Starting phenix.real_space_refine on Wed Feb 4 06:39:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kfk_62299/02_2026/9kfk_62299.map" } resolution = 2.95 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5754 2.51 5 N 1547 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9039 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1757 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2208 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 152 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 126 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 9039 At special positions: 0 Unit cell: (91.035, 117.81, 137.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1676 8.00 N 1547 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS A 24 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 362.2 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 39.1% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.650A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.810A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'I' and resid 6 through 32 removed outlier: 3.624A pdb=" N ASN I 22 " --> pdb=" O MET I 18 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG I 32 " --> pdb=" O GLU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 Processing helix chain 'I' and resid 208 through 217 removed outlier: 4.888A pdb=" N ILE I 213 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N HIS I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.935A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 removed outlier: 3.607A pdb=" N ILE I 286 " --> pdb=" O PRO I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.679A pdb=" N ALA I 301 " --> pdb=" O TYR I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 352 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'R' and resid 77 through 92 Processing helix chain 'R' and resid 93 through 103 removed outlier: 3.818A pdb=" N TRP R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 115 Processing helix chain 'R' and resid 119 through 144 removed outlier: 4.100A pdb=" N ILE R 129 " --> pdb=" O VAL R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 174 Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 199 through 234 removed outlier: 3.732A pdb=" N VAL R 209 " --> pdb=" O GLN R 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) Proline residue: R 216 - end of helix removed outlier: 3.596A pdb=" N ARG R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 275 removed outlier: 4.269A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) Proline residue: R 261 - end of helix removed outlier: 4.116A pdb=" N VAL R 272 " --> pdb=" O TRP R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 300 removed outlier: 4.453A pdb=" N PHE R 291 " --> pdb=" O GLN R 287 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 300 through 310 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 removed outlier: 3.654A pdb=" N ARG R 317 " --> pdb=" O ARG R 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.662A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.742A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 25 removed outlier: 3.812A pdb=" N ALA T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 35 removed outlier: 3.506A pdb=" N ILE T 33 " --> pdb=" O THR T 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 4.092A pdb=" N PHE B 14 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE B 15 " --> pdb=" O GLY B 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 16 through 22 removed outlier: 4.232A pdb=" N ILE A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 186 through 192 removed outlier: 3.566A pdb=" N LEU I 195 " --> pdb=" O PHE I 192 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ALA I 221 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS I 35 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE I 223 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU I 37 " --> pdb=" O ILE I 223 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N CYS I 225 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU I 39 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ALA I 227 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 183 through 185 removed outlier: 3.922A pdb=" N LEU R 190 " --> pdb=" O GLY R 