Starting phenix.real_space_refine on Thu Mar 13 14:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpt_60354/03_2025/8zpt_60354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpt_60354/03_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_60354/03_2025/8zpt_60354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpt_60354/03_2025/8zpt_60354.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpt_60354/03_2025/8zpt_60354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpt_60354/03_2025/8zpt_60354.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.66, per 1000 atoms: 0.62 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: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 2.83 Time building geometry restraints manager: 2.87 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.100 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:28.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- 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 0.033 9349 Z= 0.131 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 : 6.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP B 174 HIS 0.002 0.000 HIS A 324 PHE 0.007 0.001 PHE R 97 TYR 0.007 0.001 TYR A 30 ARG 0.003 0.000 ARG R 247 *********************** 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 : 1.172 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: 0.6676 (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: 0.6620 (m-30) REVERT: B 244 ASN cc_start: 0.8002 (m-40) cc_final: 0.7760 (m-40) REVERT: B 298 ASN cc_start: 0.6343 (p0) cc_final: 0.6092 (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: 0.5481 (t0) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 1.2175 time to fit residues: 280.2377 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 : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 261 GLN A 324 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 GLN E 179 GLN R 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156185 restraints weight = 9455.442| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.28 r_work: 0.3424 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9349 Z= 0.411 Angle : 0.749 9.805 12690 Z= 0.392 Chirality : 0.049 0.219 1440 Planarity : 0.006 0.071 1611 Dihedral : 4.945 22.518 1275 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.74 % Allowed : 12.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1144 helix: 1.68 (0.26), residues: 386 sheet: 0.73 (0.31), residues: 278 loop : -0.60 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 104 HIS 0.009 0.002 HIS E 34 PHE 0.027 0.003 PHE G 60 TYR 0.033 0.002 TYR B 269 ARG 0.009 0.001 ARG R 125 *********************** 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 205 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6407 (m-30) cc_final: 0.6168 (m-30) REVERT: A 340 ARG cc_start: 0.7106 (mmm160) cc_final: 0.6690 (tpp-160) REVERT: B 285 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6703 (ptmm) REVERT: E 166 LEU cc_start: 0.8231 (tt) cc_final: 0.7998 (tp) REVERT: E 183 GLN cc_start: 0.6608 (mt0) cc_final: 0.6299 (mt0) REVERT: G 20 MET cc_start: 0.7109 (ptm) cc_final: 0.6774 (ptm) REVERT: G 45 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7374 (tptt) REVERT: R 125 ARG cc_start: 0.4584 (mtp-110) cc_final: 0.3788 (tmm-80) REVERT: R 253 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5734 (ttm110) REVERT: R 275 ARG cc_start: 0.5802 (ttt90) cc_final: 0.5574 (ttm-80) REVERT: R 315 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7071 (tm) outliers start: 47 outliers final: 21 residues processed: 187 average time/residue: 1.1258 time to fit residues: 225.9308 Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 360 LEU 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 82 MET Chi-restraints excluded: chain E residue 141 THR 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 154 THR Chi-restraints excluded: chain R residue 165 HIS 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 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 93 ASN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN R 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.199438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.161763 restraints weight = 9471.969| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.27 r_work: 0.3465 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9349 Z= 0.191 Angle : 0.556 8.936 12690 Z= 0.287 Chirality : 0.043 0.160 1440 Planarity : 0.004 0.047 1611 Dihedral : 4.301 19.026 1275 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.34 % Allowed : 15.34 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1144 helix: 2.01 (0.27), residues: 390 sheet: 0.50 (0.31), residues: 282 loop : -0.43 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.005 0.001 HIS B 