Starting phenix.real_space_refine on Fri Oct 10 19:29:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbg_36145/10_2025/8jbg_36145.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.150 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 43 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5585 2.51 5 N 1486 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8750 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2077 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'TRP:plan': 3, 'ARG:plan': 7, 'PHE:plan': 5, 'HIS:plan': 1, 'GLU:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 62 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8750 At special positions: 0 Unit cell: (86.67, 120.91, 123.05, 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 59 16.00 O 1620 8.00 N 1486 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 275.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 81 through 113 removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'B' and resid 163 through 189 Processing helix chain 'B' and resid 196 through 221 removed outlier: 3.572A pdb=" N LYS B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 239 through 275 removed outlier: 3.864A pdb=" N GLN B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.613A pdb=" N TYR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 325 removed outlier: 3.881A pdb=" N VAL B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.624A pdb=" N PHE B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.652A pdb=" N ARG B 330 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 removed outlier: 3.564A pdb=" N VAL B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.753A pdb=" N TYR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Proline residue: B 353 - end of helix removed outlier: 3.658A pdb=" N ASN B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 368 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.579A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.762A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.574A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'C' and resid 8 through 33 removed outlier: 4.076A pdb=" N VAL C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 210 through 216 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 260 through 270 removed outlier: 3.642A pdb=" N GLU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.654A pdb=" N ASP C 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 319 removed outlier: 3.579A pdb=" N PHE C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.349A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.500A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.729A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.636A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.645A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.630A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.642A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.532A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.665A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 190 removed outlier: 4.533A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 221 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE C 257 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE C 223 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 259 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 225 " --> pdb=" O ASN C 259 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2823 1.34 - 1.46: 1965 1.46 - 1.58: 4062 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8938 Sorted by residual: bond pdb=" N ASP C 217 " pdb=" CA ASP C 217 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.44e+00 bond pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB ASN D 268 " pdb=" CG ASN D 268 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.00e-01 bond pdb=" CG PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.503 1.534 -0.031 3.40e-02 8.65e+02 8.45e-01 bond pdb=" CB ASP C 217 " pdb=" CG ASP C 217 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.04e-01 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 11984 1.86 - 3.72: 133 3.72 - 5.58: 18 5.58 - 7.44: 7 7.44 - 9.30: 2 Bond angle restraints: 12144 Sorted by residual: angle pdb=" CA LEU B 328 " pdb=" CB LEU B 328 " pdb=" CG LEU B 328 " ideal model delta sigma weight residual 116.30 125.60 -9.30 3.50e+00 8.16e-02 7.06e+00 angle pdb=" CB MET B 346 " pdb=" CG MET B 346 " pdb=" SD MET B 346 " ideal model delta sigma weight residual 112.70 120.44 -7.74 3.00e+00 1.11e-01 6.66e+00 angle pdb=" C LEU A 9 " pdb=" N MET A 10 " pdb=" CA MET A 10 " ideal model delta sigma weight residual 121.70 125.98 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" CB GLN E 82 " pdb=" CG GLN E 82 " pdb=" CD GLN E 82 " ideal model delta sigma weight residual 112.60 116.62 -4.02 1.70e+00 3.46e-01 5.58e+00 angle pdb=" CA LEU B 101 " pdb=" CB LEU B 101 " pdb=" CG LEU B 101 " ideal model delta sigma weight residual 116.30 123.66 -7.36 3.50e+00 8.16e-02 4.42e+00 ... (remaining 12139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4495 17.72 - 35.45: 552 35.45 - 53.17: 188 53.17 - 70.89: 25 70.89 - 88.62: 8 Dihedral angle restraints: 5268 sinusoidal: 1954 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ASN B 138 " pdb=" C ASN B 138 " pdb=" N THR B 139 " pdb=" CA THR B 139 