Starting phenix.real_space_refine on Sat Jul 4 21:41:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402.map" model { file = "/net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unh_42402/07_2026/8unh_42402_trim.cif" } resolution = 3.21 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12960 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 67 5.16 5 C 8409 2.51 5 N 2218 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 13244 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "E" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1503 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "G" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "F" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.20, per 1000 atoms: 0.24 Number of scatterers: 13244 At special positions: 0 Unit cell: (96.416, 119.472, 124.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 6 15.00 Mg 2 11.99 O 2542 8.00 N 2218 7.00 C 8409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.17 Conformation dependent library (CDL) restraints added in 621.9 milliseconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 13 sheets defined 49.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 20 through 24 removed outlier: 4.288A pdb=" N ILE B 24 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.005A pdb=" N VAL B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 247 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.142A pdb=" N SER B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 294 removed outlier: 3.615A pdb=" N TYR B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 302 through 316 Processing helix chain 'E' and resid 26 through 39 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.585A pdb=" N GLN E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 145 through 152 removed outlier: 3.700A pdb=" N SER E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 183 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.876A pdb=" N VAL E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 215 Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 235 through 245 Processing helix chain 'E' and resid 246 through 258 removed outlier: 3.882A pdb=" N ALA E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 273 through 276 removed outlier: 4.249A pdb=" N VAL E 276 " --> pdb=" O TYR E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.952A pdb=" N ILE E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 315 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.541A pdb=" N ARG C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 4.396A pdb=" N ALA C 259 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.065A pdb=" N PHE C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 4.188A pdb=" N ILE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.732A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 246 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 277 through 294 removed outlier: 4.389A pdb=" N ILE D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.759A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.630A pdb=" N LYS A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.944A pdb=" N GLU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.157A pdb=" N GLU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 119 through 134 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'H' and resid 119 through 134 Processing helix chain 'F' and resid 1004 through 1015 Processing helix chain 'F' and resid 1056 through 1067 removed outlier: 3.538A pdb=" N LEU F1066 " --> pdb=" O GLY F1062 " (cutoff:3.500A) Processing helix chain 'F' and resid 1096 through 1100 removed outlier: 3.588A pdb=" N VAL F1100 " --> pdb=" O PRO F1097 " (cutoff:3.500A) Processing helix chain 'F' and resid 1119 through 1134 removed outlier: 3.506A pdb=" N ARG F1131 " --> pdb=" O LEU F1127 " (cutoff:3.500A) Processing helix chain 'F' and resid 1185 through 1187 No H-bonds generated for 'chain 'F' and resid 1185 through 1187' Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 75 removed outlier: 6.568A pdb=" N LYS B 102 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 135 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 104 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR B 137 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 106 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'G' and resid 26 through 32 removed outlier: 6.156A pdb=" N GLN G 27 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 41 " --> pdb=" O ASN G 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AA5, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'G' and resid 142 through 143 removed outlier: 7.138A pdb=" N ILE G 147 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS G 164 " --> pdb=" O PHE F1091 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 178 through 179 Processing sheet with id=AA8, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 32 removed outlier: 5.264A pdb=" N GLN H 27 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 208 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 75 removed outlier: 6.578A pdb=" N ILE F1147 " --> pdb=" O LEU F1169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F1180 " --> pdb=" O ILE F1140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 168 through 171 removed outlier: 6.343A pdb=" N THR H 168 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE H 149 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 170 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 180 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 142 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE H 178 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 1021 through 1023 Processing sheet with id=AB4, first strand: chain 'F' and resid 1026 through 1032 removed outlier: 5.939A pdb=" N GLN F1027 " --> pdb=" O ILE F1044 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F1041 " --> pdb=" O ASN F1215 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F1210 " --> pdb=" O LYS F1195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F1114 " --> pdb=" O LEU F1198 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4386 1.37 - 1.51: 3754 1.51 - 1.66: 5225 1.66 - 1.80: 84 1.80 - 1.95: 30 Bond restraints: 13479 Sorted by residual: bond pdb=" O3B AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " ideal model delta sigma weight residual 