Starting phenix.real_space_refine on Fri Aug 22 21:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qj2_18442/08_2025/8qj2_18442.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5146 2.51 5 N 1395 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8108 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1781 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2547 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 922 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1853 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 587 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 1.89, per 1000 atoms: 0.23 Number of scatterers: 8108 At special positions: 0 Unit cell: (76.95, 102.6, 149.625, 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 61 16.00 O 1506 8.00 N 1395 7.00 C 5146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 40 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 481.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 34.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 13 through 39 removed outlier: 3.786A pdb=" N LYS B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.587A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 removed outlier: 3.569A pdb=" N ALA B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.511A pdb=" N GLU B 299 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 300' Processing helix chain 'B' and resid 333 through 351 removed outlier: 3.745A pdb=" N ALA B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 391 removed outlier: 3.775A pdb=" N ARG B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.658A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.527A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.532A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.932A pdb=" N GLU G 47 " --> pdb=" O HIS G 44 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 48' Processing helix chain 'A' and resid 52 through 72 removed outlier: 4.294A pdb=" N ASN A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 103 removed outlier: 3.506A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 122 through 153 removed outlier: 3.573A pdb=" N ASP A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 187 removed outlier: 3.653A pdb=" N TYR A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 225 Processing helix chain 'A' and resid 241 through 271 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.698A pdb=" N CYS A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.692A pdb=" N LEU A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.179A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 207 through 213 removed outlier: 6.676A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL B 224 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N LEU B 45 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N ALA B 243 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL B 247 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 46 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.707A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.102A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.624A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151 removed outlier: 3.725A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.221A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.642A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.726A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.508A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 18 through 19 removed outlier: 3.609A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET N 83 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.773A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 3.640A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA D 97 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 106 " --> pdb=" O THR D 99 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2645 1.35 - 1.46: 1970 1.46 - 1.58: 3558 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 8258 Sorted by residual: bond pdb=" C THR D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.340 1.370 -0.030 2.76e-02 1.31e+03 1.15e+00 bond pdb=" C GLN A 273 " pdb=" N ASN A 274 " ideal model delta sigma weight residual 1.331 1.350 -0.019 2.07e-02 2.33e+03 8.11e-01 bond pdb=" CB ILE A 129 " pdb=" CG2 ILE A 129 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.70e-01 bond pdb=" N PRO A 275 " pdb=" CA PRO A 275 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.12e-01 bond pdb=" C THR C 243 " pdb=" N GLY C 244 " ideal model delta sigma weight residual 1.330 1.324 0.006 8.50e-03 1.38e+04 5.60e-01 ... (remaining 8253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 10878 1.21 - 2.41: 257 2.41 - 3.62: 57 3.62 - 4.82: 12 4.82 - 6.03: 3 Bond angle restraints: 11207 Sorted by residual: angle pdb=" C ASP B 368 " pdb=" N THR B 369 " pdb=" CA THR B 369 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.93e+00 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 110.65 113.37 -2.72 1.26e+00 6.30e-01 4.65e+00 angle pdb=" C GLN A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta sigma weight residual 121.80 127.03 -5.23 2.44e+00 1.68e-01 4.59e+00 angle pdb=" C CYS A 257 " pdb=" N TRP A 258 " pdb=" CA TRP A 258 " ideal model delta sigma weight residual 122.36 118.84 3.52 1.72e+00 3.38e-01 4.18e+00 angle pdb=" N THR D 40 " pdb=" CA THR D 40 " pdb=" C THR D 40 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 ... (remaining 11202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4658 17.69 - 35.38: 195 35.38 - 53.07: 41 53.07 - 70.77: 5 70.77 - 88.46: 4 Dihedral angle restraints: 4903 sinusoidal: 1810 harmonic: 3093 Sorted by residual: dihedral pdb=" CA ASN A 274 " pdb=" C ASN A 274 " pdb=" N PRO A 275 " pdb=" CA PRO A 275 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU C 226 " pdb=" CG GLU C 226 " pdb=" CD GLU C 226 " pdb=" OE1 GLU C 226 " ideal model delta sinusoidal sigma weight residual 0.00 -87.92 87.92 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLN A 273 " pdb=" C GLN A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 ... (remaining 4900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 750 0.026 - 0.052: 329 0.052 - 0.078: 143 0.078 - 0.104: 57 0.104 - 0.131: 30 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 1306 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO G 49 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 88 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C VAL A 88 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 88 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 89 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 87 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ALA A 87 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA A 87 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 696 2.74 - 3.28: 7875 3.28 - 3.82: 12470 3.82 - 4.36: 14046 4.36 - 4.90: 25359 Nonbonded interactions: 60446 Sorted by model distance: nonbonded pdb=" O PHE A 184 " pdb=" OG SER A 188 " model vdw 2.203 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.242 3.040 nonbonded pdb=" OG SER C 147 " pdb=" O MET C 188 " model vdw 2.250 3.040 nonbonded pdb=" N ASP C 186 " pdb=" OD1 ASP C 186 " model vdw 2.306 3.120 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.331 3.040 ... (remaining 60441 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 0.034 8262 Z= 0.121 Angle : 0.491 6.031 11215 Z= 0.269 Chirality : 0.040 0.131 1309 Planarity : 0.003 0.060 1419 Dihedral : 10.541 88.457 2883 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.47 % Allowed : 6.93 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.27), residues: 1032 helix: 1.71 (0.30), residues: 336 sheet: -0.43 (0.33), residues: 243 loop : -1.92 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 98 TYR 0.012 0.001 TYR N 60 PHE 0.011 0.001 PHE C 241 TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8258) covalent geometry : angle 0.49044 (11207) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.70887 ( 8) hydrogen bonds : bond 0.16054 ( 365) hydrogen bonds : angle 6.16862 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ILE cc_start: 0.8494 (tp) cc_final: 0.8160 (tt) REVERT: B 250 SER cc_start: 0.8541 (t) cc_final: 0.8338 (t) REVERT: B 265 ARG cc_start: 0.6988 (mtt180) cc_final: 0.6731 (mtt180) REVERT: B 271 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8074 (mmmm) REVERT: B 283 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7296 (tpp80) REVERT: C 59 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 61 MET cc_start: 0.7980 (ppp) cc_final: 0.7737 (ppp) REVERT: C 74 SER cc_start: 0.8613 (t) cc_final: 0.8381 (t) REVERT: C 118 ASP cc_start: 0.7354 (t70) cc_final: 0.6820 (t0) REVERT: C 217 MET cc_start: 0.6378 (mmm) cc_final: 0.6177 (mmm) REVERT: C 226 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 247 ASP cc_start: 0.6884 (t0) cc_final: 0.6513 (t0) REVERT: C 251 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7911 (mtt90) REVERT: G 48 ASP cc_start: 0.8156 (t70) cc_final: 0.7865 (t0) REVERT: N 27 PHE cc_start: 0.7607 (p90) cc_final: 0.7220 (p90) REVERT: A 207 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6262 (mt) REVERT: A 214 HIS cc_start: 0.7778 (t70) cc_final: 0.7559 (t70) REVERT: A 287 TYR cc_start: 0.8067 (m-10) cc_final: 0.7800 (m-10) REVERT: D 101 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7744 (mtp-110) outliers start: 21 outliers final: 12 residues processed: 194 average