Starting phenix.real_space_refine on Thu Mar 13 07:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbg_36145/03_2025/8jbg_36145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbg_36145/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jbg_36145/03_2025/8jbg_36145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbg_36145/03_2025/8jbg_36145.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbg_36145/03_2025/8jbg_36145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbg_36145/03_2025/8jbg_36145.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 7} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 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: 5.12, per 1000 atoms: 0.59 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.61 Time building geometry restraints manager: 2.73 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- 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= 0.143 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (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 TRP 0.012 0.001 TRP B 275 HIS 0.005 0.001 HIS C 324 PHE 0.029 0.001 PHE A 6 TYR 0.009 0.001 TYR D 264 ARG 0.005 0.000 ARG C 250 *********************** 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 : 0.863 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: 1.2142 time to fit residues: 247.5423 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 : 0.773 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119990 restraints weight = 9793.606| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.61 r_work: 0.3117 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8938 Z= 0.339 Angle : 0.651 8.665 12144 Z= 0.344 Chirality : 0.047 0.164 1391 Planarity : 0.005 0.054 1538 Dihedral : 7.245 62.237 1273 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.64 % Allowed : 26.25 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1119 helix: 1.00 (0.27), residues: 382 sheet: 0.43 (0.34), residues: 260 loop : -0.74 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 63 HIS 0.011 0.002 HIS C 324 PHE 0.015 0.002 PHE D 151 TYR 0.014 0.002 TYR B 315 ARG 0.006 0.001 ARG E 72 *********************** 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 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 1.066 Fit side-chains REVERT: B 142 ASN cc_start: 0.8240 (m-40) cc_final: 0.7787 (m110) REVERT: B 210 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7287 (tm) REVERT: B 359 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7346 (mm) REVERT: D 46 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7937 (ttm110) REVERT: D 57 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8933 (ptpp) REVERT: D 75 GLN cc_start: 0.8723 (mt0) cc_final: 0.8371 (mt0) REVERT: D 181 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8107 (m) REVERT: D 220 GLN cc_start: 0.8707 (tt0) cc_final: 0.8431 (mt0) REVERT: E 63 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7908 (t) REVERT: G 21 MET cc_start: 0.6132 (OUTLIER) cc_final: 0.5931 (ppp) REVERT: C 53 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6401 (mpp) REVERT: C 250 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7443 (mtt-85) REVERT: C 276 GLU cc_start: 0.6058 (mp0) cc_final: 0.5827 (mp0) outliers start: 61 outliers final: 31 residues processed: 189 average time/residue: 1.1569 time to fit residues: 233.3112 Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 202 ILE 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 57 LYS Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 181 THR 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 63 THR 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 197 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 21 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 340 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN C 231 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 = 0.3885 r_free = 0.3885 target = 0.171014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123834 restraints weight = 10014.543| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.62 r_work: 0.3174 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1513 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= 0.178 Angle : 0.555 9.698 12144 Z= 0.290 Chirality : 0.043 0.154 1391 Planarity : 0.004 0.052 1538 Dihedral : 6.504 64.143 1250 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.88 % Allowed : 27.02 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1119 helix: 1.35 (0.27), residues: 384 sheet: 0.46 (0.33), residues: 262 loop : -0.70 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 169 HIS 0.006 0.001 HIS C 324 PHE 0.020 0.001 PHE A 6 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG E 72 *********************** 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 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.885 Fit side-chains REVERT: B 210 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7071 (tm) REVERT: B 359 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7427 (mm) REVERT: D 46 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7894 (ttm110) REVERT: D 59 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: D 220 GLN cc_start: 0.8614 (tt0) cc_final: 0.8396 (mt0) REVERT: E 46 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: C 53 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6415 (mpp) REVERT: C 250 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7376 (mtt-85) REVERT: C 276 GLU cc_start: 0.6256 (mp0) cc_final: 0.5941 (mp0) outliers start: 54 outliers final: 23 residues processed: 179 average time/residue: 1.2127 time to fit residues: 230.8626 