1.664 1.575 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O3A AGS B 401 " pdb=" PA AGS B 401 " ideal model delta sigma weight residual 1.664 1.585 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.20e-02 6.94e+03 1.27e+01 ... (remaining 13474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 18003 2.07 - 4.14: 206 4.14 - 6.21: 12 6.21 - 8.29: 7 8.29 - 10.36: 7 Bond angle restraints: 18235 Sorted by residual: angle pdb=" N ALA A 56 " pdb=" CA ALA A 56 " pdb=" C ALA A 56 " ideal model delta sigma weight residual 113.43 108.71 4.72 1.26e+00 6.30e-01 1.40e+01 angle pdb=" N ASN A 48 " pdb=" CA ASN A 48 " pdb=" C ASN A 48 " ideal model delta sigma weight residual 111.14 115.01 -3.87 1.08e+00 8.57e-01 1.28e+01 angle pdb=" O3A AGS B 401 " pdb=" PB AGS B 401 " pdb=" O3B AGS B 401 " ideal model delta sigma weight residual 100.38 110.74 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" PB AGS E 401 " pdb=" O3B AGS E 401 " pdb=" PG AGS E 401 " ideal model delta sigma weight residual 129.21 119.07 10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O3A AGS E 401 " pdb=" PB AGS E 401 " pdb=" O3B AGS E 401 " ideal model delta sigma weight residual 100.38 110.32 -9.94 3.00e+00 1.11e-01 1.10e+01 ... (remaining 18230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 7863 33.18 - 66.36: 317 66.36 - 99.54: 43 99.54 - 132.72: 0 132.72 - 165.91: 1 Dihedral angle restraints: 8224 sinusoidal: 3316 harmonic: 4908 Sorted by residual: dihedral pdb=" O1A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual 82.37 -83.54 165.91 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA LEU A 10 " pdb=" C LEU A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" O2A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual -52.28 41.24 -93.52 1 3.00e+01 1.11e-03 1.13e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1740 0.054 - 0.107: 287 0.107 - 0.161: 47 0.161 - 0.215: 1 0.215 - 0.269: 2 Chirality restraints: 2077 Sorted by residual: chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS E 401 " pdb=" C2' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" O3' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA MET C 316 " pdb=" N MET C 316 " pdb=" C MET C 316 " pdb=" CB MET C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 2074 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 254 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO D 255 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 164 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C LYS H 164 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS H 164 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR H 165 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 47 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C ILE A 47 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 47 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 48 " -0.010 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 174 2.56 - 3.14: 11778 3.14 - 3.73: 20612 3.73 - 4.31: 29266 4.31 - 4.90: 50016 Nonbonded interactions: 111846 Sorted by model distance: nonbonded pdb=" O2B AGS E 401 " pdb="MG MG E 402 " model vdw 1.974 2.170 nonbonded pdb=" NZ LYS B 56 " pdb="MG MG B 402 " model vdw 2.102 2.250 nonbonded pdb=" O ASN B 300 " pdb=" OG1 THR B 301 " model vdw 2.148 3.040 nonbonded pdb=" N GLU F1175 " pdb=" OE1 GLU F1175 " model vdw 2.170 3.120 nonbonded pdb=" O2B AGS E 401 " pdb=" O2G AGS E 401 " model vdw 2.195 3.040 ... (remaining 111841 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) selection = (chain 'H' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.004 0.093 13479 Z= 0.218 Angle : 0.557 10.358 18235 Z= 0.305 Chirality : 0.042 0.269 2077 Planarity : 0.003 0.077 2327 Dihedral : 17.623 165.906 5046 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 46.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 0.49 % Allowed : 22.80 % Favored : 76.71 % 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: 0.09 (0.22), residues: 1667 helix: 1.56 (0.20), residues: 698 sheet: -1.52 (0.31), residues: 309 loop : -0.69 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 119 TYR 0.011 0.001 TYR D 261 PHE 0.027 0.001 PHE B 109 TRP 0.009 0.001 TRP E 263 HIS 0.014 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (13479) covalent geometry : angle 0.55708 / 0.31 (18235) hydrogen bonds : bond 0.18252 / 12.42 ( 654) hydrogen bonds : angle 7.07220 / 5.12 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 PHE cc_start: 0.7857 (t80) cc_final: 0.7652 (t80) REVERT: B 142 ASP cc_start: 0.8768 (m-30) cc_final: 0.8534 (p0) REVERT: B 168 MET cc_start: 0.9449 (ttp) cc_final: 0.9137 (ptm) REVERT: B 169 MET cc_start: 0.9077 (mmm) cc_final: 0.8784 (mmm) REVERT: B 172 MET cc_start: 0.9456 (tpt) cc_final: 0.8856 (tpt) REVERT: B 182 HIS cc_start: 0.8834 (m90) cc_final: 0.8550 (m90) REVERT: B 261 TYR cc_start: 0.7879 (t80) cc_final: 0.7637 (t80) REVERT: B 284 MET cc_start: 0.9677 (tmm) cc_final: 0.9388 (tmm) REVERT: B 294 TYR cc_start: 0.9300 (m-80) cc_final: 0.9044 (m-80) REVERT: B 307 TYR cc_start: 0.9052 (t80) cc_final: 0.8683 (t80) REVERT: E 169 MET cc_start: 0.9463 (mtt) cc_final: 0.9079 (mtp) REVERT: E 172 MET cc_start: 0.9331 (tpt) cc_final: 0.9109 (tpt) REVERT: E 284 MET cc_start: 0.9647 (tmm) cc_final: 0.9330 (tmm) REVERT: C 302 GLU cc_start: 0.9224 (pt0) cc_final: 0.8845 (pm20) REVERT: C 317 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6946 (tp40) REVERT: D 244 ASN cc_start: 0.8730 (m110) cc_final: 0.8490 (m-40) REVERT: D 249 GLN cc_start: 0.9332 (tp40) cc_final: 0.9043 (tp-100) REVERT: D 291 ASN cc_start: 0.8666 (t0) cc_final: 0.8282 (t0) REVERT: A 4 PHE cc_start: 0.8107 (m-80) cc_final: 0.7808 (m-80) REVERT: A 21 ASP cc_start: 0.8466 (t0) cc_final: 0.7949 (t0) REVERT: A 30 ASP cc_start: 0.8947 (m-30) cc_final: 0.8716 (m-30) REVERT: A 156 LYS cc_start: 0.9599 (tmtt) cc_final: 0.9334 (tppt) REVERT: G 32 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8327 (ptm-80) REVERT: H 126 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9240 (tp) REVERT: H 134 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8884 (mm-40) REVERT: F 1055 TYR cc_start: 0.8109 (p90) cc_final: 0.7524 (p90) REVERT: F 1128 ARG cc_start: 0.9108 (mpp80) cc_final: 0.8859 (mtp85) REVERT: F 1134 GLN cc_start: 0.8878 (mp10) cc_final: 0.8674 (mp10) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 0.1162 time to fit residues: 39.8140 Evaluate