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA HIS B 148 " pdb=" C HIS B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP C 298 " pdb=" CB ASP C 298 " pdb=" CG ASP C 298 " pdb=" OD1 ASP C 298 " ideal model delta sinusoidal sigma weight residual -30.00 -89.51 59.51 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 5265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.056: 341 0.056 - 0.084: 125 0.084 - 0.112: 90 0.112 - 0.139: 14 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASP C 217 " pdb=" N ASP C 217 " pdb=" C ASP C 217 " pdb=" CB ASP C 217 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA VAL D 327 " pdb=" N VAL D 327 " pdb=" C VAL D 327 " pdb=" CB VAL D 327 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1388 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 217 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 298 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO C 299 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 299 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 299 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 253 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ILE B 253 " 0.033 2.00e-02 2.50e+03 pdb=" O ILE B 253 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 254 " -0.011 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 171 2.66 - 3.22: 7958 3.22 - 3.78: 14028 3.78 - 4.34: 19510 4.34 - 4.90: 31920 Nonbonded interactions: 73587 Sorted by model distance: nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.106 3.040 nonbonded pdb=" N GLU C 276 " pdb=" OE1 GLU C 276 " model vdw 2.223 3.120 nonbonded pdb=" O ILE C 315 " pdb=" OG SER C 319 " model vdw 2.225 3.040 nonbonded pdb=" O ASN B 138 " pdb=" ND2 ASN B 142 " model vdw 2.228 3.120 nonbonded pdb=" OD1 ASP D 228 " pdb=" NH2 ARG C 209 " model vdw 2.247 3.120 ... (remaining 73582 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: 0.490 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.031 8938 Z= 0.107 Angle : 0.542 9.299 12144 Z= 0.291 Chirality : 0.041 0.139 1391 Planarity : 0.004 0.081 1538 Dihedral : 17.536 88.617 3128 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.36 % Allowed : 30.61 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1119 helix: 0.54 (0.27), residues: 391 sheet: 0.29 (0.34), residues: 270 loop : -0.73 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 250 TYR 0.009 0.001 TYR D 264 PHE 0.029 0.001 PHE A 6 TRP 0.012 0.001 TRP B 275 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8938) covalent geometry : angle 0.54181 (12144) hydrogen bonds : bond 0.22257 ( 434) hydrogen bonds : angle 7.36727 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.289 Fit side-chains REVERT: E 79 LEU cc_start: 0.7114 (tp) cc_final: 0.6447 (tt) outliers start: 40 outliers final: 36 residues processed: 190 average time/residue: 0.5193 time to fit residues: 105.4211 Evaluate side-chains 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 142 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN E 194 ASN C 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124625 restraints weight = 10008.636| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.76 r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.135 Angle : 0.571 9.229 12144 Z= 0.303 Chirality : 0.043 0.149 1391 Planarity : 0.005 0.054 1538 Dihedral : 6.550 57.355 1273 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.77 % Allowed : 25.93 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1119 helix: 1.04 (0.27), residues: 395 sheet: 0.57 (0.34), residues: 256 loop : -0.66 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 250 TYR 0.011 0.001 TYR E 190 PHE 0.011 0.001 PHE C 215 TRP 0.014 0.001 TRP D 169 HIS 0.008 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8938) covalent geometry : angle 0.57072 (12144) hydrogen bonds : bond 0.04534 ( 434) hydrogen bonds : angle 5.03243 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.344 Fit side-chains REVERT: B 210 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7068 (tm) REVERT: B 359 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7329 (mm) REVERT: D 46 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7932 (ttm110) REVERT: D 228 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: E 63 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7895 (t) REVERT: C 250 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7349 (mtt-85) REVERT: C 276 GLU cc_start: 0.6098 (mp0) cc_final: 0.5865 (mp0) outliers start: 53 outliers final: 24 residues processed: 188 average time/residue: 0.5646 time to fit residues: 113.1254 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 332 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.167237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118855 restraints weight = 9897.559| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.62 r_work: 0.3096 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8938 Z= 0.244 Angle : 0.664 9.694 12144 Z= 0.346 Chirality : 0.047 0.164 1391 Planarity : 0.005 0.052 1538 Dihedral : 6.652 67.011 1243 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.86 % Allowed : 25.82 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.26), residues: 1119 helix: 1.10 (0.27), residues: 384 sheet: 0.41 (0.33), residues: 271 loop : -0.82 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.017 0.002 TYR B 315 PHE 0.023 0.002 PHE A 6 TRP 0.019 0.002 