Starting phenix.real_space_refine on Thu Jan 16 02:07:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpt_60354/01_2025/8zpt_60354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpt_60354/01_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_60354/01_2025/8zpt_60354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpt_60354/01_2025/8zpt_60354.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpt_60354/01_2025/8zpt_60354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpt_60354/01_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-5571/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: 5.38, per 1000 atoms: 0.59 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 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: 1.00 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: 2.56 Time building geometry restraints manager: 2.68 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.810 Find NCS groups from input model: 0.100 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:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- 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 : 1.075 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: 1.1365 time to fit residues: 262.4108 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 : 0.961 ------------------------------------------------------------------------------- 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 = 9455.449| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.28 r_work: 0.3425 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 1.106 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.6406 (m-30) cc_final: 0.6166 (m-30) REVERT: A 340 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6694 (tpp-160) REVERT: B 285 LYS cc_start: 0.7272 (mmtt) cc_final: 0.6706 (ptmm) REVERT: E 166 LEU cc_start: 0.8234 (tt) cc_final: 0.8000 (tp) REVERT: E 183 GLN cc_start: 0.6604 (mt0) cc_final: 0.6301 (mt0) REVERT: G 20 MET cc_start: 0.7111 (ptm) cc_final: 0.6776 (ptm) REVERT: G 45 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7368 (tptt) REVERT: R 125 ARG cc_start: 0.4582 (mtp-110) cc_final: 0.3789 (tmm-80) REVERT: R 253 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5713 (ttm110) REVERT: R 275 ARG cc_start: 0.5800 (ttt90) cc_final: 0.5571 (ttm-80) REVERT: R 315 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7074 (tm) outliers start: 47 outliers final: 21 residues processed: 187 average time/residue: 1.1475 time to fit residues: 230.1075 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.0040 chunk 70 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 54 GLN R 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.199359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.161644 restraints weight = 9481.804| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.28 r_work: 0.3463 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3547 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 : 0.557 8.933 12690 Z= 0.288 Chirality : 0.043 0.159 1440 Planarity : 0.004 0.047 1611 Dihedral : 4.315 19.170 1275 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.24 % Allowed : 15.34 % Favored : 80.42 % 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: 0.56 (0.31), residues: 277 loop : -0.47 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.004 0.001 HIS B 188 PHE 0.010 0.001 PHE G 60 TYR 0.012 0.001 TYR B 269 ARG 0.005 0.001 ARG R 247 *********************** 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 185 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASP cc_start: 0.8234 (m-30) cc_final: 0.7972 (m-30) REVERT: B 285 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6699 (ptmm) REVERT: E 166 LEU cc_start: 0.8187 (tt) cc_final: 0.7954 (tp) REVERT: E 183 GLN cc_start: 0.6752 (mt0) cc_final: 0.6390 (mt0) REVERT: G 45 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7438 (tptt) REVERT: R 125 ARG cc_start: 0.4494 (mtp-110) cc_final: 0.4020 (ttt180) REVERT: R 167 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5302 (pp) REVERT: R 315 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7117 (tm) outliers start: 42 outliers final: 20 residues processed: 166 average time/residue: 1.1885 time to fit residues: 211.4104 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 195 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 80 GLN B 181 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.199717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162515 restraints weight = 9546.587| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.06 r_work: 0.3499 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3674 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= 0.159 Angle : 0.531 8.529 12690 Z= 0.272 Chirality : 0.042 0.152 1440 Planarity : 0.004 0.042 1611 Dihedral : 4.107 18.764 1275 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.14 % Allowed : 17.05 % Favored : 78.81 % 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: 0.96 (0.25), residues: 1144 helix: 2.02 (0.27), residues: 392 sheet: 0.57 (0.31), residues: 276 loop : -0.47 (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 