Starting phenix.real_space_refine on Wed Sep 17 13:52:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpt_60354/09_2025/8zpt_60354.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5827 2.51 5 N 1601 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9151 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1875 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2577 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 403 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 161 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2352 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.58, per 1000 atoms: 0.28 Number of scatterers: 9151 At special positions: 0 Unit cell: (82.62, 123.12, 133.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1670 8.00 N 1601 7.00 C 5827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 358.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.450A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.531A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.856A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.583A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.575A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.857A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.544A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'L' and resid 4 through 11 removed outlier: 4.148A pdb=" N SER L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.597A pdb=" N TYR R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 Processing helix chain 'R' and resid 93 through 123 Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 132 through 164 removed outlier: 4.016A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 172 through 198 removed outlier: 3.612A pdb=" N SER R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.640A pdb=" N LEU R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA R 226 " --> pdb=" O ARG R 222 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU R 229 " --> pdb=" O TYR R 225 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) Proline residue: R 237 - end of helix Processing helix chain 'R' and resid 267 through 304 removed outlier: 3.613A pdb=" N TRP R 291 " --> pdb=" O PHE R 287 " (cutoff:3.500A) Proline residue: R 293 - end of helix Processing helix chain 'R' and resid 309 through 336 removed outlier: 4.733A pdb=" N GLY R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU R 315 " --> pdb=" O TYR R 311 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.503A pdb=" N ALA R 336 " --> pdb=" O PRO R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.805A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.709A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 7.028A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.904A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.533A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.843A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.585A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.809A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.154A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.154A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.606A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.539A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 199 through 201 450 hydrogen bonds defined for protein. 1257 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: 1.53 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2993 1.34 - 1.46: 2178 1.46 - 1.58: 4104 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9349 Sorted by residual: bond pdb=" N ALA A 7 " pdb=" CA ALA A 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ASP B 10 " pdb=" CA ASP B 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ALA G 9 " pdb=" CA ALA G 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N VAL E 1 " pdb=" CA VAL E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR L 1 " pdb=" CA THR L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 12231 0.99 - 1.97: 366 1.97 - 2.96: 51 2.96 - 3.95: 36 3.95 - 4.93: 6 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N ARG B 73 " pdb=" CA ARG B 73 " pdb=" C ARG B 73 " ideal model delta sigma weight residual 113.43 110.06 3.37 1.26e+00 6.30e-01 7.15e+00 angle pdb=" N THR B 92 " pdb=" CA THR B 92 " pdb=" CB THR B 92 " ideal model delta sigma weight residual 113.65 109.90 3.75 1.47e+00 4.63e-01 6.52e+00 angle pdb=" N THR B 201 " pdb=" CA THR B 201 " pdb=" CB THR B 201 " ideal model delta sigma weight residual 113.65 110.30 3.35 1.47e+00 4.63e-01 5.20e+00 angle pdb=" N GLN R 58 " pdb=" CA GLN R 58 " pdb=" CB GLN R 58 " ideal model delta sigma weight residual 113.65 110.37 3.28 1.47e+00 4.63e-01 4.98e+00 angle pdb=" N VAL R 82 " pdb=" CA VAL R 82 " pdb=" C VAL R 82 " ideal model delta sigma weight residual 112.76 