side-chains 184 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN G 124 GLN H 13 ASN H 153 ASN F1179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.039164 restraints weight = 51049.242| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 4.40 r_work: 0.2450 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13479 Z= 0.210 Angle : 0.681 9.142 18235 Z= 0.354 Chirality : 0.046 0.221 2077 Planarity : 0.004 0.055 2327 Dihedral : 11.195 177.043 1876 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 3.36 % Allowed : 20.49 % Favored : 76.15 % 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: -0.25 (0.21), residues: 1667 helix: 1.13 (0.19), residues: 722 sheet: -1.69 (0.28), residues: 321 loop : -0.72 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 162 TYR 0.022 0.002 TYR C 307 PHE 0.025 0.002 PHE B 109 TRP 0.014 0.001 TRP D 318 HIS 0.011 0.002 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (13479) covalent geometry : angle 0.68117 / 0.35 (18235) hydrogen bonds : bond 0.04749 / 3.23 ( 654) hydrogen bonds : angle 5.27297 / 3.82 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7836 (ppp) cc_final: 0.7511 (ppp) REVERT: B 97 PHE cc_start: 0.8544 (t80) cc_final: 0.8227 (t80) REVERT: B 106 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9160 (mm) REVERT: B 120 HIS cc_start: 0.9272 (OUTLIER) cc_final: 0.8809 (m90) REVERT: B 142 ASP cc_start: 0.9353 (m-30) cc_final: 0.8942 (p0) REVERT: B 169 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (mmt) REVERT: B 172 MET cc_start: 0.9440 (tpt) cc_final: 0.8951 (tpt) REVERT: B 182 HIS cc_start: 0.8986 (m90) cc_final: 0.8535 (m90) REVERT: B 281 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 284 MET cc_start: 0.9792 (tmm) cc_final: 0.9438 (tmm) REVERT: B 307 TYR cc_start: 0.9305 (t80) cc_final: 0.9030 (t80) REVERT: E 120 HIS cc_start: 0.9024 (m170) cc_final: 0.8769 (m170) REVERT: E 137 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8541 (p) REVERT: E 169 MET cc_start: 0.9586 (mtt) cc_final: 0.9377 (mtp) REVERT: E 240 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.9047 (tm-30) REVERT: E 284 MET cc_start: 0.9735 (tmm) cc_final: 0.9471 (tmm) REVERT: E 316 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8812 (mmm) REVERT: C 284 MET cc_start: 0.9532 (tmm) cc_final: 0.9321 (ppp) REVERT: C 302 GLU cc_start: 0.9572 (OUTLIER) cc_final: 0.9185 (pm20) REVERT: C 305 LEU cc_start: 0.9588 (mm) cc_final: 0.9264 (mp) REVERT: D 244 ASN cc_start: 0.8731 (m110) cc_final: 0.8455 (m-40) REVERT: D 249 GLN cc_start: 0.9639 (tp40) cc_final: 0.9394 (tp-100) REVERT: D 261 TYR cc_start: 0.8793 (t80) cc_final: 0.8521 (t80) REVERT: D 270 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9222 (pt0) REVERT: D 284 MET cc_start: 0.9537 (tmm) cc_final: 0.9073 (tmm) REVERT: D 291 ASN cc_start: 0.8949 (t0) cc_final: 0.8673 (t0) REVERT: A 4 PHE cc_start: 0.8573 (m-80) cc_final: 0.8162 (m-80) REVERT: A 21 ASP cc_start: 0.9075 (t0) cc_final: 0.8755 (t0) REVERT: A 30 ASP cc_start: 0.9343 (m-30) cc_final: 0.9141 (m-30) REVERT: A 156 LYS cc_start: 0.9664 (tmtt) cc_final: 0.9323 (tppt) REVERT: A 168 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8589 (mmmt) REVERT: A 172 LYS cc_start: 0.9038 (mppt) cc_final: 0.8757 (mmtm) REVERT: G 30 MET cc_start: 0.9080 (ptt) cc_final: 0.8623 (ptm) REVERT: G 32 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8067 (ttt-90) REVERT: G 51 ASP cc_start: 0.9400 (OUTLIER) cc_final: 0.9053 (m-30) REVERT: H 30 MET cc_start: 0.9122 (ptp) cc_final: 0.8689 (ptp) REVERT: H 172 TYR cc_start: 0.9138 (t80) cc_final: 0.8913 (t80) REVERT: F 1030 MET cc_start: 0.9075 (ptt) cc_final: 0.8806 (ptt) REVERT: F 1055 TYR cc_start: 0.8539 (p90) cc_final: 0.8217 (p90) REVERT: F 1134 GLN cc_start: 0.9019 (mp10) cc_final: 0.8814 (mp10) outliers start: 48 outliers final: 12 residues processed: 241 average time/residue: 0.1194 time to fit residues: 42.5351 Evaluate side-chains 202 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain F residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.039217 restraints weight = 52368.186| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 4.33 r_work: 0.2514 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13479 Z= 0.184 Angle : 0.624 8.136 18235 Z= 0.320 Chirality : 0.045 0.308 2077 Planarity : 0.004 0.049 2327 Dihedral : 10.426 179.647 1868 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.34 % Rotamer: Outliers : 3.29 % Allowed : 21.05 % Favored : 75.66 % 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: -0.24 (0.20), residues: 1667 helix: 1.17 (0.19), residues: 726 sheet: -1.65 (0.28), residues: 309 loop : -0.81 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F1131 TYR 0.019 0.002 TYR D 285 PHE 0.017 0.002 PHE B 109 TRP 0.012 0.001 TRP D 318 HIS 0.009 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (13479) covalent geometry : angle 0.62392 / 0.32 (18235) hydrogen bonds : bond 0.04305 / 2.93 ( 654) hydrogen bonds : angle 4.94272 / 3.57 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 PHE cc_start: 0.8481 (t80) cc_final: 0.8224 (t80) REVERT: B 169 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9124 (mmt) REVERT: B 172 MET cc_start: 0.9445 (tpt) cc_final: 0.8896 (tpt) REVERT: B 182 HIS cc_start: 0.9018 (m90) cc_final: 0.8470 (m90) REVERT: B 281 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8893 (tt) REVERT: B 284 MET cc_start: 0.9788 (tmm) cc_final: 0.9353 (tmm) REVERT: B 307 TYR cc_start: 0.9214 (t80) cc_final: 0.8919 (t80) REVERT: E 70 ASP cc_start: 0.9210 (t0) cc_final: 0.8981 (t0) REVERT: E 120 HIS cc_start: 0.9041 (m170) cc_final: 0.8799 (m170) REVERT: E 137 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.8479 (p) REVERT: E 284 MET cc_start: 0.9783 (tmm) cc_final: 0.9580 (tmm) REVERT: E 316 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8944 (mmm) REVERT: C 302 GLU cc_start: 0.9522 (OUTLIER) cc_final: 0.9177 (pm20) REVERT: C 305 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9276 (mp) REVERT: C 307 TYR cc_start: 0.9433 (t80) cc_final: 0.9168 (t80) REVERT: C 311 GLN cc_start: 0.9588 (OUTLIER) cc_final: 0.9378 (mt0) REVERT: D 244 ASN cc_start: 0.8785 (m110) cc_final: 0.8480 (m-40) REVERT: D 249 GLN cc_start: 0.9680 (tp40) cc_final: 0.9436 (tp-100) REVERT: D 270 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9110 (pt0) REVERT: D 284 MET cc_start: 0.9599 (tmm) cc_final: 0.9054 (tmm) REVERT: D 315 GLU cc_start: 