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 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 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 123 ILE 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 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 204 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.168871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.121027 restraints weight = 9898.077| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.61 r_work: 0.3127 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8938 Z= 0.266 Angle : 0.602 9.944 12144 Z= 0.312 Chirality : 0.044 0.168 1391 Planarity : 0.005 0.048 1538 Dihedral : 6.356 63.207 1242 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.32 % Allowed : 26.91 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1119 helix: 1.37 (0.27), residues: 384 sheet: 0.36 (0.33), residues: 258 loop : -0.74 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.007 0.001 HIS C 324 PHE 0.016 0.002 PHE A 6 TYR 0.013 0.002 TYR B 315 ARG 0.004 0.001 ARG E 72 *********************** 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 203 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.882 Fit side-chains REVERT: B 138 ASN cc_start: 0.8470 (t0) cc_final: 0.8056 (t0) REVERT: B 142 ASN cc_start: 0.8111 (m-40) cc_final: 0.7586 (m-40) REVERT: B 210 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7290 (tm) REVERT: B 299 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: B 302 ILE cc_start: 0.8295 (tt) cc_final: 0.7688 (mm) REVERT: B 359 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7486 (mm) REVERT: D 46 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7923 (ttm110) REVERT: D 217 MET cc_start: 0.7906 (pp-130) cc_final: 0.7593 (ppp) REVERT: D 220 GLN cc_start: 0.8651 (tt0) cc_final: 0.8376 (mt0) REVERT: D 262 MET cc_start: 0.8261 (tpp) cc_final: 0.8044 (mtt) REVERT: E 46 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 53 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6391 (mpp) REVERT: C 276 GLU cc_start: 0.6170 (mp0) cc_final: 0.5817 (mp0) outliers start: 58 outliers final: 35 residues processed: 178 average time/residue: 1.3210 time to fit residues: 250.3119 Evaluate side-chains 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 72 SER 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 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 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 197 SER Chi-restraints excluded: chain E residue 210 THR 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 201 VAL 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 46 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.171861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124916 restraints weight = 9947.522| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.61 r_work: 0.3189 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8938 Z= 0.159 Angle : 0.548 10.499 12144 Z= 0.282 Chirality : 0.042 0.149 1391 Planarity : 0.004 0.040 1538 Dihedral : 6.071 60.664 1242 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.56 % Allowed : 28.32 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1119 helix: 1.63 (0.27), residues: 384 sheet: 0.40 (0.33), residues: 264 loop : -0.63 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.005 0.001 HIS C 324 PHE 0.021 0.001 PHE A 6 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG C 250 *********************** 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 201 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.001 Fit side-chains REVERT: B 210 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7080 (tm) REVERT: B 299 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7961 (mtmm) REVERT: B 302 ILE cc_start: 0.8212 (tt) cc_final: 0.7659 (mm) REVERT: B 359 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 23 LYS cc_start: 0.7430 (tmtm) cc_final: 0.6080 (ptmm) REVERT: D 46 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7907 (ttm110) REVERT: D 217 MET cc_start: 0.7953 (pp-130) cc_final: 0.7652 (ppp) REVERT: D 220 GLN cc_start: 0.8573 (tt0) cc_final: 0.8362 (mt0) REVERT: D 256 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8377 (mtm180) REVERT: C 25 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8350 (ttmm) REVERT: C 53 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6408 (mpp) REVERT: C 250 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7423 (mtt-85) REVERT: C 276 GLU cc_start: 0.6332 (mp0) cc_final: 0.6030 (mp0) outliers start: 51 outliers final: 30 residues processed: 187 average time/residue: 1.5695 time to fit residues: 313.2645 Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 226 VAL 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 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 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU 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 210 THR 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 Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 231 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 = 0.3891 r_free = 0.3891 target = 0.171720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.125561 restraints weight = 9934.702| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.75 r_work: 0.3142 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8938 Z= 0.177 Angle : 0.571 10.651 12144 Z= 0.290 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.043 1538 Dihedral : 5.400 56.285 1237 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.12 % Allowed : 29.63 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1119 helix: 1.64 (0.27), residues: 385 sheet: 0.39 (0.33), residues: 