time/residue: 0.1161 time to fit residues: 28.2901 Evaluate side-chains 174 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN C 119 ASN C 220 GLN C 259 GLN N 31 ASN N 39 GLN A 283 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128095 restraints weight = 12013.822| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.39 r_work: 0.3504 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8262 Z= 0.107 Angle : 0.517 14.841 11215 Z= 0.270 Chirality : 0.041 0.155 1309 Planarity : 0.003 0.064 1419 Dihedral : 5.631 49.172 1165 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.47 % Allowed : 11.87 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.27), residues: 1032 helix: 2.22 (0.29), residues: 347 sheet: -0.30 (0.33), residues: 245 loop : -1.91 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 342 TYR 0.009 0.001 TYR N 60 PHE 0.009 0.001 PHE B 376 TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8258) covalent geometry : angle 0.51714 (11207) SS BOND : bond 0.00227 ( 4) SS BOND : angle 0.67615 ( 8) hydrogen bonds : bond 0.04488 ( 365) hydrogen bonds : angle 4.67576 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8622 (t) cc_final: 0.8383 (t) REVERT: B 265 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7217 (mtt180) REVERT: B 283 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7458 (tpp80) REVERT: C 59 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8063 (t80) REVERT: C 98 SER cc_start: 0.8788 (m) cc_final: 0.8432 (p) REVERT: C 118 ASP cc_start: 0.7580 (t70) cc_final: 0.7083 (t0) REVERT: C 150 ARG cc_start: 0.8098 (mmt180) cc_final: 0.7840 (mmt180) REVERT: C 163 ASP cc_start: 0.7326 (p0) cc_final: 0.7101 (p0) REVERT: C 214 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7031 (mtt180) REVERT: C 217 MET cc_start: 0.7044 (mmm) cc_final: 0.6710 (mmm) REVERT: C 226 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7322 (mt-10) REVERT: C 247 ASP cc_start: 0.7136 (t0) cc_final: 0.6649 (t0) REVERT: C 251 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7768 (mmm-85) REVERT: N 27 PHE cc_start: 0.7482 (p90) cc_final: 0.7085 (p90) REVERT: N 28 THR cc_start: 0.8485 (p) cc_final: 0.8218 (p) REVERT: N 72 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7306 (ttm170) REVERT: A 207 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6269 (mt) REVERT: A 292 MET cc_start: 0.6679 (mmt) cc_final: 0.6107 (mmm) REVERT: D 32 ASN cc_start: 0.8135 (t0) cc_final: 0.7882 (t0) outliers start: 21 outliers final: 13 residues processed: 176 average time/residue: 0.1102 time to fit residues: 24.4333 Evaluate side-chains 164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121556 restraints weight = 12056.940| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.45 r_work: 0.3458 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8262 Z= 0.156 Angle : 0.544 7.560 11215 Z= 0.288 Chirality : 0.042 0.212 1309 Planarity : 0.004 0.068 1419 Dihedral : 5.519 49.890 1157 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.94 % Allowed : 13.28 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.27), residues: 1032 helix: 2.10 (0.29), residues: 348 sheet: -0.33 (0.32), residues: 249 loop : -1.96 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 342 TYR 0.015 0.001 TYR N 60 PHE 0.014 0.002 PHE C 235 TRP 0.011 0.001 TRP C 169 HIS 0.011 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8258) covalent geometry : angle 0.54428 (11207) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.69608 ( 8) hydrogen bonds : bond 0.05006 ( 365) hydrogen bonds : angle 4.64106 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8692 (t) cc_final: 0.8438 (t) REVERT: B 283 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7395 (tpp80) REVERT: B 390 GLN cc_start: 0.8303 (tp40) cc_final: 0.8030 (tp-100) REVERT: C 59 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 118 ASP cc_start: 0.7614 (t70) cc_final: 0.7076 (t0) REVERT: C 214 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7055 (mtt180) REVERT: C 217 MET cc_start: 0.7084 (mmm) cc_final: 0.6733 (mmm) REVERT: C 226 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 247 ASP cc_start: 0.7197 (t0) cc_final: 0.6811 (t0) REVERT: C 251 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7899 (mtt90) REVERT: C 273 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (mp) REVERT: N 28 THR cc_start: 0.8475 (p) cc_final: 0.8171 (p) REVERT: A 207 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6414 (mt) REVERT: A 257 CYS cc_start: 0.8107 (m) cc_final: 0.7827 (p) REVERT: A 292 MET cc_start: 0.6791 (mmt) cc_final: 0.6051 (mmm) REVERT: D 32 ASN cc_start: 0.8192 (t0) cc_final: 0.7912 (t0) outliers start: 25 outliers final: 17 residues processed: 169 average time/residue: 0.1159 time to fit residues: 