0.9105 (tp30) cc_final: 0.8772 (tt0) REVERT: A 4 PHE cc_start: 0.8785 (m-80) cc_final: 0.8381 (m-80) REVERT: A 21 ASP cc_start: 0.9258 (t0) cc_final: 0.8959 (t0) REVERT: A 99 MET cc_start: 0.9211 (mmm) cc_final: 0.8865 (mmm) REVERT: A 156 LYS cc_start: 0.9668 (tmtt) cc_final: 0.9441 (tppt) REVERT: A 168 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8712 (mmmt) REVERT: A 172 LYS cc_start: 0.9154 (mppt) cc_final: 0.8855 (mmtm) REVERT: G 16 THR cc_start: 0.9549 (m) cc_final: 0.9308 (p) REVERT: G 30 MET cc_start: 0.9228 (ptt) cc_final: 0.8816 (ptm) REVERT: G 32 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8511 (ptm-80) REVERT: G 51 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9165 (m-30) REVERT: G 210 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: H 30 MET cc_start: 0.9121 (ptp) cc_final: 0.8809 (ptp) REVERT: H 172 TYR cc_start: 0.9219 (t80) cc_final: 0.8782 (t80) REVERT: F 1001 MET cc_start: 0.8810 (ptt) cc_final: 0.8493 (ptp) REVERT: F 1030 MET cc_start: 0.9198 (ptt) cc_final: 0.8980 (ptt) REVERT: F 1055 TYR cc_start: 0.8450 (p90) cc_final: 0.8117 (p90) outliers start: 47 outliers final: 19 residues processed: 233 average time/residue: 0.1142 time to fit residues: 39.7478 Evaluate side-chains 201 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 95 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.040220 restraints weight = 51168.728| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 4.50 r_work: 0.2497 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13479 Z= 0.126 Angle : 0.599 9.575 18235 Z= 0.302 Chirality : 0.044 0.307 2077 Planarity : 0.003 0.047 2327 Dihedral : 8.918 175.718 1866 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 3.57 % Allowed : 21.40 % Favored : 75.03 % 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: -0.17 (0.21), residues: 1667 helix: 1.14 (0.19), residues: 728 sheet: -1.51 (0.28), residues: 314 loop : -0.73 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 162 TYR 0.019 0.002 TYR B 214 PHE 0.015 0.001 PHE A 63 TRP 0.011 0.001 TRP E 263 HIS 0.006 0.001 HIS D 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13479) covalent geometry : angle 0.59861 / 0.30 (18235) hydrogen bonds : bond 0.03839 / 2.60 ( 654) hydrogen bonds : angle 4.73765 / 3.41 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8089 (ppp) cc_final: 0.7777 (ppp) REVERT: B 71 MET cc_start: 0.9095 (tmm) cc_final: 0.8866 (tmm) REVERT: B 97 PHE cc_start: 0.8626 (t80) cc_final: 0.8313 (t80) REVERT: B 169 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9134 (mmt) REVERT: B 172 MET cc_start: 0.9428 (tpt) cc_final: 0.8965 (tpt) REVERT: B 182 HIS cc_start: 0.9001 (m90) cc_final: 0.8498 (m-70) REVERT: B 284 MET cc_start: 0.9767 (tmm) cc_final: 0.9424 (tmm) REVERT: B 307 TYR cc_start: 0.9240 (t80) cc_final: 0.8988 (t80) REVERT: E 70 ASP cc_start: 0.9124 (t0) cc_final: 0.8908 (t0) REVERT: E 120 HIS cc_start: 0.9077 (m170) cc_final: 0.8796 (m170) REVERT: E 137 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8212 (p) REVERT: E 316 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8769 (mmm) REVERT: C 284 MET cc_start: 0.9597 (tmm) cc_final: 0.9346 (ppp) REVERT: C 302 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9161 (pm20) REVERT: C 305 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9288 (mt) REVERT: D 244 ASN cc_start: 0.8721 (m110) cc_final: 0.8424 (m-40) REVERT: D 249 GLN cc_start: 0.9691 (tp40) cc_final: 0.9488 (tp-100) REVERT: D 261 TYR cc_start: 0.8903 (t80) cc_final: 0.8606 (t80) REVERT: D 270 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9074 (pt0) REVERT: D 284 MET cc_start: 0.9652 (tmm) cc_final: 0.9172 (tmm) REVERT: D 304 HIS cc_start: 0.9572 (OUTLIER) cc_final: 0.9188 (t70) REVERT: A 4 PHE cc_start: 0.8578 (m-80) cc_final: 0.8061 (m-80) REVERT: A 21 ASP cc_start: 0.9089 (t0) cc_final: 0.8801 (t0) REVERT: A 99 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8750 (mmm) REVERT: A 156 LYS cc_start: 0.9647 (tmtt) cc_final: 0.9387 (tppt) REVERT: A 168 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8412 (mmmt) REVERT: A 172 LYS cc_start: 0.9142 (mppt) cc_final: 0.8821 (mmtm) REVERT: G 16 THR cc_start: 0.9479 (m) cc_final: 0.9235 (p) REVERT: G 22 MET cc_start: 0.9473 (ttm) cc_final: 0.8898 (tpp) REVERT: G 30 MET cc_start: 0.9177 (ptt) cc_final: 0.8719 (ptm) REVERT: G 32 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8204 (ttt-90) REVERT: G 38 THR cc_start: 0.9613 (OUTLIER) cc_final: 0.9305 (m) REVERT: G 51 ASP cc_start: 0.9394 (OUTLIER) cc_final: 0.9154 (m-30) REVERT: G 165 TYR cc_start: 0.9094 (t80) cc_final: 0.8694 (t80) REVERT: G 210 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: H 30 MET cc_start: 0.9052 (ptp) cc_final: 0.8494 (ptp) REVERT: H 87 ARG cc_start: 0.8840 (mpp80) cc_final: 0.8563 (mpp80) REVERT: H 117 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8629 (tm-30) REVERT: H 172 TYR cc_start: 0.9208 (t80) cc_final: 0.8651 (t80) REVERT: H 184 MET cc_start: 0.9340 (mmm) cc_final: 0.9130 (mmm) REVERT: F 1001 MET cc_start: 0.8616 (ptt) cc_final: 0.8315 (ptp) REVERT: F 1030 MET cc_start: 0.9146 (ptt) cc_final: 0.8945 (ptt) REVERT: F 1055 TYR cc_start: 0.8348 (p90) cc_final: 0.8018 (p90) outliers start: 51 outliers final: 22 residues processed: 248 average time/residue: 0.1115 time to fit residues: 41.3727 Evaluate side-chains 210 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN F1179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.039597 restraints weight = 51588.085| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 4.47 r_work: 0.2480 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13479 Z= 0.148 Angle : 0.605 8.929 18235 Z= 0.306 Chirality : 0.044 0.269 2077 Planarity : 0.003 0.044 2327 Dihedral : 8.326 171.825 1866 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.72 % Favored : 96.04 % Rotamer: Outliers : 3.71 % Allowed : 22.31 % Favored : 73.99 % 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: -0.10 (0.21), residues: 1667 helix: 1.20 (0.19), residues: 730 sheet: -1.45 (0.28), residues: 314 loop : -0.72 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 162 TYR 0.025 0.002 TYR C 307 PHE 0.017 0.001 PHE E 264 TRP 0.009 0.001 TRP D 318 HIS 0.017 0.002 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13479) covalent geometry : angle 0.60511 / 0.31 (18235) hydrogen bonds : bond 0.03823 / 2.60 ( 654) hydrogen bonds : angle 4.74416 / 3.41 