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.507A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.749A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.108A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AA7, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.625A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 46 through 52 removed outlier: 5.689A pdb=" N THR T 47 " --> pdb=" O ASN T 340 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN T 340 " --> pdb=" O THR T 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 58 through 63 removed outlier: 3.560A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY T 115 " --> pdb=" O MET T 101 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS T 103 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA T 113 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR T 105 " --> pdb=" O TYR T 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR T 111 " --> pdb=" O TYR T 105 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.465A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 191 through 192 removed outlier: 3.655A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP T 212 " --> pdb=" O CYS T 218 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS T 218 " --> pdb=" O ASP T 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 229 through 234 removed outlier: 3.523A pdb=" N ARG T 251 " --> pdb=" O THR T 243 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS T 250 " --> pdb=" O THR T 263 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR T 263 " --> pdb=" O CYS T 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU T 252 " --> pdb=" O LEU T 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 273 through 278 removed outlier: 3.727A pdb=" N GLY T 306 " --> pdb=" O VAL T 296 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP T 298 " --> pdb=" O ARG T 304 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG T 304 " --> pdb=" O ASP T 298 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2866 1.34 - 1.46: 2317 1.46 - 1.59: 3962 1.59 - 1.71: 0 1.71 - 1.84: 86 Bond restraints: 9231 Sorted by residual: bond pdb=" C VAL R 117 " pdb=" O VAL R 117 " ideal model delta sigma weight residual 1.237 1.210 0.026 9.80e-03 1.04e+04 7.29e+00 bond pdb=" CA VAL R 117 " pdb=" C VAL R 117 " ideal model delta sigma weight residual 1.526 1.500 0.025 1.17e-02 7.31e+03 4.66e+00 bond pdb=" CA MET S 83 " pdb=" C MET S 83 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" C VAL T 327 " pdb=" O VAL T 327 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.11e-02 8.12e+03 2.91e+00 bond pdb=" CA VAL R 117 " pdb=" CB VAL R 117 " ideal model delta sigma weight residual 1.543 1.521 0.022 1.27e-02 6.20e+03 2.90e+00 ... (remaining 9226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 12261 2.14 - 4.28: 215 4.28 - 6.42: 36 6.42 - 8.56: 7 8.56 - 10.70: 4 Bond angle restraints: 12523 Sorted by residual: angle pdb=" N VAL R 117 " pdb=" CA VAL R 117 " pdb=" C VAL R 117 " ideal model delta sigma weight residual 112.96 102.26 10.70 1.00e+00 1.00e+00 1.14e+02 angle pdb=" N SER T 161 " pdb=" CA SER T 161 " pdb=" C SER T 161 " ideal model delta sigma weight residual 108.74 117.28 -8.54 1.38e+00 5.25e-01 3.83e+01 angle pdb=" N ALA T 326 " pdb=" CA ALA T 326 " pdb=" C ALA T 326 " ideal model delta sigma weight residual 109.50 116.59 -7.09 1.58e+00 4.01e-01 2.01e+01 angle pdb=" N SER T 160 " pdb=" CA SER T 160 " pdb=" C SER T 160 " ideal model delta sigma weight residual 109.50 103.43 6.07 1.58e+00 4.01e-01 1.48e+01 angle pdb=" C PHE R 283 " pdb=" N TYR R 284 " pdb=" CA TYR R 284 " ideal model delta sigma weight residual 122.56 116.84 5.72 1.50e+00 4.44e-01 1.46e+01 ... (remaining 12518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4901 17.38 - 34.77: 443 34.77 - 52.15: 79 52.15 - 69.54: 11 69.54 - 86.92: 10 Dihedral angle restraints: 5444 sinusoidal: 2073 harmonic: 3371 Sorted by residual: dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS A 11 " pdb=" CB CYS A 11 " ideal model delta sinusoidal sigma weight residual -86.00 -156.60 70.60 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS A 24 " pdb=" CB CYS A 24 " ideal model delta sinusoidal sigma weight residual -86.00 -137.24 51.24 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA TYR I 297 " pdb=" C TYR I 297 " pdb=" N ASP I 298 " pdb=" CA ASP I 298 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 959 0.044 - 0.088: 344 0.088 - 0.132: 110 0.132 - 0.176: 11 0.176 - 0.220: 3 Chirality restraints: 1427 Sorted