24.4502 Evaluate side-chains 168 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 222 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122139 restraints weight = 12226.505| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.48 r_work: 0.3463 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.134 Angle : 0.519 6.653 11215 Z= 0.276 Chirality : 0.041 0.153 1309 Planarity : 0.004 0.068 1419 Dihedral : 5.438 50.075 1155 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.70 % Allowed : 14.10 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.27), residues: 1032 helix: 2.38 (0.29), residues: 335 sheet: -0.28 (0.32), residues: 254 loop : -2.02 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.014 0.001 TYR N 60 PHE 0.012 0.001 PHE C 235 TRP 0.010 0.001 TRP C 169 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8258) covalent geometry : angle 0.51885 (11207) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.65212 ( 8) hydrogen bonds : bond 0.04553 ( 365) hydrogen bonds : angle 4.54153 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8660 (t) cc_final: 0.8392 (t) REVERT: B 283 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7413 (tpp80) REVERT: C 59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8211 (t80) REVERT: C 98 SER cc_start: 0.8820 (m) cc_final: 0.8478 (p) REVERT: C 118 ASP cc_start: 0.7637 (t70) cc_final: 0.7023 (t0) REVERT: C 214 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7047 (mtt180) REVERT: C 217 MET cc_start: 0.7066 (mmm) cc_final: 0.6715 (mmm) REVERT: C 226 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 247 ASP cc_start: 0.7176 (t0) cc_final: 0.6649 (t0) REVERT: C 273 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8083 (mp) REVERT: N 28 THR cc_start: 0.8477 (p) cc_final: 0.8166 (p) REVERT: N 72 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7544 (ttm170) REVERT: A 207 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6408 (mt) REVERT: A 257 CYS cc_start: 0.8085 (m) cc_final: 0.7822 (p) REVERT: A 292 MET cc_start: 0.6794 (mmt) cc_final: 0.6013 (mmm) REVERT: D 32 ASN cc_start: 0.8178 (t0) cc_final: 0.7880 (t0) REVERT: D 101 ARG cc_start: 0.8396 (mtm110) cc_final: 0.8138 (mtp-110) outliers start: 23 outliers final: 15 residues processed: 169 average time/residue: 0.1009 time to fit residues: 21.3856 Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123819 restraints weight = 12284.940| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.49 r_work: 0.3483 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8262 Z= 0.101 Angle : 0.502 8.477 11215 Z= 0.264 Chirality : 0.040 0.148 1309 Planarity : 0.003 0.061 1419 Dihedral : 5.310 49.527 1155 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.17 % Allowed : 14.45 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.27), residues: 1032 helix: 2.40 (0.29), residues: 341 sheet: -0.16 (0.33), residues: 249 loop : -1.90 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 251 TYR 0.010 0.001 TYR N 60 PHE 0.009 0.001 PHE B 212 TRP 0.010 0.001 TRP C 169 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8258) covalent geometry : angle 0.50202 (11207) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.55127 ( 8) hydrogen bonds : bond 0.03934 ( 365) hydrogen bonds : angle 4.37293 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8654 (t) cc_final: 0.8375 (t) REVERT: B 265 ARG cc_start: 0.7286 (mtm110) cc_final: 0.7031 (mtm110) REVERT: B 283 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7416 (tpp80) REVERT: B 342 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7167 (tmm-80) REVERT: C 59 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8100 (t80) REVERT: C 98 SER cc_start: 0.8809 (m) cc_final: 0.8471 (p) REVERT: C 118 ASP cc_start: 0.7667 (t70) cc_final: 0.7091 (t0) REVERT: C 214 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7320 (mtt180) REVERT: C 217 MET cc_start: 0.7093 (mmm) cc_final: 0.6756 (mmm) REVERT: C 226 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 247 ASP cc_start: 0.7097 (t0) cc_final: 0.6518 (t0) REVERT: G 47 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7068 (mp0) REVERT: N 27 PHE cc_start: 0.7562 (p90) cc_final: 0.7090 (p90) REVERT: N 28 THR cc_start: 0.8542 (p) cc_final: 0.8285 (p) REVERT: N 72 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7557 (ttm170) REVERT: A 146 ASP cc_start: 0.8753 (t70) cc_final: 0.8418 (t0) REVERT: A 257 CYS cc_start: 0.7998 (m) cc_final: 0.7749 (p) REVERT: A 297 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7177 (tt) REVERT: D 32 ASN cc_start: 0.8152 (t0) cc_final: 0.7853 (t0) REVERT: D 101 ARG cc_start: 0.8319 (mtm110) cc_final: 0.8052 (mtp-110) outliers start: 27 outliers final: 17 residues processed: 178 average time/residue: 0.1159 time