110.13 2.63 1.27e+00 6.20e-01 4.30e+00 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5312 17.97 - 35.94: 179 35.94 - 53.92: 39 53.92 - 71.89: 4 71.89 - 89.86: 3 Dihedral angle restraints: 5537 sinusoidal: 2163 harmonic: 3374 Sorted by residual: dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -60.00 -118.25 58.25 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N ARG R 343 " pdb=" CA ARG R 343 " pdb=" CB ARG R 343 " pdb=" CG ARG R 343 " ideal model delta sinusoidal sigma weight residual -60.00 -114.86 54.86 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" CB ARG E 191 " pdb=" CG ARG E 191 " ideal model delta sinusoidal sigma weight residual -180.00 -126.28 -53.72 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 5534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 927 0.028 - 0.057: 346 0.057 - 0.085: 82 0.085 - 0.114: 63 0.114 - 0.142: 22 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA VAL E 1 " pdb=" N VAL E 1 " pdb=" C VAL E 1 " pdb=" CB VAL E 1 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 1437 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 5 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO L 6 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 6 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 6 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 73 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL R 73 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL R 73 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY R 74 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 304 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO R 305 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 305 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 305 " -0.021 5.00e-02 4.00e+02 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 63 2.56 - 3.14: 7628 3.14 - 3.73: 13873 3.73 - 4.31: 19152 4.31 - 4.90: 32580 Nonbonded interactions: 73296 Sorted by model distance: nonbonded pdb=" O ARG A 35 " pdb=" OG1 THR A 219 " model vdw 1.974 3.040 nonbonded pdb=" O ASP B 338 " pdb=" OG SER B 339 " model vdw 2.205 3.040 nonbonded pdb=" NE2 GLN B 181 " pdb=" OG1 THR B 184 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN A 359 " pdb=" OG SER R 341 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 232 " pdb=" OG SER B 250 " model vdw 2.233 3.040 ... (remaining 73291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.002 0.101 9350 Z= 0.149 Angle : 0.450 4.934 12690 Z= 0.256 Chirality : 0.038 0.142 1440 Planarity : 0.003 0.045 1611 Dihedral : 10.050 89.862 3359 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.20 % Allowed : 5.25 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.26), residues: 1144 helix: 2.70 (0.28), residues: 382 sheet: 1.19 (0.32), residues: 263 loop : -0.37 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 247 TYR 0.007 0.001 TYR A 30 PHE 0.007 0.001 PHE R 97 TRP 0.009 0.001 TRP B 174 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 9349) covalent geometry : angle 0.45024 (12690) hydrogen bonds : bond 0.13578 ( 446) hydrogen bonds : angle 4.74264 ( 1257) Misc. bond : bond 0.10140 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 340 ARG cc_start: 0.6653 (mmm160) cc_final: 0.6361 (tpp-160) REVERT: A 347 LYS cc_start: 0.7638 (ttpp) cc_final: 0.7116 (mtpp) REVERT: A 356 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.7268 (ttm110) REVERT: B 48 ILE cc_start: 0.7010 (mt) cc_final: 0.6677 (mt) REVERT: B 66 MET cc_start: 0.8277 (pp-130) cc_final: 0.7876 (pp-130) REVERT: B 217 ASP cc_start: 0.6937 (m-30) cc_final: 0.6625 (m-30) REVERT: B 244 ASN cc_start: 0.8002 (m-40) cc_final: 0.7761 (m-40) REVERT: B 298 ASN cc_start: 0.6343 (p0) cc_final: 0.6091 (p0) REVERT: B 340 PHE cc_start: 0.8186 (m-10) cc_final: 0.7981 (m-10) REVERT: E 79 PHE cc_start: 0.6927 (m-80) cc_final: 0.6660 (m-80) REVERT: E 166 LEU cc_start: 0.7979 (tt) cc_final: 0.7743 (tp) REVERT: G 23 ASN cc_start: 0.5707 (m-40) cc_final: 0.5474 (m-40) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.5721 time to fit residues: 131.5263 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 204 GLN A 324 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 93 ASN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN R 92 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.200996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163838 restraints weight = 9637.296| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.05 r_work: 0.3542 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9350 Z= 0.176 Angle : 0.627 8.872 12690 Z= 0.324 Chirality : 0.045 0.178 1440 Planarity : 0.005 0.074 1611 Dihedral : 4.174 17.738 1275 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.83 % Allowed : 12.71 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.25), residues: 