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8094 (ppp) cc_final: 0.7764 (ppp) REVERT: B 71 MET cc_start: 0.9088 (tmm) cc_final: 0.8864 (tmm) REVERT: B 97 PHE cc_start: 0.8633 (t80) cc_final: 0.8309 (t80) REVERT: B 106 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9035 (mm) REVERT: B 172 MET cc_start: 0.9414 (tpt) cc_final: 0.8985 (tpt) REVERT: B 182 HIS cc_start: 0.8977 (m90) cc_final: 0.8499 (m-70) REVERT: B 284 MET cc_start: 0.9777 (tmm) cc_final: 0.9427 (tmm) REVERT: B 307 TYR cc_start: 0.9160 (t80) cc_final: 0.8868 (t80) REVERT: E 70 ASP cc_start: 0.9129 (t0) cc_final: 0.8914 (t0) REVERT: E 112 SER cc_start: 0.8082 (m) cc_final: 0.7599 (p) REVERT: E 120 HIS cc_start: 0.9050 (m170) cc_final: 0.8767 (m170) REVERT: E 137 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8297 (p) REVERT: E 168 MET cc_start: 0.9127 (mtt) cc_final: 0.8317 (mtt) REVERT: E 316 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8768 (mmm) REVERT: C 284 MET cc_start: 0.9574 (tmm) cc_final: 0.9364 (ppp) REVERT: C 302 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9167 (pm20) REVERT: C 305 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9334 (mt) REVERT: D 244 ASN cc_start: 0.8740 (m110) cc_final: 0.8441 (m-40) REVERT: D 249 GLN cc_start: 0.9695 (tp40) cc_final: 0.9495 (tp-100) REVERT: D 270 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9081 (pt0) REVERT: D 284 MET cc_start: 0.9646 (tmm) cc_final: 0.9135 (tmm) REVERT: A 4 PHE cc_start: 0.8611 (m-80) cc_final: 0.8114 (m-80) REVERT: A 21 ASP cc_start: 0.9078 (t0) cc_final: 0.8763 (t0) REVERT: A 99 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8733 (mmm) REVERT: A 156 LYS cc_start: 0.9649 (tmtt) cc_final: 0.9389 (tppt) REVERT: A 168 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8607 (mmmt) REVERT: A 171 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7876 (t) REVERT: A 172 LYS cc_start: 0.9174 (mppt) cc_final: 0.8908 (mmtm) REVERT: G 16 THR cc_start: 0.9496 (m) cc_final: 0.9258 (p) REVERT: G 22 MET cc_start: 0.9488 (ttm) cc_final: 0.8765 (ttm) REVERT: G 30 MET cc_start: 0.9166 (ptt) cc_final: 0.8815 (ptm) REVERT: G 32 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8163 (ttt-90) REVERT: G 38 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9314 (m) REVERT: G 51 ASP cc_start: 0.9406 (OUTLIER) cc_final: 0.9046 (m-30) REVERT: G 210 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: H 30 MET cc_start: 0.9055 (ptp) cc_final: 0.8662 (ptp) REVERT: H 117 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: H 162 ARG cc_start: 0.9209 (ttm110) cc_final: 0.8491 (ptp-110) REVERT: H 172 TYR cc_start: 0.9216 (t80) cc_final: 0.8686 (t80) REVERT: H 184 MET cc_start: 0.9361 (mmm) cc_final: 0.9023 (mmm) REVERT: F 1001 MET cc_start: 0.8600 (ptt) cc_final: 0.8315 (ptp) REVERT: F 1055 TYR cc_start: 0.8384 (p90) cc_final: 0.8023 (p90) REVERT: F 1163 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9043 (t) outliers start: 53 outliers final: 31 residues processed: 223 average time/residue: 0.1109 time to fit residues: 37.0433 Evaluate side-chains 220 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 120 optimal weight: 9.9990 chunk 62 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.040536 restraints weight = 51330.157| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 4.51 r_work: 0.2513 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13479 Z= 0.119 Angle : 0.611 11.406 18235 Z= 0.303 Chirality : 0.044 0.304 2077 Planarity : 0.003 0.044 2327 Dihedral : 7.676 164.050 1866 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 3.50 % Allowed : 22.59 % Favored : 73.92 % 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: 0.02 (0.21), residues: 1667 helix: 1.31 (0.19), residues: 730 sheet: -1.36 (0.28), residues: 314 loop : -0.67 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 162 TYR 0.018 0.002 TYR B 261 PHE 0.017 0.001 PHE A 63 TRP 0.009 0.001 TRP E 263 HIS 0.023 0.002 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13479) covalent geometry : angle 0.61094 / 0.30 (18235) hydrogen bonds : bond 0.03674 / 2.49 ( 654) hydrogen bonds : angle 4.69006 / 3.37 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8100 (ppp) cc_final: 0.7754 (ppp) REVERT: B 58 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9210 (m) REVERT: B 71 MET cc_start: 0.9107 (tmm) cc_final: 0.8856 (tmm) REVERT: B 97 PHE cc_start: 0.8612 (t80) cc_final: 0.8278 (t80) REVERT: B 106 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9000 (mm) REVERT: B 172 MET cc_start: 0.9442 (tpt) cc_final: 0.8927 (tpt) REVERT: B 182 HIS cc_start: 0.8985 (m90) cc_final: 0.8485 (m-70) REVERT: B 284 MET cc_start: 0.9795 (tmm) cc_final: 0.9465 (tmm) REVERT: B 307 TYR cc_start: 0.9132 (t80) cc_final: 0.8860 (t80) REVERT: E 70 ASP cc_start: 0.9112 (t0) cc_final: 0.8903 (t0) REVERT: E 112 SER cc_start: 0.7833 (m) cc_final: 0.7381 (p) REVERT: E 120 HIS cc_start: 0.9116 (m170) cc_final: 0.8823 (m170) REVERT: E 137 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8200 (p) REVERT: E 316 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8720 (mmm) REVERT: C 276 VAL cc_start: 0.8988 (t) cc_final: 0.8738 (t) REVERT: C 279 GLN cc_start: 0.9302 (pp30) cc_final: 0.9054 (pp30) REVERT: C 302 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9118 (pm20) REVERT: C 305 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9332 (mt) REVERT: D 270 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9126 (pt0) REVERT: D 284 MET cc_start: 0.9660 (tmm) cc_final: 0.9108 (tmm) REVERT: A 4 PHE cc_start: 0.8602 (m-80) cc_final: 0.8082 (m-80) REVERT: A 12 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8725 (tp30) REVERT: A 21 ASP cc_start: 0.9035 (t0) cc_final: 0.8710 (t0) REVERT: A 63 PHE cc_start: 0.9151 (t80) cc_final: 0.8934 (t80) REVERT: A 99 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8557 (mmm) REVERT: A 156 LYS cc_start: 0.9627 (tmtt) cc_final: 0.9360 (tppt) REVERT: A 168 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8642 (mmmt) REVERT: A 171 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7915 (t) REVERT: A 172 LYS cc_start: 0.9203 (mppt) cc_final: 0.8922 (mmtm) REVERT: G 16 THR cc_start: 0.9450 (m) cc_final: 0.9202 (p) REVERT: G 22 MET cc_start: 0.9483 (ttm) cc_final: 0.8815 (ttm) REVERT: G 30 MET cc_start: 0.9210 (ptt) cc_final: 0.8897 (ptm) REVERT: G 32 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8078 (ttt-90) REVERT: G 51 ASP cc_start: 0.9402 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: G 189 MET cc_start: 0.9635 (pmm) cc_final: 0.9391 (pmm) REVERT: G 210 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: H 30 MET cc_start: 0.9064 (ptp) cc_final: 0.8673 (ptp) REVERT: H 87 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8537 (mpp80) REVERT: H 137 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9296 (m) REVERT: H 162 ARG cc_start: 0.9221 (ttm110) cc_final: 0.8545 (ptp-110) REVERT: H 172 TYR cc_start: 0.9209 (t80) cc_final: 0.8716 (t80) REVERT: F 1001 MET cc_start: 0.8617 (ptt) cc_final: 0.8367 (ptp) REVERT: F 1055 TYR cc_start: 0.8351 (p90) cc_final: 0.7987 (p90) REVERT: F 1087 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8110 (ttp-110) REVERT: F 1163 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9099 (t) outliers start: 50 outliers final: 26 residues processed: 231 average time/residue: 0.1031 time to fit residues: 34.8657 Evaluate side-chains 222 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1184 MET Chi-restraints excluded: chain F residue 1189 MET Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 GLN B 120 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.038439 restraints weight = 52620.531| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 4.36 r_work: 0.2470 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13479 Z= 0.236 Angle : 0.663 11.486 18235 Z= 0.333 Chirality : 0.045 0.331 2077 Planarity : 0.003 0.040 2327 Dihedral : 7.536 156.376 1866 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.14 % Rotamer: Outliers : 3.78 % Allowed : 22.94 % Favored : 73.29 % 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: 0.07 (0.21), residues: 1667 helix: 1.27 (0.19), residues: 736 sheet: -1.32 (0.28), residues: 316 loop : -0.56 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 275 TYR 0.021 0.002 TYR C 307 PHE 0.020 0.002 PHE E 264 TRP 0.010 0.001 TRP E 318 HIS 0.016 0.002 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (13479) covalent geometry : angle 0.66280 / 0.33 (18235) hydrogen bonds : bond 0.03977 / 2.70 ( 654) hydrogen bonds : angle 4.85914 / 3.49 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8178 (ppp) cc_final: 0.7825 (ppp) REVERT: B 13 GLN cc_start: 0.9857 (OUTLIER) cc_final: 0.9372 (mp10) REVERT: B 97 PHE cc_start: 0.8631 (t80) cc_final: 0.8279 (t80) REVERT: B 106 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9073 (mm) REVERT: B 182 HIS cc_start: 0.9024 (m90) cc_final: 0.8515 (m-70) REVERT: B 284 MET cc_start: 0.9825 (tmm) cc_final: 0.9480 (tmm) REVERT: B 307 TYR cc_start: 0.9178 (t80) cc_final: 0.8867 (t80) REVERT: E 112 SER cc_start: 0.8329 (m) cc_final: 0.7862 (p) REVERT: E 137 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.8538 (p) REVERT: E 256 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8931 (tttp) REVERT: E 316 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8913 (mmm) REVERT: C 276 VAL cc_start: 0.8962 (t) cc_final: 0.8716 (t) REVERT: C 279 GLN cc_start: 0.9314 (pp30) cc_final: 0.9088 (pp30) REVERT: C 302 GLU cc_start: 0.9433 (OUTLIER) cc_final: 0.9151 (pm20) REVERT: C 305 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9353 (mp) REVERT: D 270 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9104 (pt0) REVERT: D 284 MET cc_start: 0.9675 (tmm) cc_final: 0.9115 (tmm) REVERT: D 304 HIS cc_start: 0.9665 (OUTLIER) cc_final: 0.9392 (t70) REVERT: A 4 PHE cc_start: 0.8798 (m-80) cc_final: 0.8251 (m-80) REVERT: A 21 ASP cc_start: 0.9227 (t0) cc_final: 0.8928 (t0) REVERT: A 99 MET cc_start: 0.9172 (mmm) cc_final: 0.8830 (mmm) REVERT: A 117 ASP cc_start: 0.8895 (t0) cc_final: 0.8574 (t0) REVERT: A 156 LYS cc_start: 0.9658 (tmtt) cc_final: 0.9415 (tppt) REVERT: A 168 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8698 (mmmt) REVERT: A 171 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 172 LYS cc_start: 0.9278 (mppt) cc_final: 0.8998 (mmtm) REVERT: G 16 THR cc_start: 0.9501 (m) cc_final: 0.9262 (p) REVERT: G 30 MET cc_start: 0.9235 (ptt) cc_final: 0.8829 (ptm) REVERT: G 32 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8275 (ttt-90) REVERT: G 51 ASP cc_start: 0.9376 (OUTLIER) cc_final: 0.9110 (m-30) REVERT: G 210 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: H 117 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8837 (tm-30) REVERT: H 162 ARG cc_start: 0.9211 (ttm110) cc_final: 0.8737 (ptp-110) REVERT: H 172 TYR cc_start: 0.9243 (t80) cc_final: 0.8690 (t80) REVERT: F 1001 MET cc_start: 0.8738 (ptt) cc_final: 0.8490 (ptp) REVERT: F 1030 MET cc_start: 0.9469 (ptm) cc_final: 0.9196 (ptp) REVERT: F 1055 TYR cc_start: 0.8448 (p90) cc_final: 0.8066 (p90) REVERT: F 1087 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8217 (ttp-110) REVERT: F 1163 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9182 (t) outliers start: 54 outliers final: 34 residues processed: 219 average time/residue: 0.1025 time to fit residues: 33.1275 Evaluate side-chains 218 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain E residue 314 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.040710 restraints weight = 51899.693| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.37 r_work: 0.2593 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13479 Z= 0.131 Angle : 0.657 12.142 18235 Z= 0.321 Chirality : 0.045 0.328 2077 Planarity : 0.003 0.042 2327 Dihedral : 7.292 148.839 1866 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.90 % Favored : 95.92 % Rotamer: Outliers : 3.29 % Allowed : 23.64 % Favored : 73.08 % 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: 0.17 (0.21), residues: 1667 helix: 1.37 (0.19), residues: 731 sheet: -1.29 (0.28), residues: 314 loop : -0.52 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 275 TYR 0.026 0.002 TYR C 273 PHE 0.027 0.001 PHE C 264 TRP 0.010 0.001 TRP E 263 HIS 0.013 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13479) covalent geometry : angle 0.65746 / 0.32 (18235) hydrogen bonds : bond 0.03672 / 2.51 ( 654) hydrogen bonds : angle 4.78500 / 3.43 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8110 (ppp) cc_final: 0.7755 (ppp) REVERT: B 13 GLN cc_start: 0.9855 (OUTLIER) cc_final: 0.9412 (mp10) REVERT: B 97 PHE cc_start: 0.8551 (t80) cc_final: 0.8181 (t80) REVERT: B 106 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9147 (mm) REVERT: B 169 MET cc_start: 0.9261 (mmt) cc_final: 0.8943 (mmt) REVERT: B 182 HIS cc_start: 0.8993 (m90) cc_final: 0.8435 (m-70) REVERT: B 284 MET cc_start: 0.9779 (tmm) cc_final: 0.9493 (tmm) REVERT: B 307 TYR cc_start: 0.9115 (t80) cc_final: 0.8806 (t80) REVERT: E 70 ASP cc_start: 0.9262 (t0) cc_final: 0.9052 (t0) REVERT: E 112 SER cc_start: 0.8237 (m) cc_final: 0.7840 (p) REVERT: E 120 HIS cc_start: 0.8990 (m170) cc_final: 0.8785 (m170) REVERT: E 137 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.8471 (p) REVERT: E 168 MET cc_start: 0.9245 (mmt) cc_final: 0.9018 (mmt) REVERT: E 256 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8928 (tttt) REVERT: E 316 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8877 (mmm) REVERT: C 276 VAL cc_start: 0.8924 (t) cc_final: 0.8657 (t) REVERT: C 284 MET cc_start: 0.9301 (ppp) cc_final: 0.9077 (ppp) REVERT: C 302 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9095 (pm20) REVERT: C 305 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9283 (mt) REVERT: D 270 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9082 (pt0) REVERT: D 284 MET cc_start: 0.9652 (tmm) cc_final: 0.9082 (tmm) REVERT: D 304 HIS cc_start: 0.9596 (OUTLIER) cc_final: 0.9368 (t70) REVERT: A 4 PHE cc_start: 0.8800 (m-80) cc_final: 0.8282 (m-80) REVERT: A 12 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8612 (tp30) REVERT: A 21 ASP cc_start: 0.9285 (t0) cc_final: 0.9015 (t0) REVERT: A 99 MET cc_start: 0.9075 (mmm) cc_final: 0.8779 (mmm) REVERT: A 117 ASP cc_start: 0.8945 (t0) cc_final: 0.8600 (t0) REVERT: A 156 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9402 (tppt) REVERT: A 168 LYS cc_start: 0.9287 (mmmt) cc_final: 0.8742 (mmmt) REVERT: A 171 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 172 LYS cc_start: 0.9294 (mppt) cc_final: 0.8988 (mmtm) REVERT: G 16 THR cc_start: 0.9454 (m) cc_final: 0.9201 (p) REVERT: G 30 MET cc_start: 0.9216 (ptt) cc_final: 0.9009 (ptm) REVERT: G 32 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8367 (ttt-90) REVERT: G 51 ASP cc_start: 0.9413 (OUTLIER) cc_final: 0.9099 (m-30) REVERT: G 124 GLN cc_start: 0.9298 (pt0) cc_final: 0.8271 (pp30) REVERT: G 128 ARG cc_start: 0.9451 (mtt90) cc_final: 0.8944 (mtt90) REVERT: G 189 MET cc_start: 0.9681 (pmm) cc_final: 0.9287 (pmm) REVERT: G 210 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: H 87 ARG cc_start: 0.8752 (mpp80) cc_final: 0.8489 (mpp80) REVERT: H 117 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8871 (tm-30) REVERT: H 162 ARG cc_start: 0.9229 (ttm110) cc_final: 0.8617 (ptp-110) REVERT: H 172 TYR cc_start: 0.9206 (t80) cc_final: 0.8703 (t80) REVERT: F 1030 MET cc_start: 0.9432 (ptm) cc_final: 0.9206 (ptp) REVERT: F 1055 TYR cc_start: 0.8329 (p90) cc_final: 0.7956 (p90) REVERT: F 1087 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: F 1163 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9285 (t) outliers start: 47 outliers final: 30 residues processed: 226 average time/residue: 0.1132 time to fit residues: 37.4024 Evaluate side-chains 221 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 0.0170 chunk 84 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.040146 restraints weight = 52519.348| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.44 r_work: 0.2527 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13479 Z= 0.143 Angle : 0.666 13.535 18235 Z= 0.325 Chirality : 0.045 0.305 2077 Planarity : 0.003 0.042 2327 Dihedral : 7.214 146.587 1866 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Rotamer: Outliers : 3.29 % Allowed : 24.55 % Favored : 72.17 % 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: 0.22 (0.21), residues: 1667 helix: 1.36 (0.19), residues: 732 sheet: -1.24 (0.28), residues: 316 loop : -0.43 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 275 TYR 0.023 0.002 TYR C 307 PHE 0.023 0.001 PHE A 63 TRP 0.009 0.001 TRP E 263 HIS 0.013 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13479) covalent geometry : angle 0.66563 / 0.33 (18235) hydrogen bonds : bond 0.03707 / 2.53 ( 654) hydrogen bonds : angle 4.76214 / 3.40 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8115 (ppp) cc_final: 0.7752 (ppp) REVERT: B 13 GLN cc_start: 0.9855 (OUTLIER) cc_final: 0.9410 (mp10) REVERT: B 97 PHE cc_start: 0.8605 (t80) cc_final: 0.8217 (t80) REVERT: B 106 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9024 (mm) REVERT: B 182 HIS cc_start: 0.8984 (m90) cc_final: 0.8430 (m-70) REVERT: B 284 MET cc_start: 0.9807 (tmm) cc_final: 0.9488 (tmm) REVERT: B 307 TYR cc_start: 0.9138 (t80) cc_final: 0.8837 (t80) REVERT: E 70 ASP cc_start: 0.9221 (t0) cc_final: 0.9006 (t0) REVERT: E 112 SER cc_start: 0.8260 (m) cc_final: 0.7838 (p) REVERT: E 120 HIS cc_start: 0.9044 (m170) cc_final: 0.8827 (m170) REVERT: E 137 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.8464 (p) REVERT: E 168 MET cc_start: 0.9215 (mmt) cc_final: 0.8967 (mmt) REVERT: E 169 MET cc_start: 0.9299 (mmm) cc_final: 0.9074 (mmm) REVERT: E 316 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8854 (mmm) REVERT: C 276 VAL cc_start: 0.8911 (t) cc_final: 0.8640 (t) REVERT: C 284 MET cc_start: 0.9321 (ppp) cc_final: 0.9086 (ppp) REVERT: C 302 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9080 (pm20) REVERT: C 305 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9420 (mp) REVERT: D 270 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9053 (pt0) REVERT: D 284 MET cc_start: 0.9674 (tmm) cc_final: 0.9189 (tmm) REVERT: D 285 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.8570 (t80) REVERT: D 304 HIS cc_start: 0.9628 (OUTLIER) cc_final: 0.9412 (t70) REVERT: A 4 PHE cc_start: 0.8826 (m-80) cc_final: 0.8265 (m-80) REVERT: A 12 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8640 (tp30) REVERT: A 21 ASP cc_start: 0.9241 (t0) cc_final: 0.8949 (t0) REVERT: A 99 MET cc_start: 0.9073 (mmm) cc_final: 0.8748 (mmm) REVERT: A 117 ASP cc_start: 0.8893 (t0) cc_final: 0.8546 (t0) REVERT: A 156 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9386 (tppt) REVERT: A 168 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8830 (mmmt) REVERT: A 171 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8396 (t) REVERT: A 172 LYS cc_start: 0.9271 (mppt) cc_final: 0.8933 (mmtm) REVERT: G 16 THR cc_start: 0.9444 (m) cc_final: 0.9208 (p) REVERT: G 30 MET cc_start: 0.9259 (ptt) cc_final: 0.9014 (ptm) REVERT: G 32 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8323 (ttt-90) REVERT: G 51 ASP