0.009 0.001 TYR B 269 ARG 0.004 0.000 ARG R 301 *********************** 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: 41 poor density : 139 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 ARG cc_start: 0.6776 (mtt180) cc_final: 0.6520 (mpt-90) REVERT: B 48 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 62 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7637 (pttp) REVERT: B 64 TYR cc_start: 0.7934 (m-80) cc_final: 0.7681 (m-80) REVERT: B 158 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: B 222 MET cc_start: 0.7718 (ptp) cc_final: 0.7302 (pp-130) REVERT: B 285 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6625 (ptmm) REVERT: E 166 LEU cc_start: 0.8109 (tt) cc_final: 0.7897 (tp) REVERT: E 183 GLN cc_start: 0.6786 (mt0) cc_final: 0.6471 (mt0) REVERT: R 125 ARG cc_start: 0.4713 (mtp-110) cc_final: 0.3899 (tmm-80) REVERT: R 167 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5321 (pp) REVERT: R 315 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7063 (tm) outliers start: 41 outliers final: 21 residues processed: 158 average time/residue: 1.1362 time to fit residues: 192.8854 Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 101 ASN 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: 4.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 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 = 0.4148 r_free = 0.4148 target = 0.189688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153767 restraints weight = 9524.209| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.31 r_work: 0.3326 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 9349 Z= 0.438 Angle : 0.731 8.592 12690 Z= 0.380 Chirality : 0.050 0.210 1440 Planarity : 0.005 0.045 1611 Dihedral : 5.230 27.783 1275 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.75 % Allowed : 16.75 % Favored : 77.50 % 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: 0.30 (0.25), residues: 1144 helix: 1.33 (0.26), residues: 387 sheet: 0.27 (0.30), residues: 283 loop : -0.75 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 104 HIS 0.008 0.002 HIS E 34 PHE 0.026 0.003 PHE G 60 TYR 0.022 0.002 TYR B 269 ARG 0.006 0.001 ARG R 170 *********************** 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 197 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.988 Fit side-chains REVERT: A 186 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: A 188 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7597 (mttm) REVERT: B 28 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7116 (ttpt) REVERT: B 210 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 285 LYS cc_start: 0.7514 (mmtt) cc_final: 0.6878 (ptmm) REVERT: B 308 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (p0) REVERT: E 79 PHE cc_start: 0.8385 (m-80) cc_final: 0.8135 (m-80) REVERT: E 166 LEU cc_start: 0.8193 (tt) cc_final: 0.7967 (tp) REVERT: E 183 GLN cc_start: 0.6940 (mt0) cc_final: 0.6621 (mt0) REVERT: G 45 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7323 (tptt) REVERT: R 167 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5491 (pp) REVERT: R 168 ARG cc_start: 0.4765 (ttp80) cc_final: 0.4434 (ptt90) REVERT: R 253 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5671 (ttm170) REVERT: R 315 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7148 (tm) REVERT: R 334 ILE cc_start: 0.7256 (tt) cc_final: 0.6853 (tp) outliers start: 57 outliers final: 30 residues processed: 171 average time/residue: 1.1863 time to fit residues: 217.7952 Evaluate side-chains 167 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 G residue 45 LYS 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: 0.9990 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.193283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156812 restraints weight = 9467.413| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.25 r_work: 0.3374 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4558 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= 0.212 Angle : 0.595 8.969 12690 Z= 0.306 Chirality : 0.043 0.164 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.662 22.820 1275 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.73 % Allowed : 19.68 % 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 (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: 0.55 (0.25), residues: 1144 helix: 1.63 (0.26), residues: 391 sheet: 0.44 (0.32), residues: 260 loop : -0.67 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 322 HIS 0.015 0.001 HIS B 271 PHE 0.020 0.002 PHE R 297 TYR 0.012 0.001 TYR B 269 ARG 0.003 0.000 ARG E 17 *********************** 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 177 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7595 (mttm) REVERT: A 337 GLU cc_start: 0.7097 (tp30) cc_final: 0.6856 (mt-10) REVERT: B 28 LYS cc_start: 0.7529 (mmtp) cc_final: 0.7058 (ttpt) REVERT: B 158 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 222 MET cc_start: 0.7851 (ptp) cc_final: 0.7399 (pp-130) REVERT: B 285 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6796 (ptmm) REVERT: B 308 ASP cc_start: 0.7913 (p0) cc_final: 0.7638 (p0) REVERT: E 166 LEU cc_start: 0.8187 (tt) cc_final: 0.7960 (tp) REVERT: E 183 GLN cc_start: 0.7014 (mt0) cc_final: 0.6634 (mt0) REVERT: E 222 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5667 (pt0) REVERT: G 45 LYS cc_start: 0.7594 (tppp) cc_final: 0.7302 (tptt) REVERT: R 167 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5353 (pp) REVERT: R 168 ARG cc_start: 0.4691 (ttp80) cc_final: 0.4472 (ptt90) REVERT: R 315 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7027 (tm) REVERT: R 334 ILE cc_start: 0.7128 (tt) cc_final: 0.6751 (tp) outliers start: 37 outliers final: 22 residues processed: 161 average time/residue: 1.1739 time to fit residues: 202.5764 Evaluate side-chains 157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.0570 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 B 80 GLN B 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159682 restraints weight = 9607.167| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.20 r_work: 0.3424 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4468 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= 0.165 Angle : 0.553 8.210 12690 Z= 0.283 Chirality : 0.042 0.158 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.284 19.072 1275 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.33 % Allowed : 20.99 % Favored : 75.68 % 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: 0.68 (0.25), residues: 1144 helix: 1.74 (0.26), residues: 393 sheet: 0.45 (0.31), residues: 272 loop : -0.60 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 302 HIS 0.009 0.001 HIS A 329 PHE 0.022 0.001 PHE R 297 TYR 0.009 0.001 TYR A 306 ARG 0.003 0.000 ARG R 301 *********************** 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 171 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7204 (tt0) cc_final: 0.6659 (tm-30) REVERT: A 195 ASN cc_start: 0.7775 (m-40) cc_final: 0.7425 (m-40) REVERT: B 28 LYS cc_start: 0.7508 (mmtp) cc_final: 0.7168 (ttpt) REVERT: B 158 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: B 222 MET cc_start: 0.7896 (ptp) cc_final: 0.7451 (pp-130) REVERT: B 285 LYS cc_start: 0.7417 (mmtt) cc_final: 0.6771 (ptmm) REVERT: B 308 ASP cc_start: 0.7849 (p0) cc_final: 0.7601 (p0) REVERT: E 166 LEU cc_start: 0.8174 (tt) cc_final: 0.7954 (tp) REVERT: E 183 GLN cc_start: 0.6983 (mt0) cc_final: 0.6591 (mt0) REVERT: G 45 LYS cc_start: 0.7510 (tppp) cc_final: 0.7256 (tptt) REVERT: R 167 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5231 (pp) REVERT: R 315 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.7001 (tm) REVERT: R 334 ILE cc_start: 0.7101 (tt) cc_final: 0.6766 (tp) outliers start: 33 outliers final: 22 residues processed: 159 average time/residue: 1.2314 time to fit residues: 209.2264 Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 250 ARG 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 42 optimal weight: 0.0970 chunk 25 optimal weight: 0.0970 chunk 18 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.196180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159550 restraints weight = 9710.488| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.28 r_work: 0.3437 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9349 Z= 0.157 Angle : 0.553 8.162 12690 Z= 0.282 Chirality : 0.042 0.164 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.151 18.698 1275 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.03 % Allowed : 22.20 % Favored : 74.77 % 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: 0.77 (0.25), residues: 1144 helix: 1.82 (0.27), residues: 395 sheet: 0.46 (0.32), residues: 274 loop : -0.53 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.008 0.001 HIS A 329 PHE 0.025 0.002 PHE R 297 TYR 0.008 0.001 TYR B 129 ARG 0.004 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 168 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7181 (tt0) cc_final: 0.6657 (tm-30) REVERT: A 195 ASN cc_start: 0.7885 (m-40) cc_final: 0.7546 (m-40) REVERT: B 28 LYS cc_start: 0.7518 (mmtp) cc_final: 0.7187 (ttpt) REVERT: B 158 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: B 222 MET cc_start: 0.7880 (ptp) cc_final: 0.7498 (pp-130) REVERT: B 285 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6779 (ptmm) REVERT: B 308 ASP cc_start: 0.7817 (p0) cc_final: 0.7579 (p0) REVERT: E 166 LEU cc_start: 0.8145 (tt) cc_final: 0.7939 (tp) REVERT: E 183 GLN cc_start: 0.6971 (mt0) cc_final: 0.6561 (mt0) REVERT: G 45 LYS cc_start: 0.7435 (tppp) cc_final: 0.7191 (tptt) REVERT: R 315 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7038 (tm) REVERT: R 334 ILE cc_start: 0.7062 (tt) cc_final: 0.6734 (tp) outliers start: 30 outliers final: 17 residues processed: 154 average time/residue: 1.2095 time to fit residues: 199.7054 Evaluate side-chains 153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 271 HIS ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.193605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154578 restraints weight = 9548.132| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.42 r_work: 0.3445 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4683 