1144 helix: 2.24 (0.27), residues: 386 sheet: 0.90 (0.31), residues: 270 loop : -0.35 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 208 TYR 0.023 0.002 TYR B 269 PHE 0.017 0.002 PHE B 258 TRP 0.019 0.002 TRP B 104 HIS 0.006 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9349) covalent geometry : angle 0.62715 (12690) hydrogen bonds : bond 0.04729 ( 446) hydrogen bonds : angle 4.25272 ( 1257) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6346 (m-30) cc_final: 0.6084 (m-30) REVERT: A 340 ARG cc_start: 0.7009 (mmm160) cc_final: 0.6622 (tpp-160) REVERT: A 356 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7393 (ttm110) REVERT: B 222 MET cc_start: 0.7620 (ptp) cc_final: 0.7107 (pp-130) REVERT: B 285 LYS cc_start: 0.6634 (mmtt) cc_final: 0.6271 (ptmm) REVERT: B 298 ASN cc_start: 0.6807 (p0) cc_final: 0.6588 (p0) REVERT: B 340 PHE cc_start: 0.8376 (m-10) cc_final: 0.8164 (m-10) REVERT: G 20 MET cc_start: 0.7090 (ptm) cc_final: 0.6885 (ptm) REVERT: G 23 ASN cc_start: 0.5927 (m-40) cc_final: 0.5613 (m-40) REVERT: G 54 PRO cc_start: 0.6488 (Cg_exo) cc_final: 0.6266 (Cg_endo) REVERT: R 125 ARG cc_start: 0.4388 (mtp-110) cc_final: 0.3648 (ttt180) REVERT: R 253 ARG cc_start: 0.6236 (OUTLIER) cc_final: 0.5716 (ttm170) REVERT: R 275 ARG cc_start: 0.5640 (ttt90) cc_final: 0.5431 (ttm-80) REVERT: R 315 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6951 (tm) outliers start: 38 outliers final: 20 residues processed: 175 average time/residue: 0.5894 time to fit residues: 110.1680 Evaluate side-chains 152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 213 GLN A 245 ASN B 80 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 101 ASN R 317 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.199338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161612 restraints weight = 9576.979| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.28 r_work: 0.3487 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9350 Z= 0.143 Angle : 0.567 8.773 12690 Z= 0.293 Chirality : 0.043 0.158 1440 Planarity : 0.004 0.051 1611 Dihedral : 4.201 19.437 1275 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.74 % Allowed : 14.43 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1144 helix: 2.11 (0.27), residues: 388 sheet: 0.73 (0.31), residues: 279 loop : -0.43 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 247 TYR 0.015 0.001 TYR B 269 PHE 0.012 0.002 PHE G 60 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9349) covalent geometry : angle 0.56664 (12690) hydrogen bonds : bond 0.04366 ( 446) hydrogen bonds : angle 4.10411 ( 1257) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6844 (tp30) REVERT: A 192 ASP cc_start: 0.6328 (m-30) cc_final: 0.6075 (m-30) REVERT: A 340 ARG cc_start: 0.6958 (mmm160) cc_final: 0.6688 (tpp-160) REVERT: B 222 MET cc_start: 0.7754 (ptp) cc_final: 0.7314 (pp-130) REVERT: B 248 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8280 (p) REVERT: B 285 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6528 (ptmm) REVERT: B 298 ASN cc_start: 0.6957 (p0) cc_final: 0.6741 (p0) REVERT: E 183 GLN cc_start: 0.6608 (mt0) cc_final: 0.6391 (mt0) REVERT: G 45 LYS cc_start: 0.7516 (tppp) cc_final: 0.7276 (tptt) REVERT: R 125 ARG cc_start: 0.4334 (mtp-110) cc_final: 0.4016 (ttt180) REVERT: R 167 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5273 (pp) REVERT: R 253 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5690 (ttm170) REVERT: R 275 ARG cc_start: 0.5610 (ttt90) cc_final: 0.5405 (ttm-80) REVERT: R 315 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7030 (tm) outliers start: 47 outliers final: 20 residues processed: 167 average time/residue: 0.5453 time to fit residues: 97.6843 Evaluate side-chains 152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 245 ASN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN R 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.193732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157995 restraints weight = 9667.511| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.38 r_work: 0.3381 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9350 Z= 0.189 Angle : 0.619 8.051 12690 Z= 0.324 Chirality : 0.045 0.168 1440 Planarity : 0.005 0.042 1611 Dihedral : 4.719 22.657 1275 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.05 % Allowed : 16.35 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1144 helix: 1.86 (0.26), residues: 390 sheet: 0.50 (0.31), residues: 266 loop : -0.67 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.020 0.002 TYR B 269 PHE 0.019 0.002 PHE G 60 TRP 0.017 0.002 TRP B 104 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9349) covalent geometry : angle 0.61908 (12690) hydrogen bonds : bond 0.04785 ( 446) hydrogen bonds : angle 4.41390 ( 1257) Misc. bond : bond 0.00087 