Starting phenix.real_space_refine on Mon May 12 04:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbg_36145/05_2025/8jbg_36145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbg_36145/05_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_36145/05_2025/8jbg_36145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbg_36145/05_2025/8jbg_36145.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbg_36145/05_2025/8jbg_36145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbg_36145/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.06, per 1000 atoms: 0.58 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 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: 0.95 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: 2.54 Time building geometry restraints manager: 2.53 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8938 Z= 0.107 Angle : 0.542 9.299 12144 Z= 0.291 Chirality : 0.041 0.139 1391 Planarity : 0.004 0.081 1538 Dihedral : 17.536 88.617 3128 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.36 % Allowed : 30.61 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.22257 ( 434) hydrogen bonds : angle 7.36727 ( 1230) covalent geometry : bond 0.00224 ( 8938) covalent geometry : angle 0.54181 (12144) *********************** 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 : 0.911 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: 1.1069 time to fit residues: 225.4617 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 : 1.145 ------------------------------------------------------------------------------- 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 = 74)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119902 restraints weight = 9793.606| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.62 r_work: 0.3154 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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= 0.221 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 Details of bonding type rmsd hydrogen bonds : bond 0.04990 ( 434) hydrogen bonds : angle 5.19528 ( 1230) covalent geometry : bond 0.00517 ( 8938) covalent geometry : angle 0.65118 (12144) *********************** 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 : 0.965 Fit side-chains REVERT: B 142 ASN cc_start: 0.8239 (m-40) cc_final: 0.7785 (m110) REVERT: B 210 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7292 (tm) REVERT: B 359 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7335 (mm) REVERT: D 46 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7923 (ttm110) REVERT: D 57 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8931 (ptpp) REVERT: D 75 GLN cc_start: 0.8725 (mt0) cc_final: 0.8375 (mt0) REVERT: D 181 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8089 (m) REVERT: D 220 GLN cc_start: 0.8703 (tt0) cc_final: 0.8424 (mt0) REVERT: E 63 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7904 (t) REVERT: C 53 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6397 (mpp) REVERT: C 250 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7441 (mtt-85) REVERT: C 276 GLU cc_start: 0.6051 (mp0) cc_final: 0.5820 (mp0) outliers start: 61 outliers final: 31 residues processed: 189 average time/residue: 1.1166 time to fit residues: 225.3220 Evaluate side-chains 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.171202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123995 restraints weight = 10011.604| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.61 r_work: 0.3173 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8938 Z= 0.121 Angle : 0.555 9.631 12144 Z= 0.289 Chirality : 0.042 0.152 1391 Planarity : 0.004 0.051 1538 Dihedral : 6.476 63.682 1250 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: 1.36 (0.27), residues: 384 sheet: 0.46 (0.33), residues: 256 loop : -0.70 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 169 HIS 0.005 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 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 434) hydrogen bonds : angle 4.74639 ( 1230) covalent geometry : bond 0.00267 ( 8938) covalent geometry : angle 0.55513 (12144) *********************** 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 199 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.900 Fit side-chains REVERT: B 210 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7076 (tm) REVERT: B 359 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7437 (mm) REVERT: D 46 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7887 (ttm110) REVERT: D 59 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: D 214 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7613 (mpt-90) REVERT: D 220 GLN cc_start: 0.8634 (tt0) cc_final: 0.8422 (mt0) REVERT: E 46 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: C 53 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: C 250 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7391 (mtt-85) REVERT: C 276 GLU cc_start: 0.6214 (mp0) cc_final: 0.5917 (mp0) outliers start: 54 outliers final: 24 residues processed: 181 average time/residue: 1.1720 time to fit residues: 225.9290 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 102 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.165711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120683 restraints weight = 9876.822| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.71 r_work: 0.3055 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.007 0.063 8938 Z= 0.286 Angle : 0.702 9.686 12144 Z= 0.365 