188 PHE 0.011 0.002 PHE G 60 TYR 0.012 0.001 TYR B 269 ARG 0.005 0.000 ARG R 343 *********************** 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 186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASP cc_start: 0.8229 (m-30) cc_final: 0.7956 (m-30) REVERT: B 285 LYS cc_start: 0.7258 (mmtt) cc_final: 0.6705 (ptmm) REVERT: E 166 LEU cc_start: 0.8182 (tt) cc_final: 0.7940 (tp) REVERT: E 183 GLN cc_start: 0.6752 (mt0) cc_final: 0.6387 (mt0) REVERT: G 45 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7429 (tptt) REVERT: R 125 ARG cc_start: 0.4485 (mtp-110) cc_final: 0.4011 (ttt180) REVERT: R 167 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5082 (pp) REVERT: R 315 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7124 (tm) outliers start: 43 outliers final: 18 residues processed: 165 average time/residue: 1.1302 time to fit residues: 199.9905 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain B residue 183 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 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 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 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 45 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 80 GLN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162257 restraints weight = 9536.047| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.15 r_work: 0.3502 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9349 Z= 0.156 Angle : 0.528 8.714 12690 Z= 0.271 Chirality : 0.042 0.152 1440 Planarity : 0.004 0.042 1611 Dihedral : 4.086 18.521 1275 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.04 % Allowed : 16.75 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1144 helix: 2.05 (0.27), residues: 393 sheet: 0.60 (0.31), residues: 275 loop : -0.46 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.003 0.001 HIS B 188 PHE 0.014 0.001 PHE R 297 TYR 0.010 0.001 TYR B 269 ARG 0.003 0.000 ARG A 309 *********************** 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 180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6565 (mpt-90) REVERT: B 48 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7711 (mt) REVERT: B 57 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7807 (mtt90) REVERT: B 62 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7637 (pttp) REVERT: B 64 TYR cc_start: 0.7914 (m-80) cc_final: 0.7671 (m-80) REVERT: B 158 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: B 222 MET cc_start: 0.7722 (ptp) cc_final: 0.7307 (pp-130) REVERT: B 285 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6644 (ptmm) REVERT: E 166 LEU cc_start: 0.8113 (tt) cc_final: 0.7898 (tp) REVERT: E 183 GLN cc_start: 0.6801 (mt0) cc_final: 0.6481 (mt0) REVERT: G 45 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7291 (tptt) REVERT: R 125 ARG cc_start: 0.4753 (mtp-110) cc_final: 0.3946 (tmm-80) REVERT: R 167 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5275 (pp) REVERT: R 315 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7091 (tm) outliers start: 40 outliers final: 21 residues processed: 158 average time/residue: 1.1405 time to fit residues: 193.7539 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP 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 239 PHE Chi-restraints excluded: chain B residue 248 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 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 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B 345 ASN R 298 ASN R 317 GLN R 321 HIS R 331 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.187272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150413 restraints weight = 9524.934| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.32 r_work: 0.3305 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 9349 Z= 0.554 Angle : 0.806 9.371 12690 Z= 0.421 Chirality : 0.053 0.252 1440 Planarity : 0.006 0.049 1611 Dihedral : 5.563 30.065 1275 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.55 % Allowed : 17.56 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1144 helix: 1.04 (0.25), residues: 387 sheet: 0.08 (0.30), residues: 289 loop : -0.80 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 104 HIS 0.007 0.002 HIS E 34 PHE 0.031 0.003 PHE G 60 TYR 0.021 0.003 TYR B 269 ARG 0.007 0.001 ARG B 139 *********************** 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 193 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 1.060 Fit side-chains REVERT: A 32 ARG cc_start: 0.6148 (mtm-85) cc_final: 0.5528 (tpt170) REVERT: A 186 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: A 188 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7584 (mttm) REVERT: A 189 PHE cc_start: 0.7564 (p90) cc_final: 0.7280 (p90) REVERT: A 337 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6946 (tp30) REVERT: B 28 LYS cc_start: 0.7546 (mmtp) cc_final: 0.7098 (ttpt) REVERT: B 57 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8063 (mtt90) REVERT: B 210 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (p0) REVERT: B 285 LYS cc_start: 0.7510 (mmtt) cc_final: 0.6910 (tttp) REVERT: B 308 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7686 (p0) REVERT: E 166 LEU cc_start: 0.8260 (tt) cc_final: 0.8008 (tp) REVERT: E 183 GLN cc_start: 0.7041 (mt0) cc_final: 0.6732 (mt0) REVERT: E 222 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5758 (pt0) REVERT: G 45 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7319 (tptt) REVERT: R 167 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5643 (pp) REVERT: R 168 ARG cc_start: 0.4955 (ttp80) cc_final: 0.4729 (ptt90) REVERT: R 253 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5601 (ttm170) REVERT: R 315 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7162 (tm) REVERT: R 334 ILE cc_start: 0.7296 (tt) cc_final: 0.6865 (tp) outliers start: 55 outliers final: 30 residues processed: 170 average time/residue: 1.1560 time to fit residues: 210.8695 Evaluate side-chains 164 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 62 LYS 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 158 ASP 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 210 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 308 ASP 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 117 THR Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL 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 253 ARG Chi-restraints excluded: chain R residue 281 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 39 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 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 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 = 0.4178 r_free = 0.4178 target = 0.193071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156909 restraints weight = 9499.573| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.24 r_work: 0.3379 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9349 Z= 0.203 Angle : 0.594 9.053 12690 Z= 0.307 Chirality : 0.043 0.171 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.707 22.733 1275 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.14 % Allowed : 19.88 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1144 helix: 1.54 (0.26), residues: 392 sheet: 0.34 (0.31), residues: 266 loop : -0.68 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.018 0.001 HIS B 271 PHE 0.022 0.002 PHE R 297 TYR 0.013 0.001 TYR B 269 ARG 0.003 0.000 ARG R 301 *********************** 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 180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6826 (tp30) REVERT: B 28 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7110 (ttpt) REVERT: B 57 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7978 (mtt90) REVERT: B 158 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8031 (m-30) REVERT: B 222 MET cc_start: 0.7851 (ptp) cc_final: 0.7401 (pp-130) REVERT: B 285 LYS cc_start: 0.7385 (mmtt) cc_final: 0.6760 (ptmm) REVERT: B 308 ASP cc_start: 0.7894 (p0) cc_final: 0.7615 (p0) REVERT: E 79 PHE cc_start: 0.8220 (m-80) cc_final: 0.7985 (m-80) REVERT: E 166 LEU cc_start: 0.8183 (tt) cc_final: 0.7954 (tp) REVERT: E 183 GLN cc_start: 0.7037 (mt0) cc_final: 0.6723 (mt0) REVERT: E 222 GLU cc_start: 0.5976 (mm-30) cc_final: 0.5661 (pt0) REVERT: G 45 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7307 (tptt) REVERT: R 167 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5408 (pp) REVERT: R 315 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7023 (tm) REVERT: R 334 ILE cc_start: 0.7115 (tt) cc_final: 0.6690 (tp) outliers start: 41 outliers final: 19 residues processed: 162 average time/residue: 1.1492 time to fit residues: 199.6824 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 : 1.031 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 0.0370 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 329 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157276 restraints weight = 9571.878| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.22 r_work: 0.3411 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9349 Z= 0.185 Angle : 0.572 8.030 12690 Z= 0.294 Chirality : 0.042 0.148 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.436 21.266 1275 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.23 % Allowed : 21.49 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1144 helix: 1.64 (0.26), residues: 394 sheet: 0.31 (0.31), residues: 279 loop : -0.58 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.007 0.001 HIS A 329 PHE 0.023 0.002 PHE R 297 TYR 0.009 0.001 TYR B 129 ARG 0.004 0.000 ARG E 17 *********************** 