cc_start: 0.9394 (OUTLIER) cc_final: 0.9060 (m-30) REVERT: G 124 GLN cc_start: 0.9278 (pt0) cc_final: 0.8326 (pp30) REVERT: G 128 ARG cc_start: 0.9421 (mtt90) cc_final: 0.8901 (mtt90) REVERT: G 187 MET cc_start: 0.9623 (mmm) cc_final: 0.9286 (mmm) REVERT: G 189 MET cc_start: 0.9651 (pmm) cc_final: 0.9440 (pmm) REVERT: G 210 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: H 117 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8821 (tm-30) REVERT: H 162 ARG cc_start: 0.9212 (ttm110) cc_final: 0.8597 (ptp-110) REVERT: H 172 TYR cc_start: 0.9218 (t80) cc_final: 0.8678 (t80) REVERT: F 1001 MET cc_start: 0.8493 (ptt) cc_final: 0.8209 (ptp) REVERT: F 1030 MET cc_start: 0.9464 (ptm) cc_final: 0.9169 (ptp) REVERT: F 1055 TYR cc_start: 0.8322 (p90) cc_final: 0.7933 (p90) REVERT: F 1087 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8172 (ttp-110) REVERT: F 1163 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9242 (t) outliers start: 47 outliers final: 30 residues processed: 216 average time/residue: 0.1103 time to fit residues: 35.1676 Evaluate side-chains 219 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.039370 restraints weight = 52740.966| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 4.42 r_work: 0.2503 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13479 Z= 0.184 Angle : 0.683 13.623 18235 Z= 0.336 Chirality : 0.045 0.313 2077 Planarity : 0.003 0.043 2327 Dihedral : 7.192 143.586 1866 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.56 % Rotamer: Outliers : 3.15 % Allowed : 24.62 % Favored : 72.24 % 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: 0.23 (0.21), residues: 1667 helix: 1.35 (0.19), residues: 734 sheet: -1.21 (0.29), residues: 319 loop : -0.41 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 275 TYR 0.032 0.002 TYR D 261 PHE 0.029 0.001 PHE C 264 TRP 0.010 0.001 TRP C 263 HIS 0.012 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (13479) covalent geometry : angle 0.68303 / 0.34 (18235) hydrogen bonds : bond 0.03817 / 2.60 ( 654) hydrogen bonds : angle 4.81841 / 3.44 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8125 (ppp) cc_final: 0.7767 (ppp) REVERT: B 13 GLN cc_start: 0.9851 (OUTLIER) cc_final: 0.9392 (mp10) REVERT: B 97 PHE cc_start: 0.8677 (t80) cc_final: 0.8314 (t80) REVERT: B 106 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9022 (mm) REVERT: B 169 MET cc_start: 0.9253 (mmt) cc_final: 0.8978 (mmt) REVERT: B 182 HIS cc_start: 0.8986 (m90) cc_final: 0.8429 (m-70) REVERT: B 284 MET cc_start: 0.9815 (tmm) cc_final: 0.9485 (tmm) REVERT: B 307 TYR cc_start: 0.9192 (t80) cc_final: 0.8873 (t80) REVERT: E 112 SER cc_start: 0.8248 (m) cc_final: 0.7826 (p) REVERT: E 137 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.8500 (p) REVERT: E 168 MET cc_start: 0.9233 (mmt) cc_final: 0.9013 (mmt) REVERT: E 169 MET cc_start: 0.9315 (mmm) cc_final: 0.9102 (mmm) REVERT: E 316 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8859 (mmm) REVERT: C 276 VAL cc_start: 0.8838 (t) cc_final: 0.8581 (t) REVERT: C 284 MET cc_start: 0.9316 (ppp) cc_final: 0.9099 (ppp) REVERT: C 302 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9103 (pm20) REVERT: C 305 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9413 (mp) REVERT: D 270 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9066 (pt0) REVERT: D 284 MET cc_start: 0.9654 (tmm) cc_final: 0.9110 (tmm) REVERT: D 304 HIS cc_start: 0.9648 (OUTLIER) cc_final: 0.9364 (t70) REVERT: A 4 PHE cc_start: 0.8875 (m-80) cc_final: 0.8274 (m-80) REVERT: A 21 ASP cc_start: 0.9250 (t0) cc_final: 0.8949 (t0) REVERT: A 99 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8780 (mmm) REVERT: A 117 ASP cc_start: 0.8956 (t0) cc_final: 0.8617 (t0) REVERT: A 156 LYS cc_start: 0.9635 (tmtt) cc_final: 0.9405 (tppt) REVERT: A 168 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8849 (mmmt) REVERT: A 171 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 172 LYS cc_start: 0.9275 (mppt) cc_final: 0.8930 (mmtm) REVERT: G 16 THR cc_start: 0.9487 (m) cc_final: 0.9249 (p) REVERT: G 22 MET cc_start: 0.9494 (ttm) cc_final: 0.8825 (ttm) REVERT: G 30 MET cc_start: 0.9236 (ptt) cc_final: 0.8989 (ptm) REVERT: G 32 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8341 (ttt-90) REVERT: G 51 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.9077 (m-30) REVERT: G 187 MET cc_start: 0.9611 (mmm) cc_final: 0.9386 (mmm) REVERT: G 210 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8575 (tm-30) REVERT: H 117 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8821 (tm-30) REVERT: H 162 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8577 (ptp-110) REVERT: H 172 TYR cc_start: 0.9236 (t80) cc_final: 0.8680 (t80) REVERT: F 1001 MET cc_start: 0.8430 (ptt) cc_final: 0.8148 (ptp) REVERT: F 1030 MET cc_start: 0.9498 (ptm) cc_final: 0.9191 (ptp) REVERT: F 1055 TYR cc_start: 0.8373 (p90) cc_final: 0.7980 (p90) REVERT: F 1087 ARG cc_start: 0.8687 (ttp-110) cc_final: 0.8130 (ttp-110) REVERT: F 1163 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9229 (t) outliers start: 45 outliers final: 29 residues processed: 208 average time/residue: 0.1058 time to fit residues: 32.9391 Evaluate side-chains 214 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 304 HIS Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 118 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 77 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.041395 restraints weight = 52135.001| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 4.46 r_work: 0.2568 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13479 Z= 0.122 Angle : 0.678 14.000 18235 Z= 0.329 Chirality : 0.045 0.317 2077 Planarity : 0.003 0.045 2327 Dihedral : 7.110 143.335 1866 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 2.80 % Allowed : 24.90 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1667 helix: 1.39 (0.19), residues: 731 sheet: -1.17 (0.29), residues: 317 loop : -0.45 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 275 TYR 0.039 0.002 TYR C 307 PHE 0.025 0.001 PHE A 63 TRP 0.010 0.001 TRP E 263 HIS 0.011 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13479) covalent geometry : angle 0.67762 / 0.33 (18235) hydrogen bonds : bond 0.03570 / 2.44 ( 654) hydrogen bonds : angle 4.72976 / 3.38 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.47 seconds wall clock time: 53 minutes 47.09 seconds (3227.09 seconds total)