by residual: chirality pdb=" CG LEU T 30 " pdb=" CB LEU T 30 " pdb=" CD1 LEU T 30 " pdb=" CD2 LEU T 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ALA T 326 " pdb=" N ALA T 326 " pdb=" C ALA T 326 " pdb=" CB ALA T 326 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR S 172 " pdb=" CA THR S 172 " pdb=" OG1 THR S 172 " pdb=" CG2 THR S 172 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1424 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 195 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO R 196 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 284 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C TYR R 284 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR R 284 " 0.016 2.00e-02 2.50e+03 pdb=" N THR R 285 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE T 235 " 0.039 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO T 236 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO T 236 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO T 236 " 0.033 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1549 2.76 - 3.30: 8652 3.30 - 3.83: 15365 3.83 - 4.37: 18473 4.37 - 4.90: 31774 Nonbonded interactions: 75813 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.227 3.040 nonbonded pdb=" O SER S 106 " pdb=" OG SER S 106 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN G 59 " pdb=" ND2 ASN T 340 " model vdw 2.298 3.120 nonbonded pdb=" NE ARG T 283 " pdb=" OD1 ASP T 298 " model vdw 2.300 3.120 nonbonded pdb=" O LYS I 278 " pdb=" OG SER I 282 " model vdw 2.311 3.040 ... (remaining 75808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 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 : 0.006 0.042 9236 Z= 0.248 Angle : 0.736 10.696 12533 Z= 0.416 Chirality : 0.049 0.220 1427 Planarity : 0.005 0.063 1586 Dihedral : 13.838 86.922 3253 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.41 % Allowed : 0.83 % Favored : 98.76 % 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: -0.82 (0.24), residues: 1147 helix: 0.53 (0.26), residues: 407 sheet: -0.39 (0.32), residues: 265 loop : -1.53 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 251 TYR 0.024 0.002 TYR S 190 PHE 0.020 0.002 PHE R 283 TRP 0.037 0.002 TRP R 268 HIS 0.007 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 9231) covalent geometry : angle 0.73608 (12523) SS BOND : bond 0.00248 ( 5) SS BOND : angle 1.11790 ( 10) hydrogen bonds : bond 0.17366 ( 435) hydrogen bonds : angle 6.50568 ( 1215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.348 Fit side-chains REVERT: I 10 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7775 (mtpp) REVERT: I 25 GLU cc_start: 0.6096 (tm-30) cc_final: 0.5836 (tm-30) REVERT: I 341 THR cc_start: 0.7575 (m) cc_final: 0.7364 (m) REVERT: R 275 ASP cc_start: 0.6448 (p0) cc_final: 0.6187 (p0) REVERT: R 287 GLN cc_start: 0.6511 (tp-100) cc_final: 0.5948 (tp-100) REVERT: S 86 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7074 (mt) REVERT: S 171 ASN cc_start: 0.7978 (m110) cc_final: 0.7636 (m110) REVERT: T 43 ILE cc_start: 0.7487 (pt) cc_final: 0.7286 (pp) REVERT: T 134 ARG cc_start: 0.7071 (ptt90) cc_final: 0.6832 (ptt90) REVERT: T 198 LEU cc_start: 0.8517 (mt) cc_final: 0.8179 (mt) REVERT: T 221 THR cc_start: 0.8150 (m) cc_final: 0.7940 (m) REVERT: T 228 ASP cc_start: 0.7264 (p0) cc_final: 0.6698 (p0) REVERT: T 246 ASP cc_start: 0.6874 (m-30) cc_final: 0.6503 (m-30) REVERT: T 277 SER cc_start: 0.8194 (m) cc_final: 0.7935 (t) outliers start: 4 outliers final: 1 residues processed: 158 average time/residue: 0.4837 time to fit residues: 81.9826 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 321 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140024 restraints weight = 12261.790| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.11 r_work: 0.3555 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9236 Z= 0.181 Angle : 0.635 11.581 12533 Z= 0.328 Chirality : 0.045 0.151 1427 Planarity : 0.005 0.060 1586 Dihedral : 5.228 45.903 1264 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.35 % Allowed : 9.74 % Favored : 88.91 % 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: -0.52 (0.25), residues: 1147 helix: 0.88 (0.27), residues: 403 sheet: -0.40 (0.31), residues: 283 loop : -1.35 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 251 TYR 0.023 0.002 TYR S 190 PHE 0.017 0.002 PHE S 29 TRP 0.025 0.002 TRP R 268 HIS 0.005 