258 loop : -0.58 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.024 0.001 PHE A 6 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG C 250 *********************** 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 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.881 Fit side-chains REVERT: B 210 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7036 (tm) REVERT: B 299 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: B 302 ILE cc_start: 0.8233 (tt) cc_final: 0.7670 (mm) REVERT: D 23 LYS cc_start: 0.7406 (tmtm) cc_final: 0.6039 (ptmm) REVERT: D 46 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7891 (ttm110) REVERT: D 217 MET cc_start: 0.7988 (pp-130) cc_final: 0.7684 (ppp) REVERT: D 220 GLN cc_start: 0.8545 (tt0) cc_final: 0.8267 (mt0) REVERT: E 46 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: C 53 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6364 (mpp) REVERT: C 250 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7380 (mtt-85) REVERT: C 276 GLU cc_start: 0.6331 (mp0) cc_final: 0.5938 (mp0) outliers start: 47 outliers final: 31 residues processed: 176 average time/residue: 1.3282 time to fit residues: 247.7225 Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 226 VAL 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 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 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 156 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR 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 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 259 GLN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.168509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120575 restraints weight = 9999.470| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8938 Z= 0.290 Angle : 0.636 10.153 12144 Z= 0.324 Chirality : 0.045 0.159 1391 Planarity : 0.005 0.046 1538 Dihedral : 5.337 55.342 1235 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.79 % Allowed : 29.96 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1119 helix: 1.47 (0.27), residues: 385 sheet: 0.33 (0.33), residues: 271 loop : -0.67 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 211 HIS 0.006 0.001 HIS C 324 PHE 0.024 0.002 PHE A 6 TYR 0.017 0.002 TYR C 230 ARG 0.005 0.001 ARG C 250 *********************** 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 182 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.883 Fit side-chains REVERT: B 210 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7353 (tm) REVERT: B 299 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: B 302 ILE cc_start: 0.8273 (tt) cc_final: 0.7665 (mm) REVERT: D 23 LYS cc_start: 0.7439 (tmtm) cc_final: 0.6060 (ptmm) REVERT: D 46 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7852 (ttm110) REVERT: D 75 GLN cc_start: 0.8691 (mt0) cc_final: 0.8320 (mt0) REVERT: D 217 MET cc_start: 0.7911 (pp-130) cc_final: 0.7650 (ppp) REVERT: D 220 GLN cc_start: 0.8664 (tt0) cc_final: 0.8352 (mt0) REVERT: D 262 MET cc_start: 0.8357 (tpp) cc_final: 0.7977 (mtt) REVERT: E 46 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: C 53 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6332 (mpp) REVERT: C 250 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7348 (mtt-85) REVERT: C 276 GLU cc_start: 0.6187 (mp0) cc_final: 0.5818 (mp0) outliers start: 44 outliers final: 31 residues processed: 167 average time/residue: 1.2832 time to fit residues: 227.4915 Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 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 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 231 ASN Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 259 GLN G 59 ASN C 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.170012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124920 restraints weight = 10032.120| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.73 r_work: 0.3130 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8938 Z= 0.205 Angle : 0.592 10.500 12144 Z= 0.301 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.043 1538 Dihedral : 4.983 55.681 1233 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.25 % Allowed : 30.28 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1119 helix: 1.55 (0.27), residues: 385 sheet: 0.39 (0.33), residues: 264 loop : -0.64 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.021 0.001 PHE A 6 TYR 0.011 0.001 TYR B 315 ARG 0.004 0.000 ARG D 197 *********************** 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: 39 poor density : 136 time to evaluate : 0.915 Fit side-chains REVERT: B 210 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7133 (tm) REVERT: B 299 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: B 302 ILE cc_start: 0.8278 (tt) cc_final: 0.7681 (mm) REVERT: D 23 LYS cc_start: 0.7454 (tmtm) cc_final: 0.6071 (ptmm) REVERT: D 46 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7892 (ttm110) REVERT: D 75 GLN cc_start: 0.8663 (mt0) cc_final: 0.8359 (mt0) REVERT: D 217 MET cc_start: 0.7974 (pp-130) cc_final: 0.7675 (ppp) REVERT: D 220 GLN cc_start: 0.8600 (tt0) cc_final: 0.8316 (mt0) REVERT: D 262 MET cc_start: 0.8371 (tpp) cc_final: 0.8122 (mtt) REVERT: E 46 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: C 53 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6343 (mpp) REVERT: C 250 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7376 (mtt-85) REVERT: C 276 GLU cc_start: 0.6240 (mp0) cc_final: 0.5845 (mp0) outliers start: 39 outliers final: 29 residues processed: 164 average time/residue: 1.3149 time to fit residues: 228.9063 Evaluate side-chains 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 