Chirality : 0.049 0.173 1391 Planarity : 0.006 0.056 1538 Dihedral : 6.790 67.416 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 6.97 % Allowed : 26.80 % Favored : 66.23 % 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: 0.05 (0.26), residues: 1119 helix: 1.06 (0.27), residues: 384 sheet: 0.24 (0.33), residues: 264 loop : -0.89 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 63 HIS 0.008 0.002 HIS C 324 PHE 0.018 0.002 PHE D 151 TYR 0.018 0.002 TYR B 315 ARG 0.006 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 434) hydrogen bonds : angle 5.06504 ( 1230) covalent geometry : bond 0.00679 ( 8938) covalent geometry : angle 0.70223 (12144) *********************** 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 204 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 0.928 Fit side-chains REVERT: B 142 ASN cc_start: 0.8309 (m-40) cc_final: 0.7995 (m-40) REVERT: B 210 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7319 (tm) REVERT: B 299 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8124 (mtmm) REVERT: B 359 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7354 (mm) REVERT: D 46 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (ttm110) REVERT: D 57 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9064 (ptpp) REVERT: D 75 GLN cc_start: 0.8760 (mt0) cc_final: 0.8341 (mt0) REVERT: D 217 MET cc_start: 0.7892 (pp-130) cc_final: 0.7620 (ppp) REVERT: E 46 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: C 53 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6265 (mpp) REVERT: C 276 GLU cc_start: 0.6185 (mp0) cc_final: 0.5884 (mp0) outliers start: 64 outliers final: 40 residues processed: 179 average time/residue: 1.1568 time to fit residues: 220.7211 Evaluate side-chains 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 255 VAL Chi-restraints excluded: chain B residue 258 PHE 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 57 LYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 275 SER 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 11 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 197 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 A residue 10 MET 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: 4.9990 chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN G 59 ASN C 234 GLN C 352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.170500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123176 restraints weight = 9943.887| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.62 r_work: 0.3163 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8938 Z= 0.122 Angle : 0.566 10.575 12144 Z= 0.294 Chirality : 0.043 0.151 1391 Planarity : 0.004 0.046 1538 Dihedral : 6.344 65.737 1242 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.68 % Allowed : 29.74 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.26), residues: 1119 helix: 1.48 (0.27), residues: 383 sheet: 0.41 (0.33), residues: 262 loop : -0.76 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.023 0.001 PHE A 6 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 434) hydrogen bonds : angle 4.65613 ( 1230) covalent geometry : bond 0.00273 ( 8938) covalent geometry : angle 0.56615 (12144) *********************** 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 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.889 Fit side-chains REVERT: B 210 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7273 (tm) REVERT: B 351 TYR cc_start: 0.7446 (m-10) cc_final: 0.7173 (m-10) REVERT: B 359 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 46 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7883 (ttm110) REVERT: D 217 MET cc_start: 0.7948 (pp-130) cc_final: 0.7674 (ppp) REVERT: E 6 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: C 53 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: C 250 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7431 (mtt-85) REVERT: C 276 GLU cc_start: 0.6140 (mp0) cc_final: 0.5817 (mp0) outliers start: 43 outliers final: 28 residues processed: 166 average time/residue: 1.2247 time to fit residues: 215.8408 Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 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 318 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 115 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: 0.9990 chunk 35 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** 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 = 0.3870 r_free = 0.3870 target = 0.169752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124656 restraints weight = 9922.451| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.70 r_work: 0.3136 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8938 Z= 0.133 Angle : 0.575 8.210 12144 Z= 0.298 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.044 1538 Dihedral : 6.023 60.522 1240 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.23 % Allowed : 29.85 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.26), residues: 1119 helix: 1.55 (0.27), residues: 384 sheet: 0.37 (0.33), residues: 264 loop : -0.65 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.028 0.001 PHE A 6 TYR 0.011 0.001 TYR C 306 ARG 0.006 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 434) hydrogen bonds : angle 4.61872 ( 1230) covalent geometry : bond 0.00303 ( 8938) covalent geometry : angle 0.57547 (12144) *********************** 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 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.893 