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: A 337 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6790 (tp30) REVERT: A 340 ARG cc_start: 0.7123 (mmm160) cc_final: 0.6920 (tpp-160) REVERT: B 57 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7880 (mtt90) REVERT: B 222 MET cc_start: 0.7767 (ptp) cc_final: 0.7298 (pp-130) REVERT: B 285 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6747 (ptmm) REVERT: B 308 ASP cc_start: 0.7878 (p0) cc_final: 0.7596 (p0) REVERT: E 79 PHE cc_start: 0.8162 (m-80) cc_final: 0.7958 (m-80) REVERT: E 183 GLN cc_start: 0.6835 (mt0) cc_final: 0.6572 (mt0) REVERT: G 45 LYS cc_start: 0.7609 (tppp) cc_final: 0.7316 (tptt) REVERT: R 167 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5245 (pp) REVERT: R 253 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5772 (ttm110) REVERT: R 315 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7111 (tm) outliers start: 50 outliers final: 28 residues processed: 167 average time/residue: 0.5684 time to fit residues: 101.3757 Evaluate side-chains 163 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.0050 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN R 317 GLN R 321 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.197878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.160075 restraints weight = 9556.787| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.26 r_work: 0.3451 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9350 Z= 0.114 Angle : 0.532 8.402 12690 Z= 0.275 Chirality : 0.042 0.156 1440 Planarity : 0.004 0.051 1611 Dihedral : 4.222 18.600 1275 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.24 % Allowed : 17.76 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1144 helix: 1.99 (0.27), residues: 393 sheet: 0.60 (0.32), residues: 268 loop : -0.51 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 125 TYR 0.009 0.001 TYR B 129 PHE 0.018 0.001 PHE R 297 TRP 0.012 0.001 TRP B 302 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9349) covalent geometry : angle 0.53228 (12690) hydrogen bonds : bond 0.03927 ( 446) hydrogen bonds : angle 4.07895 ( 1257) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6989 (tp30) REVERT: A 340 ARG cc_start: 0.7049 (mmm160) cc_final: 0.6803 (tpp-160) REVERT: B 57 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7827 (mtt90) REVERT: B 62 LYS cc_start: 0.8061 (pttp) cc_final: 0.7717 (pttp) REVERT: B 222 MET cc_start: 0.7802 (ptp) cc_final: 0.7411 (pp-130) REVERT: B 285 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6717 (ptmm) REVERT: B 308 ASP cc_start: 0.7839 (p0) cc_final: 0.7562 (p0) REVERT: E 183 GLN cc_start: 0.6796 (mt0) cc_final: 0.6506 (mt0) REVERT: G 45 LYS cc_start: 0.7496 (tppp) cc_final: 0.7249 (tptt) REVERT: R 125 ARG cc_start: 0.4551 (mtp-110) cc_final: 0.3945 (mtp180) REVERT: R 167 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.4960 (pp) REVERT: R 315 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7064 (tm) outliers start: 42 outliers final: 23 residues processed: 161 average time/residue: 0.6105 time to fit residues: 104.7739 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 68 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.198289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.160422 restraints weight = 9671.896| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.16 r_work: 0.3492 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9350 Z= 0.110 Angle : 0.528 8.679 12690 Z= 0.272 Chirality : 0.042 0.196 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.099 18.390 1275 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.44 % Allowed : 18.67 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1144 helix: 2.01 (0.26), residues: 391 sheet: 0.53 (0.31), residues: 289 loop : -0.52 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 125 TYR 0.010 0.001 TYR B 129 PHE 0.019 0.001 PHE R 297 TRP 0.013 0.001 TRP R 322 HIS 0.002 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9349) covalent geometry : angle 0.52794 (12690) hydrogen bonds : bond 0.03807 ( 446) hydrogen bonds : angle 4.05077 ( 1257) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6851 (tp30) REVERT: A 192 ASP cc_start: 0.6208 (m-30) cc_final: 0.6000 (m-30) REVERT: A 195 ASN cc_start: 0.7756 (m-40) cc_final: 0.7367 (m-40) REVERT: A 337 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6670 (tp30) REVERT: A 340 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6672 (tpp-160) REVERT: B 222 MET cc_start: 0.7788 (ptp) cc_final: 0.7390 (pp-130) REVERT: B 285 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6666 (ptmm) REVERT: B 308 ASP cc_start: 0.7727 (p0) cc_final: 0.7487 (p0) REVERT: E 117 THR cc_start: 0.7502 (p) cc_final: 0.7214 (m) REVERT: E 183 GLN cc_start: 0.6772 (mt0) cc_final: 0.6479 (mt0) REVERT: G 45 LYS cc_start: 