TRP D 63 HIS 0.009 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8938) covalent geometry : angle 0.66362 (12144) hydrogen bonds : bond 0.04809 ( 434) hydrogen bonds : angle 5.03293 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 0.344 Fit side-chains REVERT: B 142 ASN cc_start: 0.8196 (m-40) cc_final: 0.7666 (m110) REVERT: B 210 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7332 (tm) REVERT: B 359 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7351 (mm) REVERT: D 46 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7956 (ttm110) REVERT: D 57 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9036 (ptpp) REVERT: D 75 GLN cc_start: 0.8714 (mt0) cc_final: 0.8319 (mt0) REVERT: E 46 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: E 63 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7961 (t) REVERT: C 53 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6506 (mpp) REVERT: C 198 MET cc_start: 0.9127 (ttp) cc_final: 0.8879 (ttp) REVERT: C 250 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7386 (mtt-85) REVERT: C 276 GLU cc_start: 0.6110 (mp0) cc_final: 0.5814 (mp0) outliers start: 63 outliers final: 37 residues processed: 183 average time/residue: 0.6157 time to fit residues: 119.5116 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN G 59 ASN C 231 ASN C 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119409 restraints weight = 10058.709| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.63 r_work: 0.3123 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8938 Z= 0.186 Angle : 0.617 9.793 12144 Z= 0.320 Chirality : 0.045 0.156 1391 Planarity : 0.005 0.057 1538 Dihedral : 6.618 66.208 1243 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.75 % Allowed : 26.58 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1119 helix: 1.20 (0.27), residues: 384 sheet: 0.26 (0.33), residues: 269 loop : -0.83 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.014 0.002 TYR B 315 PHE 0.018 0.002 PHE A 6 TRP 0.017 0.002 TRP D 63 HIS 0.007 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8938) covalent geometry : angle 0.61748 (12144) hydrogen bonds : bond 0.04251 ( 434) hydrogen bonds : angle 4.84028 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 0.356 Fit side-chains REVERT: B 138 ASN cc_start: 0.8510 (t0) cc_final: 0.8085 (t0) REVERT: B 142 ASN cc_start: 0.8153 (m-40) cc_final: 0.7600 (m-40) REVERT: B 210 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7315 (tm) REVERT: B 359 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7330 (mm) REVERT: D 46 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7927 (ttm110) REVERT: D 57 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8952 (ptpp) REVERT: D 123 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8443 (mp) REVERT: D 175 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7183 (mp-120) REVERT: D 214 ARG cc_start: 0.7813 (ptt-90) cc_final: 0.7574 (mpt-90) REVERT: G 14 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5831 (mttm) REVERT: C 53 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6545 (mpp) REVERT: C 276 GLU cc_start: 0.6061 (mp0) cc_final: 0.5762 (mp0) outliers start: 62 outliers final: 38 residues processed: 185 average time/residue: 0.6232 time to fit residues: 122.4816 Evaluate side-chains 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122917 restraints weight = 9969.987| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.74 r_work: 0.3159 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8938 Z= 0.125 Angle : 0.571 10.465 12144 Z= 0.294 Chirality : 0.043 0.174 1391 Planarity : 0.004 0.045 1538 Dihedral : 6.364 62.505 1243 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.77 % Allowed : 27.89 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1119 helix: 1.45 (0.27), residues: 384 sheet: 0.38 (0.33), residues: 258 loop : -0.74 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 250 TYR 0.012 0.001 TYR E 190 PHE 0.026 0.001 PHE A 6 TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8938) covalent geometry : angle 0.57132 (12144) hydrogen bonds : bond 0.03710 ( 434) hydrogen bonds : angle 4.63616 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.364 Fit side-chains REVERT: B 138 ASN cc_start: 0.8425 (t0) cc_final: 0.7991 (t0) REVERT: B 142 ASN cc_start: 0.8049 (m-40) cc_final: 0.7494 (m-40) REVERT: B 210 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7256 (tm) REVERT: B 299 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8042 (mtmm) REVERT: B 359 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7518 (mm) REVERT: D 46 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7888 (ttm110) REVERT: D 175 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7120 (mp-120) REVERT: E 46 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: G 14 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6141 (mttm) REVERT: C 53 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6541 (mpp) REVERT: C 182 SER cc_start: 0.8816 (t) cc_final: 0.8615 (p) REVERT: C 250 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7344 (mtt-85) REVERT: C 276 GLU cc_start: 0.6219 (mp0) cc_final: 0.5874 (mp0) outliers start: 53 outliers final: 30 residues processed: 172 average time/residue: 0.6132 time to fit residues: 111.8518 Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN G 59 ASN C 231 ASN C 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124715 