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9231) covalent geometry : angle 0.63489 (12523) SS BOND : bond 0.00243 ( 5) SS BOND : angle 1.11065 ( 10) hydrogen bonds : bond 0.04596 ( 435) hydrogen bonds : angle 4.94431 ( 1215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.350 Fit side-chains REVERT: I 10 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8026 (mtpp) REVERT: I 25 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6880 (tm-30) REVERT: R 287 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6418 (tp-100) REVERT: S 171 ASN cc_start: 0.8159 (m110) cc_final: 0.7840 (m110) REVERT: T 43 ILE cc_start: 0.7394 (pt) cc_final: 0.7183 (pp) REVERT: T 49 ARG cc_start: 0.8293 (mpt90) cc_final: 0.8022 (mmt90) REVERT: T 88 ASN cc_start: 0.8212 (m110) cc_final: 0.7914 (m110) REVERT: T 135 VAL cc_start: 0.8139 (t) cc_final: 0.7758 (p) REVERT: T 198 LEU cc_start: 0.8676 (mt) cc_final: 0.8385 (mp) REVERT: T 221 THR cc_start: 0.8296 (m) cc_final: 0.8066 (m) REVERT: T 228 ASP cc_start: 0.7808 (p0) cc_final: 0.7587 (p0) REVERT: T 246 ASP cc_start: 0.7485 (m-30) cc_final: 0.6907 (m-30) REVERT: T 277 SER cc_start: 0.8432 (m) cc_final: 0.8120 (t) REVERT: T 323 ASP cc_start: 0.7529 (p0) cc_final: 0.7247 (p0) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 0.5684 time to fit residues: 93.7646 Evaluate side-chains 149 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 107 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 257 ASN ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 132 ASN T 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142297 restraints weight = 12209.119| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.03 r_work: 0.3576 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9236 Z= 0.132 Angle : 0.566 8.018 12533 Z= 0.293 Chirality : 0.043 0.138 1427 Planarity : 0.005 0.060 1586 Dihedral : 4.835 42.777 1261 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.07 % Allowed : 12.33 % Favored : 85.60 % 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: -0.30 (0.25), residues: 1147 helix: 1.15 (0.27), residues: 405 sheet: -0.28 (0.31), residues: 278 loop : -1.33 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 48 TYR 0.018 0.001 TYR S 190 PHE 0.015 0.001 PHE R 283 TRP 0.021 0.002 TRP R 268 HIS 0.003 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9231) covalent geometry : angle 0.56591 (12523) SS BOND : bond 0.00193 ( 5) SS BOND : angle 1.01871 ( 10) hydrogen bonds : bond 0.03764 ( 435) hydrogen bonds : angle 4.53243 ( 1215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.352 Fit side-chains REVERT: I 10 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7985 (mtpp) REVERT: I 25 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6851 (tm-30) REVERT: I 257 ASN cc_start: 0.7922 (t0) cc_final: 0.7581 (t0) REVERT: R 287 GLN cc_start: 0.7067 (tp-100) cc_final: 0.6351 (tp-100) REVERT: S 147 VAL cc_start: 0.7339 (m) cc_final: 0.7056 (t) REVERT: T 43 ILE cc_start: 0.7278 (pt) cc_final: 0.7069 (pp) REVERT: T 49 ARG cc_start: 0.8320 (mpt90) cc_final: 0.8082 (mmt90) REVERT: T 88 ASN cc_start: 0.8221 (m110) cc_final: 0.7886 (m110) REVERT: T 101 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8371 (ptp) REVERT: T 135 VAL cc_start: 0.8145 (t) cc_final: 0.7795 (p) REVERT: T 197 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7099 (mmt-90) REVERT: T 221 THR cc_start: 0.8276 (m) cc_final: 0.8053 (m) REVERT: T 228 ASP cc_start: 0.7912 (p0) cc_final: 0.7380 (p0) REVERT: T 245 SER cc_start: 0.7883 (m) cc_final: 0.7613 (t) REVERT: T 246 ASP cc_start: 0.7455 (m-30) cc_final: 0.6910 (m-30) REVERT: T 277 SER cc_start: 0.8431 (m) cc_final: 0.8122 (t) REVERT: T 323 ASP cc_start: 0.7622 (p0) cc_final: 0.7372 (p0) outliers start: 20 outliers final: 12 residues processed: 157 average time/residue: 0.5634 time to fit residues: 94.8873 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 50.0000 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.0060 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 155 ASN T 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.169042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139538 restraints weight = 12390.645| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.10 r_work: 0.3545 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9236 Z= 0.179 Angle : 0.609 13.409 12533 Z= 0.311 Chirality : 0.044 0.154 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.861 