0.7489 (tppp) cc_final: 0.7257 (tptt) REVERT: R 125 ARG cc_start: 0.4497 (mtp-110) cc_final: 0.3752 (tmm-80) REVERT: R 167 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5199 (pp) REVERT: R 315 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7038 (tm) outliers start: 44 outliers final: 25 residues processed: 171 average time/residue: 0.5942 time to fit residues: 108.3318 Evaluate side-chains 167 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN B 80 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.197078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159042 restraints weight = 9666.094| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.22 r_work: 0.3472 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9350 Z= 0.120 Angle : 0.542 7.480 12690 Z= 0.279 Chirality : 0.042 0.159 1440 Planarity : 0.004 0.038 1611 Dihedral : 4.143 18.519 1275 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.94 % Allowed : 19.27 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.25), residues: 1144 helix: 1.94 (0.26), residues: 394 sheet: 0.61 (0.33), residues: 265 loop : -0.53 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 125 TYR 0.009 0.001 TYR A 358 PHE 0.020 0.001 PHE R 297 TRP 0.012 0.001 TRP B 87 HIS 0.003 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9349) covalent geometry : angle 0.54239 (12690) hydrogen bonds : bond 0.03904 ( 446) hydrogen bonds : angle 4.08708 ( 1257) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: A 195 ASN cc_start: 0.7896 (m-40) cc_final: 0.7532 (m-40) REVERT: A 337 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6646 (tp30) REVERT: A 340 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6768 (tpp-160) REVERT: B 28 LYS cc_start: 0.7595 (mmtp) cc_final: 0.7176 (ttpt) REVERT: B 222 MET cc_start: 0.7822 (ptp) cc_final: 0.7426 (pp-130) REVERT: B 285 LYS cc_start: 0.7229 (mmtt) cc_final: 0.6685 (ptmm) REVERT: B 308 ASP cc_start: 0.7783 (p0) cc_final: 0.7556 (p0) REVERT: E 79 PHE cc_start: 0.7854 (m-80) cc_final: 0.7538 (m-80) REVERT: E 117 THR cc_start: 0.7579 (p) cc_final: 0.7299 (m) REVERT: E 183 GLN cc_start: 0.6782 (mt0) cc_final: 0.6458 (mt0) REVERT: G 45 LYS cc_start: 0.7457 (tppp) cc_final: 0.7231 (tptt) REVERT: R 125 ARG cc_start: 0.4466 (mtp-110) cc_final: 0.3776 (tmm-80) REVERT: R 167 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5128 (pp) REVERT: R 315 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7035 (tm) outliers start: 39 outliers final: 25 residues processed: 159 average time/residue: 0.5574 time to fit residues: 94.6795 Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.0020 chunk 74 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159045 restraints weight = 9613.271| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.18 r_work: 0.3437 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9350 Z= 0.137 Angle : 0.564 7.562 12690 Z= 0.292 Chirality : 0.043 0.167 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.287 18.742 1275 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.63 % Allowed : 20.08 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1144 helix: 1.90 (0.26), residues: 391 sheet: 0.50 (0.33), residues: 260 loop : -0.57 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 17 TYR 0.011 0.001 TYR A 358 PHE 0.022 0.002 PHE R 297 TRP 0.014 0.001 TRP B 104 HIS 0.004 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9349) covalent geometry : angle 0.56408 (12690) hydrogen bonds : bond 0.04085 ( 446) hydrogen bonds : angle 4.18736 ( 1257) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6753 (tp30) REVERT: A 195 ASN cc_start: 0.7922 (m-40) cc_final: 0.7572 (m-40) REVERT: A 337 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6759 (tp30) REVERT: A 340 ARG cc_start: 0.7056 (mmm160) cc_final: 0.6838 (tpp-160) REVERT: B 28 LYS cc_start: 0.7553 (mmtp) cc_final: 0.7107 (ttpt) REVERT: B 222 MET cc_start: 0.7871 (ptp) cc_final: 0.7485 (pp-130) REVERT: B 285 LYS cc_start: 0.7265 (mmtt) cc_final: 0.6720 (ptmm) REVERT: B 308 ASP cc_start: 0.7856 (p0) cc_final: 0.7634 (p0) REVERT: E 117 THR cc_start: 0.7670 (p) cc_final: 0.7385 (m) REVERT: E 183 GLN cc_start: 0.6813 (mt0) cc_final: 0.6487 (mt0) REVERT: R 167 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5189 (pp) REVERT: R 253 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5770 (ttm170) REVERT: R 315 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.7018 (tm) outliers start: 36 outliers final: 25 residues processed: 156 average time/residue: 0.5912 time to fit residues: 98.5591 Evaluate side-chains 162 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN B 80 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.196367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159459 restraints weight = 9614.200| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.26 