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 169 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7291 (tt0) REVERT: A 195 ASN cc_start: 0.7835 (m-40) cc_final: 0.7525 (m-40) REVERT: A 337 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6847 (tp30) REVERT: A 359 ASN cc_start: 0.7870 (m-40) cc_final: 0.7642 (m-40) REVERT: B 28 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7145 (ttpt) REVERT: B 57 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7964 (mtt90) REVERT: B 158 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: B 177 GLU cc_start: 0.7592 (tp30) cc_final: 0.7327 (tt0) REVERT: B 222 MET cc_start: 0.7876 (ptp) cc_final: 0.7450 (pp-130) REVERT: B 285 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6795 (ptmm) REVERT: B 308 ASP cc_start: 0.7814 (p0) cc_final: 0.7559 (p0) REVERT: E 166 LEU cc_start: 0.8153 (tt) cc_final: 0.7933 (tp) REVERT: E 183 GLN cc_start: 0.7018 (mt0) cc_final: 0.6667 (mt0) REVERT: E 234 GLU cc_start: 0.8888 (pt0) cc_final: 0.8674 (pt0) REVERT: G 45 LYS cc_start: 0.7572 (ttmm) cc_final: 0.7269 (tptt) REVERT: R 315 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7049 (tm) REVERT: R 334 ILE cc_start: 0.7023 (tt) cc_final: 0.6624 (tp) outliers start: 32 outliers final: 22 residues processed: 156 average time/residue: 1.1221 time to fit residues: 187.9847 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain B residue 158 ASP 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 18 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4200 r_free = 0.4200 target = 0.195307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.158084 restraints weight = 9692.804| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.22 r_work: 0.3416 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9349 Z= 0.164 Angle : 0.564 8.377 12690 Z= 0.289 Chirality : 0.042 0.165 1440 Planarity : 0.004 0.038 1611 Dihedral : 4.274 18.597 1275 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.13 % Allowed : 22.30 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1144 helix: 1.76 (0.27), residues: 394 sheet: 0.42 (0.31), residues: 274 loop : -0.58 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.008 0.001 HIS A 329 PHE 0.028 0.002 PHE R 297 TYR 0.009 0.001 TYR B 129 ARG 0.003 0.000 ARG E 17 *********************** 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 166 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7300 (tt0) REVERT: A 195 ASN cc_start: 0.7905 (m-40) cc_final: 0.7619 (m-40) REVERT: A 337 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6742 (tp30) REVERT: B 28 LYS cc_start: 0.7597 (mmtp) cc_final: 0.7162 (ttpt) REVERT: B 57 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7967 (mtt90) REVERT: B 158 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: B 177 GLU cc_start: 0.7546 (tp30) cc_final: 0.7336 (tt0) REVERT: B 222 MET cc_start: 0.7893 (ptp) cc_final: 0.7470 (pp-130) REVERT: B 285 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6767 (ptmm) REVERT: B 308 ASP cc_start: 0.7825 (p0) cc_final: 0.7595 (p0) REVERT: E 166 LEU cc_start: 0.8147 (tt) cc_final: 0.7938 (tp) REVERT: E 183 GLN cc_start: 0.7067 (mt0) cc_final: 0.6659 (mt0) REVERT: E 234 GLU cc_start: 0.8893 (pt0) cc_final: 0.8689 (pt0) REVERT: G 45 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7251 (tptt) REVERT: R 315 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6950 (tm) REVERT: R 334 ILE cc_start: 0.7073 (tt) cc_final: 0.6737 (tp) outliers start: 31 outliers final: 22 residues processed: 152 average time/residue: 1.1764 time to fit residues: 191.8911 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP 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 332 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 80 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.195894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160179 restraints weight = 9581.431| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.21 r_work: 0.3438 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9349 Z= 0.167 Angle : 0.570 8.979 12690 Z= 0.289 Chirality : 0.042 0.162 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.232 22.616 1275 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.03 % Allowed : 23.01 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1144 helix: 1.83 (0.26), residues: 391 sheet: 0.48 (0.31), residues: 274 loop : -0.63 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.008 0.001 HIS A 329 PHE 0.031 0.001 PHE R 297 TYR 0.009 0.001 TYR A 306 ARG 0.005 0.000 ARG E 17 *********************** 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 165 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7351 (tt0) REVERT: A 195 ASN cc_start: 0.7943 (m-40) cc_final: 0.7620 (m-40) REVERT: A 200 ASP cc_start: 0.7429 (t0) cc_final: 