41.540 1261 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.90 % Allowed : 15.03 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1147 helix: 1.20 (0.27), residues: 404 sheet: -0.30 (0.30), residues: 278 loop : -1.36 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 251 TYR 0.023 0.002 TYR R 126 PHE 0.015 0.002 PHE T 151 TRP 0.019 0.002 TRP R 268 HIS 0.005 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9231) covalent geometry : angle 0.60806 (12523) SS BOND : bond 0.00221 ( 5) SS BOND : angle 1.11381 ( 10) hydrogen bonds : bond 0.03914 ( 435) hydrogen bonds : angle 4.52196 ( 1215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.357 Fit side-chains REVERT: I 10 LYS cc_start: 0.8276 (mtpp) cc_final: 0.8009 (mtpp) REVERT: I 25 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6899 (tm-30) REVERT: I 233 LEU cc_start: 0.7881 (mt) cc_final: 0.7659 (mt) REVERT: I 257 ASN cc_start: 0.8005 (t0) cc_final: 0.7654 (t0) REVERT: R 287 GLN cc_start: 0.7188 (tp-100) cc_final: 0.6409 (tp-100) REVERT: S 171 ASN cc_start: 0.8202 (m110) cc_final: 0.7887 (m110) REVERT: T 37 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6734 (mp) REVERT: T 43 ILE cc_start: 0.7328 (pt) cc_final: 0.7124 (pp) REVERT: T 49 ARG cc_start: 0.8347 (mpt90) cc_final: 0.8061 (mmt90) REVERT: T 88 ASN cc_start: 0.8284 (m110) cc_final: 0.7919 (m110) REVERT: T 228 ASP cc_start: 0.7887 (p0) cc_final: 0.7662 (p0) REVERT: T 246 ASP cc_start: 0.7575 (m-30) cc_final: 0.6999 (m-30) REVERT: T 277 SER cc_start: 0.8452 (m) cc_final: 0.8109 (t) outliers start: 28 outliers final: 16 residues processed: 163 average time/residue: 0.5631 time to fit residues: 98.5305 Evaluate side-chains 162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 179 THR Chi-restraints excluded: chain T residue 227 SER Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 281 HIS ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139479 restraints weight = 12289.728| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.06 r_work: 0.3551 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9236 Z= 0.180 Angle : 0.607 12.998 12533 Z= 0.310 Chirality : 0.044 0.136 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.813 40.200 1261 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.73 % Allowed : 14.92 % Favored : 81.35 % 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: -0.29 (0.25), residues: 1147 helix: 1.24 (0.27), residues: 405 sheet: -0.35 (0.30), residues: 279 loop : -1.35 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 251 TYR 0.020 0.002 TYR S 190 PHE 0.014 0.002 PHE T 151 TRP 0.021 0.002 TRP R 268 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9231) covalent geometry : angle 0.60624 (12523) SS BOND : bond 0.00206 ( 5) SS BOND : angle 1.01952 ( 10) hydrogen bonds : bond 0.03839 ( 435) hydrogen bonds : angle 4.50373 ( 1215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.376 Fit side-chains REVERT: I 10 LYS cc_start: 0.8273 (mtpp) cc_final: 0.8013 (mtpp) REVERT: I 25 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6867 (tm-30) REVERT: I 33 GLU cc_start: 0.8000 (tp30) cc_final: 0.7755 (tp30) REVERT: I 233 LEU cc_start: 0.7937 (mt) cc_final: 0.7724 (mt) REVERT: I 257 ASN cc_start: 0.7997 (t0) cc_final: 0.7690 (t0) REVERT: I 281 HIS cc_start: 0.4604 (OUTLIER) cc_final: 0.4231 (p90) REVERT: R 135 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7474 (tp) REVERT: R 208 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.5891 (tmm-80) REVERT: R 287 GLN cc_start: 0.7151 (tp-100) cc_final: 0.6376 (tp-100) REVERT: S 83 MET cc_start: 0.7129 (mtm) cc_final: 0.6902 (mtp) REVERT: S 171 ASN cc_start: 0.8193 (m110) cc_final: 0.7864 (m110) REVERT: T 49 ARG cc_start: 0.8349 (mpt90) cc_final: 0.8036 (mmt90) REVERT: T 88 ASN cc_start: 0.8357 (m110) cc_final: 0.7956 (m110) REVERT: T 228 ASP cc_start: 0.7914 (p0) cc_final: 0.7600 (p0) REVERT: T 246 ASP cc_start: 0.7617 (m-30) cc_final: 0.7025 (m-30) REVERT: T 277 SER cc_start: 0.8494 (m) cc_final: 0.8098 (t) outliers start: 36 outliers final: 21 residues processed: 173 average time/residue: 0.5693 time to fit residues: 105.4069 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 281 HIS Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 179 THR Chi-restraints excluded: chain T residue 227 SER Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 94 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 