restraints weight = 10017.753| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.61 r_work: 0.3179 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8938 Z= 0.112 Angle : 0.551 10.689 12144 Z= 0.283 Chirality : 0.042 0.158 1391 Planarity : 0.004 0.040 1538 Dihedral : 5.981 57.557 1242 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.90 % Allowed : 28.65 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1119 helix: 1.64 (0.27), residues: 384 sheet: 0.39 (0.33), residues: 259 loop : -0.62 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 250 TYR 0.011 0.001 TYR E 190 PHE 0.019 0.001 PHE A 6 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8938) covalent geometry : angle 0.55066 (12144) hydrogen bonds : bond 0.03437 ( 434) hydrogen bonds : angle 4.45707 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.358 Fit side-chains REVERT: B 210 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7079 (tm) REVERT: B 351 TYR cc_start: 0.7403 (m-10) cc_final: 0.7124 (m-10) REVERT: D 23 LYS cc_start: 0.7416 (tmtm) cc_final: 0.6042 (ptmm) REVERT: D 46 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7838 (ttm110) REVERT: C 53 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6500 (mpp) REVERT: C 250 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7392 (mtt-85) REVERT: C 276 GLU cc_start: 0.6352 (mp0) cc_final: 0.5968 (mp0) outliers start: 45 outliers final: 26 residues processed: 175 average time/residue: 0.6369 time to fit residues: 118.0645 Evaluate side-chains 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 81 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123689 restraints weight = 10077.637| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.63 r_work: 0.3167 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.129 Angle : 0.578 10.736 12144 Z= 0.293 Chirality : 0.043 0.159 1391 Planarity : 0.004 0.042 1538 Dihedral : 4.922 54.932 1235 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.12 % Allowed : 29.96 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1119 helix: 1.64 (0.27), residues: 385 sheet: 0.35 (0.33), residues: 259 loop : -0.59 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 250 TYR 0.011 0.001 TYR B 315 PHE 0.023 0.001 PHE A 6 TRP 0.014 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8938) covalent geometry : angle 0.57770 (12144) hydrogen bonds : bond 0.03547 ( 434) hydrogen bonds : angle 4.48698 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.336 Fit side-chains REVERT: B 210 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7074 (tm) REVERT: B 248 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7585 (m-70) REVERT: B 299 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: B 302 ILE cc_start: 0.8220 (tt) cc_final: 0.7686 (mm) REVERT: D 23 LYS cc_start: 0.7454 (tmtm) cc_final: 0.6103 (ptmm) REVERT: D 46 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7843 (ttm110) REVERT: D 123 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8329 (mp) REVERT: D 217 MET cc_start: 0.8079 (pp-130) cc_final: 0.7795 (ppp) REVERT: D 262 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: E 46 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 53 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6520 (mpp) REVERT: C 250 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7392 (mtt-85) REVERT: C 276 GLU cc_start: 0.6371 (mp0) cc_final: 0.5969 (mp0) outliers start: 47 outliers final: 30 residues processed: 167 average time/residue: 0.5809 time to fit residues: 103.1309 Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122016 restraints weight = 9947.021| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.78 r_work: 0.3102 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8938 Z= 0.152 Angle : 0.600 9.761 12144 Z= 0.308 Chirality : 0.044 0.158 1391 Planarity : 0.004 0.042 1538 Dihedral : 5.038 55.509 1234 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.47 % Allowed : 29.96 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.26), residues: 1119 helix: 1.58 (0.27), residues: 385 sheet: 0.31 (0.33), residues: 262 loop : -0.63 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 250 TYR 0.013 0.001 TYR B 315 PHE 0.023 0.002 PHE A 6 TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8938) covalent geometry : angle 0.60020 (12144) hydrogen bonds : bond 0.03740 ( 434) hydrogen bonds : angle 4.57305 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.347 Fit side-chains REVERT: B 210 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7134 (tm) REVERT: B 248 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7643 (m-70) REVERT: B 299 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7962 (mtmm) REVERT: B 302 ILE cc_start: 0.8272 (tt) cc_final: 0.7685 (mm) REVERT: D 23 LYS cc_start: 0.7436 (tmtm) cc_final: 0.6048 (ptmm) REVERT: D 46 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7921 (ttm110) REVERT: D 123 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8376 (mp) REVERT: E 46 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: C 53 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6434 (mpp) REVERT: C 250 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7366 (mtt-85) REVERT: C 276 GLU cc_start: 0.6326 (mp0) cc_final: 0.5917 (mp0) REVERT: C 309 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6838 (ttp-170) outliers start: 41 outliers final: 31 