0.7158 (t70) REVERT: A 337 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6717 (tp30) REVERT: B 28 LYS cc_start: 0.7599 (mmtp) cc_final: 0.7170 (ttpt) REVERT: B 57 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7932 (mtt90) REVERT: B 158 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 222 MET cc_start: 0.7790 (ptp) cc_final: 0.7365 (pp-130) REVERT: B 285 LYS cc_start: 0.7325 (mmtt) cc_final: 0.6757 (ptmm) REVERT: B 308 ASP cc_start: 0.7803 (p0) cc_final: 0.7584 (p0) REVERT: E 166 LEU cc_start: 0.8150 (tt) cc_final: 0.7943 (tp) REVERT: E 183 GLN cc_start: 0.7076 (mt0) cc_final: 0.6665 (mt0) REVERT: E 234 GLU cc_start: 0.8874 (pt0) cc_final: 0.8659 (pt0) REVERT: G 45 LYS cc_start: 0.7493 (ttmm) cc_final: 0.7225 (tptt) REVERT: R 315 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7007 (tm) REVERT: R 334 ILE cc_start: 0.7086 (tt) cc_final: 0.6767 (tp) outliers start: 30 outliers final: 20 residues processed: 152 average time/residue: 1.4747 time to fit residues: 240.4152 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP 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 332 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 230 LEU 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 107 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4140 r_free = 0.4140 target = 0.189281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.150774 restraints weight = 9693.154| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.53 r_work: 0.3340 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9349 Z= 0.378 Angle : 0.728 10.508 12690 Z= 0.371 Chirality : 0.048 0.175 1440 Planarity : 0.005 0.043 1611 Dihedral : 5.085 26.852 1275 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.53 % Allowed : 22.50 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1144 helix: 1.29 (0.26), residues: 395 sheet: 0.24 (0.31), residues: 277 loop : -0.68 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 87 HIS 0.008 0.002 HIS E 34 PHE 0.035 0.003 PHE R 297 TYR 0.018 0.002 TYR E 49 ARG 0.008 0.001 ARG E 17 ********************** 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 166 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.052 Fit side-chains REVERT: A 186 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7260 (tt0) REVERT: A 195 ASN cc_start: 0.8037 (m-40) cc_final: 0.7650 (m-40) REVERT: A 337 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6803 (tp30) REVERT: B 28 LYS cc_start: 0.7621 (mmtp) cc_final: 0.7177 (ttpt) REVERT: B 57 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8069 (mtt90) REVERT: B 62 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7933 (pttp) REVERT: B 158 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: B 222 MET cc_start: 0.7908 (ptp) cc_final: 0.7447 (pp-130) REVERT: B 285 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6855 (ptmm) REVERT: B 308 ASP cc_start: 0.7944 (p0) cc_final: 0.7677 (p0) REVERT: E 166 LEU cc_start: 0.8199 (tt) cc_final: 0.7961 (tp) REVERT: E 183 GLN cc_start: 0.7177 (mt0) cc_final: 0.6830 (mt0) REVERT: E 222 GLU cc_start: 0.5999 (mm-30) cc_final: 0.5664 (pt0) REVERT: G 45 LYS cc_start: 0.7592 (ttmm) cc_final: 0.7270 (tptt) REVERT: R 167 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5360 (pp) REVERT: R 214 PHE cc_start: 0.6785 (m-80) cc_final: 0.6549 (m-80) REVERT: R 315 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6945 (tm) REVERT: R 334 ILE cc_start: 0.7107 (tt) cc_final: 0.6676 (tp) outliers start: 35 outliers final: 20 residues processed: 152 average time/residue: 1.2550 time to fit residues: 204.2617 Evaluate side-chains 152 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 ASP 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 268 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 162 VAL 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 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.4182 r_free = 0.4182 target = 0.193716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155050 restraints weight = 9561.327| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.29 r_work: 0.3415 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9349 Z= 0.188 Angle : 0.617 9.475 12690 Z= 0.312 Chirality : 0.043 0.160 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.589 28.149 1275 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.83 % Allowed : 23.11 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1144 helix: 1.45 (0.26), residues: 398 sheet: 0.35 (0.32), residues: 260 loop : -0.59 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.009 0.001 HIS A 329 PHE 0.036 0.002 PHE R 297 TYR 0.015 0.001 TYR A 358 ARG 0.005 0.000 ARG E 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6467.28 seconds wall clock time: 113 minutes 32.80 seconds (6812.80 seconds total)