196 HIS ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN T 75 GLN T 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.169326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140199 restraints weight = 12327.311| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.07 r_work: 0.3565 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.130 Angle : 0.573 12.948 12533 Z= 0.293 Chirality : 0.042 0.135 1427 Planarity : 0.005 0.061 1586 Dihedral : 4.653 38.321 1261 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.32 % Allowed : 16.58 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1147 helix: 1.37 (0.27), residues: 406 sheet: -0.36 (0.30), residues: 283 loop : -1.32 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 251 TYR 0.018 0.002 TYR S 190 PHE 0.011 0.001 PHE I 197 TRP 0.018 0.001 TRP R 268 HIS 0.010 0.001 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9231) covalent geometry : angle 0.57220 (12523) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.95927 ( 10) hydrogen bonds : bond 0.03521 ( 435) hydrogen bonds : angle 4.36895 ( 1215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.289 Fit side-chains REVERT: I 10 LYS cc_start: 0.8271 (mtpp) cc_final: 0.8012 (mtpp) REVERT: I 25 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6909 (tm-30) REVERT: I 233 LEU cc_start: 0.7888 (mt) cc_final: 0.7635 (mp) REVERT: I 257 ASN cc_start: 0.7998 (t0) cc_final: 0.7645 (t0) REVERT: R 135 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7451 (tp) REVERT: R 208 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.5921 (tmm-80) REVERT: R 287 GLN cc_start: 0.7193 (tp-100) cc_final: 0.6377 (tp-100) REVERT: S 83 MET cc_start: 0.7191 (mtm) cc_final: 0.6927 (mtp) REVERT: S 171 ASN cc_start: 0.8173 (m110) cc_final: 0.7853 (m110) REVERT: T 88 ASN cc_start: 0.8346 (m110) cc_final: 0.7978 (m110) REVERT: T 135 VAL cc_start: 0.8174 (t) cc_final: 0.7838 (p) REVERT: T 228 ASP cc_start: 0.7914 (p0) cc_final: 0.7331 (p0) REVERT: T 245 SER cc_start: 0.7943 (m) cc_final: 0.7599 (t) REVERT: T 246 ASP cc_start: 0.7646 (m-30) cc_final: 0.7140 (m-30) REVERT: T 277 SER cc_start: 0.8427 (m) cc_final: 0.8103 (t) outliers start: 32 outliers final: 20 residues processed: 169 average time/residue: 0.5386 time to fit residues: 97.5341 Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 179 THR Chi-restraints excluded: chain T residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.168888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139588 restraints weight = 12272.292| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.08 r_work: 0.3552 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9236 Z= 0.157 Angle : 0.589 10.765 12533 Z= 0.301 Chirality : 0.043 0.176 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.669 36.335 1261 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.90 % Allowed : 16.48 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1147 helix: 1.39 (0.27), residues: 405 sheet: -0.36 (0.30), residues: 283 loop : -1.35 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 251 TYR 0.020 0.002 TYR S 190 PHE 0.013 0.002 PHE T 151 TRP 0.021 0.002 TRP R 268 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9231) covalent geometry : angle 0.58858 (12523) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.94370 ( 10) hydrogen bonds : bond 0.03634 ( 435) hydrogen bonds : angle 4.39183 ( 1215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.287 Fit side-chains REVERT: I 10 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7998 (mtpp) REVERT: I 25 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6867 (tm-30) REVERT: I 233 LEU cc_start: 0.7854 (mt) cc_final: 0.7605 (mp) REVERT: I 257 ASN cc_start: 0.8009 (t0) cc_final: 0.7666 (t0) REVERT: R 135 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7469 (tp) REVERT: R 208 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.5908 (tmm-80) REVERT: R 287 GLN cc_start: 0.7141 (tp-100) cc_final: 0.6332 (tp-100) REVERT: S 83 MET cc_start: 0.7133 (mtm) cc_final: 0.6835 (mtp) REVERT: S 93 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7541 (ttp) REVERT: T 88 ASN cc_start: 0.8349 (m110) cc_final: 0.7974 (m110) REVERT: T 135 VAL cc_start: 0.8152 (t) cc_final: 0.7818 (p) REVERT: T 228 ASP cc_start: 0.7893 (p0) cc_final: 0.7523 (p0) REVERT: T 246 ASP cc_start: 0.7656 (m-30) cc_final: 0.7051 (m-30) REVERT: T 277 SER cc_start: 