to fit residues: 25.8561 Evaluate side-chains 174 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN G 59 ASN N 31 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124278 restraints weight = 11944.759| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.55 r_work: 0.3455 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.143 Angle : 0.542 9.572 11215 Z= 0.283 Chirality : 0.041 0.157 1309 Planarity : 0.004 0.060 1419 Dihedral : 5.201 50.262 1153 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.17 % Allowed : 15.04 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.27), residues: 1032 helix: 2.43 (0.29), residues: 335 sheet: -0.23 (0.32), residues: 253 loop : -2.04 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.014 0.001 TYR N 60 PHE 0.014 0.001 PHE C 241 TRP 0.010 0.001 TRP C 169 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8258) covalent geometry : angle 0.54210 (11207) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.64466 ( 8) hydrogen bonds : bond 0.04545 ( 365) hydrogen bonds : angle 4.45854 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 VAL cc_start: 0.7818 (t) cc_final: 0.7343 (m) REVERT: B 250 SER cc_start: 0.8585 (t) cc_final: 0.8313 (t) REVERT: B 265 ARG cc_start: 0.7099 (mtm110) cc_final: 0.6839 (mtm110) REVERT: B 283 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7425 (tpp80) REVERT: B 342 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7066 (tmm-80) REVERT: B 390 GLN cc_start: 0.8179 (tp40) cc_final: 0.7868 (tp-100) REVERT: C 59 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.8027 (t80) REVERT: C 98 SER cc_start: 0.8729 (m) cc_final: 0.8391 (p) REVERT: C 118 ASP cc_start: 0.7465 (t70) cc_final: 0.6871 (t0) REVERT: C 214 ARG cc_start: 0.7298 (mtt180) cc_final: 0.7000 (mtt180) REVERT: C 217 MET cc_start: 0.6714 (mmm) cc_final: 0.6446 (mmm) REVERT: C 226 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7299 (mt-10) REVERT: C 247 ASP cc_start: 0.6960 (t0) cc_final: 0.6448 (t0) REVERT: C 251 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7708 (mmm-85) REVERT: G 47 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7067 (mp0) REVERT: N 28 THR cc_start: 0.8418 (p) cc_final: 0.8087 (p) REVERT: N 72 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7330 (ttm170) REVERT: A 146 ASP cc_start: 0.8511 (t70) cc_final: 0.8217 (t0) REVERT: A 207 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6236 (mt) REVERT: A 292 MET cc_start: 0.6394 (mmt) cc_final: 0.5575 (mmm) REVERT: A 297 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7176 (tt) REVERT: D 32 ASN cc_start: 0.8238 (t0) cc_final: 0.7933 (t0) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.1042 time to fit residues: 22.4828 Evaluate side-chains 175 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123671 restraints weight = 12107.485| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.63 r_work: 0.3454 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.136 Angle : 0.539 10.257 11215 Z= 0.283 Chirality : 0.041 0.153 1309 Planarity : 0.003 0.039 1419 Dihedral : 5.220 50.469 1153 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.17 % Allowed : 15.16 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.27), residues: 1032 helix: 2.35 (0.29), residues: 341 sheet: -0.31 (0.32), residues: 255 loop : -2.07 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.013 0.001 TYR N 60 PHE 0.013 0.001 PHE C 241 TRP 0.010 0.001 TRP C 169 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8258) covalent geometry : angle 0.53939 (11207) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.61908 ( 8) hydrogen bonds : bond 0.04436 ( 365) hydrogen bonds : angle 4.48029 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 VAL cc_start: 0.7844 (t) cc_final: 0.7367 (m) REVERT: B 250 SER cc_start: 0.8581 (t) cc_final: 0.8304 (t) REVERT: B 265 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6861 (mtm110) REVERT: B 283 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7439 (tpp80) REVERT: B 342 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7031 (tmm-80) REVERT: B 390 GLN cc_start: 0.8140 (tp40) cc_final: 0.7915 (tp-100) REVERT: C 59 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8062 (t80) REVERT: C 98 SER cc_start: 0.8715 (m) cc_final: 0.8393 (p) REVERT: C 118 ASP cc_start: 0.7366 (t70) cc_final: 0.6862 (t0) REVERT: C 214 ARG cc_start: 0.7341 (mtt180) cc_final: 0.7051 (mtt180) REVERT: C 217 MET cc_start: 0.6730 (mmm) cc_final: 0.6448 (mmm) REVERT: C 226 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 247 ASP cc_start: 0.6967 (t0) cc_final: 0.6452 (t0) REVERT: C 251 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7729 (mmm-85) REVERT: N 28 THR cc_start: 0.8413 (p) cc_final: 0.8088 (p) REVERT: N 72 