r_work: 0.3413 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9350 Z= 0.127 Angle : 0.554 8.446 12690 Z= 0.287 Chirality : 0.042 0.161 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.222 18.541 1275 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.33 % Allowed : 20.08 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1144 helix: 1.90 (0.26), residues: 391 sheet: 0.53 (0.33), residues: 255 loop : -0.61 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 17 TYR 0.012 0.001 TYR A 358 PHE 0.026 0.002 PHE R 297 TRP 0.012 0.001 TRP B 104 HIS 0.005 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9349) covalent geometry : angle 0.55390 (12690) hydrogen bonds : bond 0.03982 ( 446) hydrogen bonds : angle 4.17064 ( 1257) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7916 (m-40) cc_final: 0.7600 (m-40) REVERT: A 197 HIS cc_start: 0.7723 (m170) cc_final: 0.7472 (m90) REVERT: A 337 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6728 (tp30) REVERT: A 340 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6853 (tpp-160) REVERT: B 28 LYS cc_start: 0.7565 (mmtp) cc_final: 0.7100 (ttpt) REVERT: B 62 LYS cc_start: 0.7898 (pttp) cc_final: 0.7219 (pttt) REVERT: B 64 TYR cc_start: 0.8166 (m-80) cc_final: 0.7897 (m-80) REVERT: B 222 MET cc_start: 0.7893 (ptp) cc_final: 0.7482 (pp-130) REVERT: B 285 LYS cc_start: 0.7329 (mmtt) cc_final: 0.6708 (ptmm) REVERT: E 117 THR cc_start: 0.7595 (p) cc_final: 0.7343 (m) REVERT: E 183 GLN cc_start: 0.6879 (mt0) cc_final: 0.6514 (mt0) REVERT: R 315 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7030 (tm) outliers start: 33 outliers final: 25 residues processed: 150 average time/residue: 0.5742 time to fit residues: 92.1059 Evaluate side-chains 159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.195812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158883 restraints weight = 9588.191| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.18 r_work: 0.3435 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9350 Z= 0.131 Angle : 0.565 8.394 12690 Z= 0.291 Chirality : 0.043 0.164 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.270 18.675 1275 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.13 % Allowed : 20.38 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1144 helix: 1.79 (0.26), residues: 396 sheet: 0.45 (0.33), residues: 260 loop : -0.53 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 17 TYR 0.014 0.001 TYR A 358 PHE 0.029 0.002 PHE R 297 TRP 0.013 0.001 TRP B 104 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9349) covalent geometry : angle 0.56537 (12690) hydrogen bonds : bond 0.04019 ( 446) hydrogen bonds : angle 4.16438 ( 1257) Misc. bond : bond 0.00046 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7945 (m-40) cc_final: 0.7608 (m-40) REVERT: A 337 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6713 (tp30) REVERT: A 340 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6860 (tpp-160) REVERT: B 28 LYS cc_start: 0.7602 (mmtp) cc_final: 0.7156 (ttpt) REVERT: B 48 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 62 LYS cc_start: 0.7905 (pttp) cc_final: 0.7505 (pttm) REVERT: B 222 MET cc_start: 0.7845 (ptp) cc_final: 0.7450 (pp-130) REVERT: B 285 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6712 (ptmm) REVERT: E 117 THR cc_start: 0.7655 (p) cc_final: 0.7387 (m) REVERT: E 183 GLN cc_start: 0.6806 (mt0) cc_final: 0.6519 (mt0) REVERT: R 315 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7030 (tm) outliers start: 31 outliers final: 25 residues processed: 149 average time/residue: 0.5956 time to fit residues: 94.8036 Evaluate side-chains 161 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 204 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN R 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154294 restraints weight = 9476.403| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.32 r_work: 0.3370 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9350 Z= 0.199 Angle : 0.656 7.921 12690 Z= 0.339 Chirality : 0.046 0.179 1440 Planarity : 0.005 0.044 1611 Dihedral : 4.775 23.517 1275 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.53 % Allowed : 20.08 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1144 helix: 1.54 (0.26), residues: 393 sheet: 0.25 (0.33), residues: 261 loop : -0.64 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 17 TYR 0.020 0.002 TYR A 358 PHE 0.033 0.002 PHE R 297 TRP 0.018 0.002 TRP B 104 HIS 0.007 0.001 HIS R 339 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9349) covalent geometry : angle 0.65624 (12690) hydrogen bonds : bond 0.04827 ( 446) hydrogen bonds : angle 4.55150 ( 1257) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3273.55 seconds wall clock time: 56 minutes 49.34 seconds (3409.34 seconds total)