residues processed: 160 average time/residue: 0.6639 time to fit residues: 112.4837 Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.171111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125422 restraints weight = 9956.247| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.71 r_work: 0.3172 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8938 Z= 0.125 Angle : 0.579 10.792 12144 Z= 0.296 Chirality : 0.043 0.158 1391 Planarity : 0.004 0.049 1538 Dihedral : 4.869 54.933 1234 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.25 % Allowed : 29.74 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.26), residues: 1119 helix: 1.67 (0.27), residues: 385 sheet: 0.37 (0.33), residues: 260 loop : -0.59 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 250 TYR 0.011 0.001 TYR E 190 PHE 0.020 0.001 PHE A 6 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8938) covalent geometry : angle 0.57932 (12144) hydrogen bonds : bond 0.03461 ( 434) hydrogen bonds : angle 4.47319 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.297 Fit side-chains REVERT: B 210 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7139 (tm) REVERT: B 248 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7544 (m-70) REVERT: B 299 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7991 (mtmm) REVERT: B 302 ILE cc_start: 0.8223 (tt) cc_final: 0.7677 (mm) REVERT: D 23 LYS cc_start: 0.7447 (tmtm) cc_final: 0.6087 (ptmm) REVERT: D 46 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7967 (ttm110) REVERT: D 123 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8318 (mp) REVERT: D 217 MET cc_start: 0.8096 (pp-130) cc_final: 0.7764 (ppp) REVERT: E 46 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: C 53 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6469 (mpp) REVERT: C 250 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7438 (mtt-85) REVERT: C 276 GLU cc_start: 0.6447 (mp0) cc_final: 0.6011 (mp0) REVERT: C 309 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6856 (ttp-170) outliers start: 39 outliers final: 30 residues processed: 162 average time/residue: 0.6547 time to fit residues: 112.1320 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.169850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122254 restraints weight = 9956.629| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.62 r_work: 0.3141 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8938 Z= 0.151 Angle : 0.600 10.767 12144 Z= 0.308 Chirality : 0.044 0.159 1391 Planarity : 0.004 0.054 1538 Dihedral : 5.011 55.329 1234 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.47 % Allowed : 29.74 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1119 helix: 1.62 (0.26), residues: 385 sheet: 0.34 (0.33), residues: 262 loop : -0.61 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.013 0.001 TYR B 315 PHE 0.019 0.002 PHE A 6 TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8938) covalent geometry : angle 0.60008 (12144) hydrogen bonds : bond 0.03682 ( 434) hydrogen bonds : angle 4.55650 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.366 Fit side-chains REVERT: B 210 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7345 (tm) REVERT: B 248 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7621 (m-70) REVERT: B 299 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7942 (mtmm) REVERT: B 302 ILE cc_start: 0.8212 (tt) cc_final: 0.7655 (mm) REVERT: D 23 LYS cc_start: 0.7465 (tmtm) cc_final: 0.6069 (ptmm) REVERT: D 46 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7843 (ttm110) REVERT: D 57 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8479 (ptpt) REVERT: D 75 GLN cc_start: 0.8607 (mt0) cc_final: 0.8289 (mt0) REVERT: D 123 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8346 (mp) REVERT: D 217 MET cc_start: 0.8003 (pp-130) cc_final: 0.7716 (ppp) REVERT: E 46 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: C 53 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6443 (mpp) REVERT: C 250 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7365 (mtt-85) REVERT: C 276 GLU cc_start: 0.6461 (mp0) cc_final: 0.6022 (mp0) REVERT: C 309 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6780 (ttp-170) outliers start: 41 outliers final: 30 residues processed: 160 average time/residue: 0.6648 time to fit residues: 112.3941 Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN C 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120041 restraints weight = 9880.097| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.60 r_work: 0.3116 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8938 Z= 0.195 Angle : 0.642 10.753 12144 Z= 0.329 Chirality : 0.045 0.152 1391 Planarity : 0.005 0.058 1538 Dihedral : 5.328 57.133 1234 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.47 % Allowed : 29.63 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1119 helix: 1.48 (0.26), residues: 384 sheet: 0.26 (0.32), residues: 267 loop : -0.70 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 209 TYR 0.016 0.002 TYR B 315 PHE 0.022 0.002 PHE A 6 TRP 0.014 0.002 TRP C 211 HIS 0.006 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8938) covalent geometry : angle 0.64150 (12144) hydrogen bonds : bond 0.04021 ( 434) hydrogen bonds : angle 4.71873 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3953.84 seconds wall clock time: 68 minutes 0.08 seconds (4080.08 seconds total)