0.8490 (m) cc_final: 0.8116 (t) outliers start: 28 outliers final: 19 residues processed: 162 average time/residue: 0.5664 time to fit residues: 98.0222 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 241 MET Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 0.0060 chunk 93 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 293 ASN T 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141082 restraints weight = 12265.081| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.11 r_work: 0.3540 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9236 Z= 0.142 Angle : 0.570 8.283 12533 Z= 0.295 Chirality : 0.043 0.148 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.588 34.327 1261 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.32 % Allowed : 16.68 % Favored : 80.00 % 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 (0.25), residues: 1147 helix: 1.40 (0.27), residues: 406 sheet: -0.34 (0.30), residues: 283 loop : -1.32 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 251 TYR 0.020 0.002 TYR S 190 PHE 0.032 0.002 PHE R 291 TRP 0.012 0.001 TRP R 62 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9231) covalent geometry : angle 0.57008 (12523) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.93063 ( 10) hydrogen bonds : bond 0.03484 ( 435) hydrogen bonds : angle 4.32375 ( 1215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.355 Fit side-chains REVERT: G 42 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6143 (pm20) REVERT: I 10 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7939 (mtpp) REVERT: I 25 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6497 (tm-30) REVERT: I 53 MET cc_start: 0.3414 (mtt) cc_final: 0.3153 (mtt) REVERT: I 257 ASN cc_start: 0.7922 (t0) cc_final: 0.7597 (t0) REVERT: R 135 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7297 (tp) REVERT: R 208 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.5719 (tmm-80) REVERT: R 287 GLN cc_start: 0.6932 (tp-100) cc_final: 0.6190 (tp-100) REVERT: S 83 MET cc_start: 0.7105 (mtm) cc_final: 0.6889 (mtp) REVERT: S 93 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7336 (ttp) REVERT: T 88 ASN cc_start: 0.8272 (m110) cc_final: 0.7919 (m110) REVERT: T 135 VAL cc_start: 0.8085 (t) cc_final: 0.7786 (p) REVERT: T 228 ASP cc_start: 0.7788 (p0) cc_final: 0.7126 (p0) REVERT: T 245 SER cc_start: 0.7827 (m) cc_final: 0.7484 (t) REVERT: T 246 ASP cc_start: 0.7448 (m-30) cc_final: 0.6908 (m-30) REVERT: T 277 SER cc_start: 0.8262 (m) cc_final: 0.7922 (t) outliers start: 32 outliers final: 21 residues processed: 166 average time/residue: 0.5966 time to fit residues: 105.7541 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 241 MET Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 350 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 50.0000 chunk 3 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140432 restraints weight = 12197.602| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.10 r_work: 0.3545 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9236 Z= 0.178 Angle : 0.606 7.933 12533 Z= 0.311 Chirality : 0.044 0.155 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.690 32.949 1261 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.01 % Allowed : 17.72 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1147 helix: 1.33 (0.27), residues: 405 sheet: -0.39 (0.30), residues: 283 loop : -1.37 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG T 251 TYR 0.020 0.002 TYR S 190 PHE 0.028 0.002 PHE R 291 TRP 0.012 0.002 TRP R 62 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9231) covalent geometry : angle 0.60540 (12523) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.98300 ( 10) hydrogen bonds : bond 0.03720 ( 435) hydrogen bonds : angle 4.41413 ( 1215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.396 Fit side-chains REVERT: G 42 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: I 10 LYS cc_start: 0.8327 (mtpp) cc_final: 0.8071 (mtpp) REVERT: I 25 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6924 (tm-30) REVERT: I 198 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8245 (mtpp) REVERT: I 257 ASN cc_start: 0.8078 (t0) cc_final: 0.7749 (t0) REVERT: R 135 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7459 (tp) REVERT: R 208 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.5918 (tmm-80) REVERT: R 287 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6393 (tp-100) REVERT: S 83 MET cc_start: 0.7137 (mtm) cc_final: 0.6900 (mtp) REVERT: S 219 LEU cc_start: 0.8627 (mt) cc_final: 0.8372 (mp) REVERT: T 88 ASN cc_start: 0.8339 (m110) cc_final: 0.7994 (m110) REVERT: T 150 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8423 (mmt-90) REVERT: T 198 LEU cc_start: 0.8634 (mt) cc_final: 0.8416 (mp) REVERT: T 228 ASP cc_start: 0.7850 (p0) cc_final: 0.7540 (p0) REVERT: T 246 ASP cc_start: 0.7707 (m-30) cc_final: 0.7159 (m-30) REVERT: T 277 SER cc_start: 0.8426 (m) cc_final: 0.8051 (t) outliers start: 29 outliers final: 21 residues processed: 164 average time/residue: 0.5991 time to fit residues: 104.9180 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 241 MET Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 293 ASN T 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.169884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140434 restraints weight = 12254.976| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.11 r_work: 0.3545 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9236 Z= 0.178 Angle : 0.607 7.805 12533 Z= 0.311 Chirality : 0.044 0.149 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.693 31.136 1261 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.90 % Allowed : 17.72 % Favored : 79.38 % 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: -0.29 (0.25), residues: 1147 helix: 1.30 (0.27), residues: 405 sheet: -0.42 (0.30), residues: 284 loop : -1.37 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 251 TYR 0.021 0.002 TYR S 190 PHE 0.025 0.002 PHE R 291 TRP 0.013 0.002 TRP R 62 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9231) covalent geometry : angle 0.60683 (12523) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.95502 ( 10) hydrogen bonds : bond 0.03699 ( 435) hydrogen bonds : angle 4.42415 ( 1215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: G 38 MET cc_start: 0.8060 (ptp) cc_final: 0.7678 (ptm) REVERT: G 42 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: I 10 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8066 (mtpp) REVERT: I 25 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6916 (tm-30) REVERT: I 257 ASN cc_start: 0.8076 (t0) cc_final: 0.7771 (t0) REVERT: R 135 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7465 (tp) REVERT: R 208 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.5886 (tmm-80) REVERT: R 287 GLN cc_start: 0.7202 (tp-100) cc_final: 0.6410 (tp-100) REVERT: S 219 LEU cc_start: 0.8592 (mt) cc_final: 0.8335 (mp) REVERT: T 88 ASN cc_start: 0.8369 (m110) cc_final: 0.7975 (m110) REVERT: T 135 VAL cc_start: 0.8158 (t) cc_final: 0.7819 (p) REVERT: T 150 ARG cc_start: 0.8716 (mmp80) cc_final: 0.8417 (mmt-90) REVERT: T 198 LEU cc_start: 0.8624 (mt) cc_final: 0.8402 (mp) REVERT: T 228 ASP cc_start: 0.7832 (p0) cc_final: 0.7175 (p0) REVERT: T 245 SER cc_start: 0.7961 (m) cc_final: 0.7586 (t) REVERT: T 246 ASP cc_start: 0.7717 (m-30) cc_final: 0.7170 (m-30) REVERT: T 277 SER cc_start: 0.8428 (m) cc_final: 0.8052 (t) outliers start: 28 outliers final: 21 residues processed: 162 average time/residue: 0.5925 time to fit residues: 102.3835 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain T residue 37 ILE Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.169896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140489 restraints weight = 12098.808| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.10 r_work: 0.3552 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9236 Z= 0.139 Angle : 0.580 7.899 12533 Z= 0.297 Chirality : 0.043 0.140 1427 Planarity : 0.005 0.062 1586 Dihedral : 4.557 29.142 1261 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.69 % Allowed : 17.93 % Favored : 79.38 % 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: -0.19 (0.25), residues: 1147 helix: 1.40 (0.27), residues: 406 sheet: -0.38 (0.30), residues: 283 loop : -1.33 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 251 TYR 0.019 0.002 TYR S 190 PHE 0.022 0.002 PHE R 291 TRP 0.019 0.002 TRP R 268 HIS 0.003 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9231) covalent geometry : angle 0.57949 (12523) SS BOND : bond 0.00175 ( 5) SS BOND : angle 0.89188 ( 10) hydrogen bonds : bond 0.03448 ( 435) hydrogen bonds : angle 4.31848 ( 1215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.86 seconds wall clock time: 66 minutes 0.38 seconds (3960.38 seconds total)