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 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 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 231 ASN 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 14 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 259 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 = 0.169828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122642 restraints weight = 10060.879| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.81 r_work: 0.3128 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8938 Z= 0.215 Angle : 0.602 10.671 12144 Z= 0.307 Chirality : 0.043 0.160 1391 Planarity : 0.004 0.043 1538 Dihedral : 4.963 55.187 1233 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.92 % Allowed : 30.72 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1119 helix: 1.56 (0.27), residues: 385 sheet: 0.38 (0.33), residues: 264 loop : -0.62 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.024 0.002 PHE A 6 TYR 0.012 0.001 TYR C 306 ARG 0.004 0.000 ARG D 197 *********************** 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 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.898 Fit side-chains REVERT: B 210 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7143 (tm) REVERT: B 299 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7966 (mtmm) REVERT: B 302 ILE cc_start: 0.8293 (tt) cc_final: 0.7698 (mm) REVERT: D 23 LYS cc_start: 0.7463 (tmtm) cc_final: 0.6085 (ptmm) REVERT: D 46 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7887 (ttm110) REVERT: D 75 GLN cc_start: 0.8665 (mt0) cc_final: 0.8355 (mt0) REVERT: D 217 MET cc_start: 0.7967 (pp-130) cc_final: 0.7659 (ppp) REVERT: D 220 GLN cc_start: 0.8582 (tt0) cc_final: 0.8295 (mt0) REVERT: D 262 MET cc_start: 0.8342 (tpp) cc_final: 0.8132 (mtt) REVERT: E 46 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: C 53 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6355 (mpp) REVERT: C 250 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7369 (mtt-85) REVERT: C 276 GLU cc_start: 0.6251 (mp0) cc_final: 0.5858 (mp0) outliers start: 36 outliers final: 29 residues processed: 157 average time/residue: 1.7826 time to fit residues: 295.3649 Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 overall best weight: 0.8118 ------------------------------------------------------------------------------- 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 259 GLN C 231 ASN C 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.124316 restraints weight = 10056.221| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.62 r_work: 0.3180 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8938 Z= 0.174 Angle : 0.575 10.815 12144 Z= 0.294 Chirality : 0.043 0.164 1391 Planarity : 0.004 0.040 1538 Dihedral : 4.721 54.172 1233 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.81 % Allowed : 31.05 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1119 helix: 1.67 (0.27), residues: 385 sheet: 0.43 (0.33), residues: 264 loop : -0.57 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.020 0.001 PHE A 6 TYR 0.012 0.001 TYR C 306 ARG 0.004 0.000 ARG D 197 ********************** 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 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.022 Fit side-chains REVERT: B 210 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7132 (tm) REVERT: B 263 MET cc_start: 0.8320 (ptm) cc_final: 0.8091 (ptm) REVERT: B 299 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: B 302 ILE cc_start: 0.8225 (tt) cc_final: 0.7668 (mm) REVERT: D 23 LYS cc_start: 0.7455 (tmtm) cc_final: 0.6071 (ptmm) REVERT: D 46 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7848 (ttm110) REVERT: D 75 GLN cc_start: 0.8630 (mt0) cc_final: 0.8331 (mt0) REVERT: D 197 ARG cc_start: 0.7726 (mmp80) cc_final: 0.7424 (mtt-85) REVERT: D 217 MET cc_start: 0.7989 (pp-130) cc_final: 0.7689 (ppp) REVERT: D 220 GLN cc_start: 0.8532 (tt0) cc_final: 0.8283 (mt0) REVERT: E 46 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 53 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6378 (mpp) REVERT: C 250 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7356 (mtt-85) REVERT: C 276 GLU cc_start: 0.6441 (mp0) cc_final: 0.6007 (mp0) outliers start: 35 outliers final: 29 residues processed: 158 average time/residue: 1.3333 time to fit residues: 223.7286 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 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 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 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 231 ASN 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 60 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 259 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 = 0.3892 r_free = 0.3892 target = 0.171693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124532 restraints weight = 9988.130| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.83 r_work: 0.3170 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8938 Z= 0.243 Angle : 0.898 59.172 12144 Z= 0.522 Chirality : 0.044 0.380 1391 Planarity : 0.004 0.040 1538 Dihedral : 4.842 54.177 1233 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 31.48 % Favored : 64.81 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1119 helix: 1.65 (0.27), residues: 385 sheet: 0.44 (0.33), residues: 264 loop : -0.59 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.022 0.002 PHE A 6 TYR 0.013 0.001 TYR C 306 ARG 0.033 0.001 ARG D 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8179.76 seconds wall clock time: 144 minutes 10.91 seconds (8650.91 seconds total)