Fit side-chains REVERT: B 210 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7073 (tm) REVERT: B 253 ILE cc_start: 0.8418 (mm) cc_final: 0.8174 (mp) REVERT: B 359 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (mm) REVERT: D 46 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7923 (ttm110) REVERT: D 217 MET cc_start: 0.7937 (pp-130) cc_final: 0.7667 (ppp) REVERT: E 46 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: C 53 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6369 (mpp) REVERT: C 250 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7383 (mtt-85) REVERT: C 276 GLU cc_start: 0.6144 (mp0) cc_final: 0.5793 (mp0) outliers start: 48 outliers final: 35 residues processed: 169 average time/residue: 1.1964 time to fit residues: 214.9834 Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain 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 65 THR 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 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 19 LYS 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 199 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120973 restraints weight = 9980.263| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.64 r_work: 0.3129 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.042 8938 Z= 0.156 Angle : 0.594 9.975 12144 Z= 0.305 Chirality : 0.044 0.158 1391 Planarity : 0.005 0.052 1538 Dihedral : 5.971 59.722 1240 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.77 % Allowed : 29.08 % 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: 0.47 (0.26), residues: 1119 helix: 1.53 (0.27), residues: 384 sheet: 0.33 (0.33), residues: 266 loop : -0.68 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 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 B 315 ARG 0.005 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 434) hydrogen bonds : angle 4.65851 ( 1230) covalent geometry : bond 0.00362 ( 8938) covalent geometry : angle 0.59415 (12144) *********************** 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 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.900 Fit side-chains REVERT: B 210 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7354 (tm) REVERT: B 253 ILE cc_start: 0.8417 (mm) cc_final: 0.8187 (mp) REVERT: B 359 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7568 (mm) REVERT: D 46 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7917 (ttm110) REVERT: E 46 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: C 53 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6332 (mpp) REVERT: C 250 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7380 (mtt-85) REVERT: C 276 GLU cc_start: 0.6240 (mp0) cc_final: 0.5863 (mp0) outliers start: 53 outliers final: 38 residues processed: 168 average time/residue: 1.2343 time to fit residues: 220.6916 Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 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 251 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 65 THR 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 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 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain C residue 324 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.169972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122368 restraints weight = 10018.982| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.61 r_work: 0.3156 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8938 Z= 0.132 Angle : 0.586 11.222 12144 Z= 0.298 Chirality : 0.043 0.159 1391 Planarity : 0.004 0.043 1538 Dihedral : 5.839 58.659 1239 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.79 % Allowed : 30.17 % 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: 0.53 (0.26), residues: 1119 helix: 1.56 (0.27), residues: 385 sheet: 0.37 (0.33), residues: 264 loop : -0.63 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.022 0.001 PHE A 6 TYR 0.011 0.001 TYR B 315 ARG 0.004 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 434) hydrogen bonds : angle 4.58927 ( 1230) covalent geometry : bond 0.00303 ( 8938) covalent geometry : angle 0.58609 (12144) *********************** 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 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.903 Fit side-chains REVERT: B 210 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7363 (tm) REVERT: D 23 LYS cc_start: 0.7472 (tmtm) cc_final: 0.6087 (ptmm) REVERT: D 46 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7896 (ttm110) REVERT: D 217 MET cc_start: 0.8109 (pp-130) cc_final: 0.7868 (ppp) REVERT: E 46 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: C 53 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6337 (mpp) REVERT: C 250 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7409 (mtt-85) REVERT: C 276 GLU cc_start: 0.6250 (mp0) cc_final: 0.5854 (mp0) outliers start: 44 outliers final: 32 residues processed: 165 average time/residue: 1.2233 time to fit residues: 214.7661 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 251 VAL 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 65 THR 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 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 199 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET 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: 0.1980 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3865 r_free = 0.3865 target = 0.169138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121204 restraints weight = 