 0.7872 (tt0) cc_final: 0.7587 (tt0) REVERT: B 134 ARG cc_start: 0.6322 (ptp-110) cc_final: 0.5985 (ptm160) REVERT: B 156 GLN cc_start: 0.7711 (mt0) cc_final: 0.7471 (pt0) REVERT: B 217 MET cc_start: 0.7886 (ptt) cc_final: 0.7182 (pmt) REVERT: B 323 ASP cc_start: 0.7532 (p0) cc_final: 0.7288 (p0) REVERT: R 172 MET cc_start: 0.5607 (mtm) cc_final: 0.4507 (mmp) outliers start: 7 outliers final: 3 residues processed: 86 average time/residue: 0.4234 time to fit residues: 39.0555 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 126 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102024 restraints weight = 7623.925| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.38 r_work: 0.3192 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7471 Z= 0.146 Angle : 0.508 7.707 10121 Z= 0.262 Chirality : 0.042 0.195 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.577 88.521 1245 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.16 % Allowed : 14.80 % Favored : 84.04 % 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: 0.92 (0.29), residues: 902 helix: 2.26 (0.25), residues: 425 sheet: -0.85 (0.35), residues: 191 loop : -0.84 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR R 195 PHE 0.016 0.001 PHE R 361 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7470) covalent geometry : angle 0.50821 / 0.26 (10119) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 0.52033 / 0.27 ( 2) hydrogen bonds : bond 0.03565 / 2.48 ( 413) hydrogen bonds : angle 4.60929 / 3.28 ( 1197) *********************** 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 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6077 (mtm-85) cc_final: 0.5459 (mtm110) REVERT: A 197 LYS cc_start: 0.7472 (mtpp) cc_final: 0.7222 (mtpp) REVERT: A 209 LYS cc_start: 0.7332 (pttt) cc_final: 0.6632 (pptt) REVERT: A 257 LYS cc_start: 0.7148 (ptmm) cc_final: 0.6928 (pttm) REVERT: B 134 ARG cc_start: 0.6271 (ptp-110) cc_final: 0.5939 (ptm160) REVERT: B 146 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 156 GLN cc_start: 0.7691 (mt0) cc_final: 0.7454 (pt0) REVERT: B 217 MET cc_start: 0.7875 (ptt) cc_final: 0.7157 (pmt) REVERT: B 323 ASP cc_start: 0.7526 (p0) cc_final: 0.7317 (p0) REVERT: R 172 MET cc_start: 0.5573 (mtm) cc_final: 0.4482 (mmp) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.4802 time to fit residues: 44.4576 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 126 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.161561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109957 restraints weight = 7127.599| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.48 r_work: 0.3142 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7471 Z= 0.122 Angle : 0.490 7.646 10121 Z= 0.254 Chirality : 0.041 0.189 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.553 89.329 1245 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.64 % Allowed : 15.32 % Favored : 84.04 % 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: 1.00 (0.29), residues: 902 helix: 2.33 (0.25), residues: 425 sheet: -0.80 (0.35), residues: 190 loop : -0.81 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.010 0.001 TYR R 195 PHE 0.013 0.001 PHE R 361 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7470) covalent geometry : angle 0.49042 / 0.25 (10119) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 0.47693 / 0.25 ( 2) hydrogen bonds : bond 0.03422 / 2.38 ( 413) hydrogen bonds : angle 4.54420 / 3.24 ( 1197) *********************** 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 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5936 (mtm-85) cc_final: 0.5329 (mtm110) REVERT: A 197 LYS cc_start: 0.7323 (mtpp) cc_final: 0.7089 (mtpp) REVERT: A 209 LYS cc_start: 0.7211 (pttt) cc_final: 0.6492 (pptt) REVERT: A 257 LYS cc_start: 0.6996 (ptmm) cc_final: 0.6784 (pttm) REVERT: A 318 GLU cc_start: 0.7652 (tt0) cc_final: 0.7321 (tt0) REVERT: B 134 ARG cc_start: 0.6122 (ptp-110) cc_final: 0.5779 (ptm160) REVERT: B 156 GLN cc_start: 0.7483 (mt0) cc_final: 0.7256 (pt0) REVERT: B 217 MET cc_start: 0.7816 (ptt) cc_final: 0.7091 (pmt) REVERT: B 262 MET cc_start: 0.7909 (ttm) cc_final: 0.7679 (ttm) REVERT: B 323 ASP cc_start: 0.7420 (p0) cc_final: 0.7212 (p0) REVERT: R 172 MET cc_start: 0.5481 (mtm) cc_final: 0.4397 (mmp) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.4104 time to fit residues: 36.9352 Evaluate side-chains 80 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 HIS R 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108289 restraints weight = 7151.492| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.48 r_work: 0.3127 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7471 Z= 0.138 Angle : 0.500 7.665 10121 Z= 0.259 Chirality : 0.042 0.194 1160 Planarity : 0.003 0.034 1264 Dihedral : 8.493 88.628 1245 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.39 % Allowed : 15.96 % 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: 0.97 (0.29), residues: 902 helix: 2.29 (0.25), residues: 425 sheet: -0.82 (0.35), residues: 190 loop : -0.78 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.011 0.001 TYR R 195 PHE 0.017 0.002 PHE R 112 TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS R 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7470) covalent geometry : angle 0.50006 / 0.26 (10119) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 0.47057 / 0.24 ( 2) hydrogen bonds : bond 0.03512 / 2.45 ( 413) hydrogen bonds : angle 4.57852 / 3.26 ( 1197) ********************** 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 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5935 (mtm-85) cc_final: 0.5331 (mtm110) REVERT: A 197 LYS cc_start: 0.7343 (mtpp) cc_final: 0.7085 (mtpp) REVERT: A 209 LYS cc_start: 0.7201 (pttt) cc_final: 0.6480 (pptt) REVERT: A 257 LYS cc_start: 0.7000 (ptmm) cc_final: 0.6777 (pttm) REVERT: A 318 GLU cc_start: 0.7655 (tt0) cc_final: 0.7309 (tt0) REVERT: B 134 ARG cc_start: 0.6107 (ptp-110) cc_final: 0.5763 (ptm160) REVERT: B 156 GLN cc_start: 0.7490 (mt0) cc_final: 0.7275 (pt0) REVERT: B 217 MET cc_start: 0.7815 (ptt) cc_final: 0.7075 (pmt) REVERT: B 323 ASP cc_start: 0.7423 (p0) cc_final: 0.7217 (p0) REVERT: R 172 MET cc_start: 0.5469 (mtm) cc_final: 0.4381 (mmp) outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.4759 time to fit residues: 42.5901 Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.158372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106238 restraints weight = 7198.851| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.48 r_work: 0.3093 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7471 Z= 0.171 Angle : 0.522 7.712 10121 Z= 0.271 Chirality : 0.043 0.199 1160 Planarity : 0.003 0.035 1264 Dihedral : 8.583 88.223 1245 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.64 % Allowed : 15.83 % Favored : 83.53 % 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: 0.87 (0.29), residues: 902 helix: 2.19 (0.25), residues: 425 sheet: -0.89 (0.35), residues: 191 loop : -0.79 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.012 0.001 TYR R 195 PHE 0.040 0.002 PHE R 112 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 7470) covalent geometry : angle 0.52157 / 0.27 (10119) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.44450 / 0.21 ( 2) hydrogen bonds : bond 0.03696 / 2.57 ( 413) hydrogen bonds : angle 4.68968 / 3.34 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.80 seconds wall clock time: 46 minutes 1.85 seconds (2761.85 seconds total)