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7335 (ttm170) REVERT: A 146 ASP cc_start: 0.8524 (t70) cc_final: 0.8256 (t0) REVERT: A 207 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6246 (mt) REVERT: A 297 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7126 (tt) REVERT: D 32 ASN cc_start: 0.8261 (t0) cc_final: 0.7951 (t0) REVERT: D 69 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (tp) outliers start: 27 outliers final: 21 residues processed: 172 average time/residue: 0.1059 time to fit residues: 22.9833 Evaluate side-chains 179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 9 optimal weight: 0.0050 chunk 59 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN A 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127634 restraints weight = 11966.032| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.63 r_work: 0.3508 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8262 Z= 0.097 Angle : 0.513 11.933 11215 Z= 0.265 Chirality : 0.040 0.152 1309 Planarity : 0.003 0.043 1419 Dihedral : 4.980 48.925 1153 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.35 % Allowed : 16.69 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.27), residues: 1032 helix: 2.44 (0.29), residues: 346 sheet: -0.14 (0.33), residues: 250 loop : -1.95 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.008 0.001 TYR N 60 PHE 0.008 0.001 PHE B 376 TRP 0.013 0.001 TRP C 297 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8258) covalent geometry : angle 0.51347 (11207) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.49725 ( 8) hydrogen bonds : bond 0.03469 ( 365) hydrogen bonds : angle 4.30128 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 GLU cc_start: 0.7543 (tp30) cc_final: 0.7294 (tp30) REVERT: B 250 SER cc_start: 0.8523 (t) cc_final: 0.8218 (t) REVERT: B 265 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6731 (mtm110) REVERT: B 283 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7257 (tpp80) REVERT: B 342 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6741 (tmm-80) REVERT: C 59 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8025 (t80) REVERT: C 98 SER cc_start: 0.8680 (m) cc_final: 0.8321 (p) REVERT: C 118 ASP cc_start: 0.7358 (t70) cc_final: 0.6829 (t0) REVERT: C 200 VAL cc_start: 0.8474 (m) cc_final: 0.8101 (p) REVERT: C 214 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7106 (mtt180) REVERT: C 217 MET cc_start: 0.6710 (mmm) cc_final: 0.6439 (mmm) REVERT: C 226 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 247 ASP cc_start: 0.6830 (t0) cc_final: 0.6467 (t0) REVERT: G 51 LEU cc_start: 0.8224 (pt) cc_final: 0.8001 (pp) REVERT: N 27 PHE cc_start: 0.7453 (p90) cc_final: 0.6918 (p90) REVERT: N 28 THR cc_start: 0.8417 (p) cc_final: 0.8148 (p) REVERT: A 146 ASP cc_start: 0.8500 (t70) cc_final: 0.8191 (t0) REVERT: A 292 MET cc_start: 0.6272 (mmt) cc_final: 0.6065 (mmt) REVERT: A 297 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7087 (tt) REVERT: D 32 ASN cc_start: 0.8163 (t0) cc_final: 0.7891 (t0) REVERT: D 69 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7624 (tp) REVERT: D 101 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7759 (mtm-85) outliers start: 20 outliers final: 14 residues processed: 176 average time/residue: 0.1134 time to fit residues: 25.0278 Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 0.0970 chunk 49 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128225 restraints weight = 12065.857| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.49 r_work: 0.3510 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.100 Angle : 0.528 12.065 11215 Z= 0.272 Chirality : 0.040 0.158 1309 Planarity : 0.003 0.042 1419 Dihedral : 4.854 49.233 1151 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.35 % Allowed : 17.27 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.27), residues: 1032 helix: 2.40 (0.29), residues: 347 sheet: -0.08 (0.32), residues: 259 loop : -1.91 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.009 0.001 TYR N 115 PHE 0.008 0.001 PHE A 152 TRP 0.009 0.001 TRP C 297 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8258) covalent geometry : angle 0.52787 (11207) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.51590 ( 8) hydrogen bonds : bond 0.03565 ( 365) hydrogen bonds : angle 4.26783 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 GLU cc_start: 0.7731 (tp30) cc_final: 0.7457 (tp30) REVERT: B 250 SER cc_start: 0.8623 (t) cc_final: 0.8324 (t) REVERT: B 265 ARG cc_start: 0.7278 (mtm110) cc_final: 0.7024 (mtm110) REVERT: B 283 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7565 (tpp80) REVERT: B 342 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6951 (tmm-80) REVERT: C 59 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8144 (t80) REVERT: C 98 SER cc_start: 0.8756 (m) cc_final: 0.8400 (p) REVERT: C 118 ASP cc_start: 0.7552 (t70) cc_final: 0.6994 (t0) REVERT: C 200 VAL cc_start: 0.8550 (m) cc_final: 0.8194 (p) REVERT: C 214 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7456 (mtt180) REVERT: C 217 MET cc_start: 0.7102 (mmm) cc_final: 0.6762 (mmm) REVERT: C 226 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7281 (mt-10) REVERT: C 247 ASP cc_start: 0.7033 (t0) cc_final: 0.6638 (t0) REVERT: C 251 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7709 (mmm-85) REVERT: N 27 PHE cc_start: 0.7451 (p90) cc_final: 0.6933 (p90) REVERT: N 28 THR cc_start: 0.8505 (p) cc_final: 0.8247 (p) REVERT: A 146 ASP cc_start: 0.8736 (t70) cc_final: 0.8439 (t0) REVERT: A 297 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7416 (tt) REVERT: D 32 ASN cc_start: 0.8278 (t0) cc_final: 0.8026 (t0) REVERT: D 101 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7827 (mtm-85) outliers start: 20 outliers final: 15 residues processed: 170 average time/residue: 0.1027 time to fit residues: 22.0901 Evaluate side-chains 173 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain D residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 0.0670 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123801 restraints weight = 12082.112| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.59 r_work: 0.3465 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.120 Angle : 0.549 12.441 11215 Z= 0.284 Chirality : 0.041 0.147 1309 Planarity : 0.004 0.046 1419 Dihedral : 4.956 49.406 1151 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.23 % Allowed : 17.04 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.27), residues: 1032 helix: 2.32 (0.29), residues: 347 sheet: -0.10 (0.32), residues: 250 loop : -1.92 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.011 0.001 TYR A 268 PHE 0.011 0.001 PHE C 235 TRP 0.007 0.001 TRP C 169 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8258) covalent geometry : angle 0.54909 (11207) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.60266 ( 8) hydrogen bonds : bond 0.03970 ( 365) hydrogen bonds : angle 4.32767 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 230 GLU cc_start: 0.7605 (tp30) cc_final: 0.7328 (tp30) REVERT: B 250 SER cc_start: 0.8567 (t) cc_final: 0.8296 (t) REVERT: B 265 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6788 (mtm110) REVERT: B 283 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7341 (tpp80) REVERT: B 342 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6813 (tmm-80) REVERT: B 390 GLN cc_start: 0.8119 (tp40) cc_final: 0.7831 (tp-100) REVERT: C 59 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7958 (t80) REVERT: C 98 SER cc_start: 0.8696 (m) cc_final: 0.8371 (p) REVERT: C 118 ASP cc_start: 0.7322 (t70) cc_final: 0.6762 (t0) REVERT: C 200 VAL cc_start: 0.8503 (m) cc_final: 0.8145 (p) REVERT: C 214 ARG cc_start: 0.7288 (mtt180) cc_final: 0.7035 (mtt180) REVERT: C 217 MET cc_start: 0.6708 (mmm) cc_final: 0.6472 (mmm) REVERT: C 226 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7246 (mt-10) REVERT: C 247 ASP cc_start: 0.6827 (t0) cc_final: 0.6500 (t0) REVERT: N 28 THR cc_start: 0.8430 (p) cc_final: 0.8106 (p) REVERT: A 146 ASP cc_start: 0.8590 (t70) cc_final: 0.8249 (t0) REVERT: A 297 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7386 (tt) REVERT: D 32 ASN cc_start: 0.8216 (t0) cc_final: 0.7931 (t0) REVERT: D 101 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7820 (mtm-85) outliers start: 19 outliers final: 16 residues processed: 163 average time/residue: 0.1152 time to fit residues: 23.5393 Evaluate side-chains 171 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126080 restraints weight = 12055.935| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.66 r_work: 0.3468 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8262 Z= 0.122 Angle : 0.548 12.818 11215 Z= 0.284 Chirality : 0.041 0.155 1309 Planarity : 0.004 0.047 1419 Dihedral : 4.997 49.481 1151 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.23 % Allowed : 16.92 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.27), residues: 1032 helix: 2.30 (0.29), residues: 347 sheet: -0.08 (0.33), residues: 245 loop : -2.03 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.012 0.001 TYR A 268 PHE 0.010 0.001 PHE C 241 TRP 0.008 0.001 TRP C 169 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8258) covalent geometry : angle 0.54823 (11207) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.59476 ( 8) hydrogen bonds : bond 0.04019 ( 365) hydrogen bonds : angle 4.35732 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.82 seconds wall clock time: 30 minutes 42.92 seconds (1842.92 seconds total)