10024.092| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.79 r_work: 0.3132 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8938 Z= 0.158 Angle : 0.617 10.865 12144 Z= 0.316 Chirality : 0.044 0.158 1391 Planarity : 0.005 0.049 1538 Dihedral : 5.927 57.015 1239 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.90 % Allowed : 30.28 % Favored : 64.81 % 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: 0.49 (0.26), residues: 1119 helix: 1.50 (0.27), residues: 385 sheet: 0.34 (0.33), residues: 266 loop : -0.63 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.005 0.001 HIS C 324 PHE 0.031 0.002 PHE A 6 TYR 0.011 0.001 TYR B 315 ARG 0.004 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 434) hydrogen bonds : angle 4.66767 ( 1230) covalent geometry : bond 0.00369 ( 8938) covalent geometry : angle 0.61686 (12144) *********************** 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 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.959 Fit side-chains REVERT: B 210 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7371 (tm) REVERT: D 46 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7898 (ttm110) REVERT: D 262 MET cc_start: 0.8311 (tpp) cc_final: 0.7885 (mtt) REVERT: E 46 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: C 53 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: C 250 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7333 (mtt-85) REVERT: C 276 GLU cc_start: 0.6256 (mp0) cc_final: 0.5847 (mp0) outliers start: 45 outliers final: 37 residues processed: 159 average time/residue: 1.2882 time to fit residues: 217.4531 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 65 THR 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 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 19 LYS 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 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 309 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 103 optimal weight: 0.0170 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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** G 59 ASN 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 = 0.3883 r_free = 0.3883 target = 0.170878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123465 restraints weight = 10066.369| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.63 r_work: 0.3166 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1924 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= 0.125 Angle : 0.584 10.710 12144 Z= 0.300 Chirality : 0.043 0.163 1391 Planarity : 0.004 0.044 1538 Dihedral : 5.751 59.603 1239 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.47 % Allowed : 30.72 % Favored : 64.81 % 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: 0.59 (0.26), residues: 1119 helix: 1.62 (0.27), residues: 385 sheet: 0.39 (0.33), residues: 264 loop : -0.59 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.004 0.001 HIS C 324 PHE 0.028 0.001 PHE A 6 TYR 0.011 0.001 TYR C 306 ARG 0.004 0.000 ARG C 250 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 434) hydrogen bonds : angle 4.54400 ( 1230) covalent geometry : bond 0.00285 ( 8938) covalent geometry : angle 0.58382 (12144) ********************** 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 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.896 Fit side-chains REVERT: B 210 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7157 (tm) REVERT: D 23 LYS cc_start: 0.7458 (tmtm) cc_final: 0.6066 (ptmm) REVERT: D 46 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7856 (ttm110) REVERT: D 217 MET cc_start: 0.8111 (pp-130) cc_final: 0.7835 (ppp) REVERT: E 46 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 53 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6368 (mpp) REVERT: C 250 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7336 (mtt-85) REVERT: C 276 GLU cc_start: 0.6468 (mp0) cc_final: 0.6035 (mp0) outliers start: 41 outliers final: 35 residues processed: 157 average time/residue: 1.2781 time to fit residues: 212.7731 Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 65 THR 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 19 LYS 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 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 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: 0.8980 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 11 optimal weight: 0.0010 chunk 54 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.171209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123730 restraints weight = 10005.038| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.63 r_work: 0.3174 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 8938 Z= 0.198 Angle : 0.903 59.115 12144 Z= 0.528 Chirality : 0.047 0.658 1391 Planarity : 0.005 0.044 1538 Dihedral : 5.055 54.718 1234 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 4.25 % Allowed : 31.05 % Favored : 64.71 % 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: 0.59 (0.26), residues: 1119 helix: 1.62 (0.27), residues: 385 sheet: 0.38 (0.33), residues: 264 loop : -0.61 (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 0.027 0.001 PHE A 6 TYR 0.013 0.001 TYR C 306 ARG 0.006 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 434) hydrogen bonds : angle 4.54423 ( 1230) covalent geometry : bond 0.00394 ( 8938) covalent geometry : angle 0.90277 (12144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7517.43 seconds wall clock time: 129 minutes 54.13 seconds (7794.13 seconds total)