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= 0.223 Angle : 0.604 9.325 12690 Z= 0.308 Chirality : 0.043 0.169 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.420 20.914 1275 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.13 % Allowed : 22.81 % 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: 0.73 (0.25), residues: 1144 helix: 1.74 (0.26), residues: 392 sheet: 0.52 (0.32), residues: 264 loop : -0.54 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.008 0.001 HIS A 329 PHE 0.029 0.002 PHE R 297 TYR 0.010 0.001 TYR A 306 ARG 0.007 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 167 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7170 (tt0) cc_final: 0.6679 (tm-30) REVERT: A 195 ASN cc_start: 0.7944 (m-40) cc_final: 0.7599 (m-40) REVERT: A 337 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6698 (tp30) REVERT: B 28 LYS cc_start: 0.7567 (mmtp) cc_final: 0.7125 (ttpt) REVERT: B 48 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7765 (mt) REVERT: B 57 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7914 (mtt90) REVERT: B 62 LYS cc_start: 0.8071 (pttp) cc_final: 0.7504 (pttt) REVERT: B 64 TYR cc_start: 0.8107 (m-80) cc_final: 0.7890 (m-80) REVERT: B 158 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: B 222 MET cc_start: 0.7862 (ptp) cc_final: 0.7470 (pp-130) REVERT: B 285 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6776 (ptmm) REVERT: B 308 ASP cc_start: 0.7833 (p0) cc_final: 0.7597 (p0) REVERT: E 166 LEU cc_start: 0.8134 (tt) cc_final: 0.7924 (tp) REVERT: E 183 GLN cc_start: 0.7034 (mt0) cc_final: 0.6629 (mt0) REVERT: G 45 LYS cc_start: 0.7546 (tppp) cc_final: 0.7283 (tptt) REVERT: R 315 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6949 (tm) REVERT: R 334 ILE cc_start: 0.7044 (tt) cc_final: 0.6719 (tp) outliers start: 31 outliers final: 19 residues processed: 153 average time/residue: 1.2146 time to fit residues: 201.1142 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 48 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B 345 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 = 0.4162 r_free = 0.4162 target = 0.191496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154241 restraints weight = 9675.445| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.46 r_work: 0.3341 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9349 Z= 0.289 Angle : 0.657 10.067 12690 Z= 0.336 Chirality : 0.045 0.170 1440 Planarity : 0.004 0.040 1611 Dihedral : 4.751 24.279 1275 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.33 % Allowed : 22.81 % Favored : 73.86 % 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: 0.54 (0.25), residues: 1144 helix: 1.56 (0.26), residues: 389 sheet: 0.37 (0.32), residues: 265 loop : -0.58 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.009 0.001 HIS A 329 PHE 0.033 0.002 PHE R 297 TYR 0.013 0.002 TYR A 306 ARG 0.007 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 163 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7312 (tt0) cc_final: 0.6883 (tm-30) REVERT: A 195 ASN cc_start: 0.8020 (m-40) cc_final: 0.7659 (m-40) REVERT: A 337 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6747 (tp30) REVERT: B 28 LYS cc_start: 0.7609 (mmtp) cc_final: 0.7151 (ttpt) REVERT: B 48 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 57 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7978 (mtt90) REVERT: B 62 LYS cc_start: 0.8182 (pttp) cc_final: 0.7927 (pttp) REVERT: B 158 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: B 222 MET cc_start: 0.7904 (ptp) cc_final: 0.7421 (pp-130) REVERT: B 285 LYS cc_start: 0.7421 (mmtt) cc_final: 0.6827 (ptmm) REVERT: B 308 ASP cc_start: 0.7942 (p0) cc_final: 0.7717 (p0) REVERT: E 166 LEU cc_start: 0.8205 (tt) cc_final: 0.7968 (tp) REVERT: E 183 GLN cc_start: 0.7035 (mt0) cc_final: 0.6636 (mt0) REVERT: G 45 LYS cc_start: 0.7594 (tppp) cc_final: 0.7312 (tptt) REVERT: R 315 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6959 (tm) REVERT: R 334 ILE cc_start: 0.7068 (tt) cc_final: 0.6680 (tp) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 1.1494 time to fit residues: 185.0769 Evaluate side-chains 153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 59 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.195900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157419 restraints weight = 9557.276| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.26 r_work: 0.3451 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9349 Z= 0.166 Angle : 0.578 9.199 12690 Z= 0.296 Chirality : 0.042 0.161 1440 Planarity : 0.004 0.039 1611 Dihedral : 4.339 19.202 1275 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.62 % Allowed : 23.11 % Favored : 74.27 % 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: 0.65 (0.25), residues: 1144 helix: 1.70 (0.26), residues: 392 sheet: 0.45 (0.32), residues: 260 loop : -0.59 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.009 0.001 HIS A 329 PHE 0.035 0.001 PHE R 297 TYR 0.016 0.001 TYR A 358 ARG 0.004 0.000 ARG E 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6152.36 seconds wall clock time: 109 minutes 47.22 seconds (6587.22 seconds total)