Starting phenix.real_space_refine on Wed Mar 12 15:57:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qj2_18442/03_2025/8qj2_18442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qj2_18442/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qj2_18442/03_2025/8qj2_18442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qj2_18442/03_2025/8qj2_18442.map" model { file = "/net/cci-nas-00/data/ceres_data/8qj2_18442/03_2025/8qj2_18442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qj2_18442/03_2025/8qj2_18442.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLU:plan': 1, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 5.09, per 1000 atoms: 0.63 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 2.35 Time building geometry restraints manager: 2.56 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: 0.250 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.970 Find NCS groups from input model: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 8258 Z= 0.164 Angle : 0.490 6.031 11207 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 : 6.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.27), 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 TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS C 91 PHE 0.011 0.001 PHE C 241 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG D 98 *********************** 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 : 0.901 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: 0.2733 time to fit residues: 66.5809 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 : 0.800 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.0000 chunk 93 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126131 restraints weight = 11924.900| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.35 r_work: 0.3471 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8258 Z= 0.206 Angle : 0.551 14.882 11207 Z= 0.289 Chirality : 0.042 0.190 1309 Planarity : 0.004 0.068 1419 Dihedral : 5.852 49.996 1165 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.17 % Allowed : 11.52 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1032 helix: 2.11 (0.29), residues: 338 sheet: -0.36 (0.33), residues: 242 loop : -1.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 283 PHE 0.013 0.002 PHE C 241 TYR 0.014 0.001 TYR N 60 ARG 0.003 0.000 ARG N 98 *********************** 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 186 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8651 (t) cc_final: 0.8426 (t) REVERT: B 265 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7278 (mtt180) REVERT: B 283 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7364 (tpp80) REVERT: C 59 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8117 (t80) REVERT: C 98 SER cc_start: 0.8820 (m) cc_final: 0.8480 (p) REVERT: C 118 ASP cc_start: 0.7598 (t70) cc_final: 0.7074 (t0) REVERT: C 214 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7026 (mtt180) REVERT: C 217 MET cc_start: 0.7028 (mmm) cc_final: 0.6716 (mmm) REVERT: C 226 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 247 ASP cc_start: 0.7184 (t0) cc_final: 0.6666 (t0) REVERT: C 251 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8016 (mtt90) REVERT: N 27 PHE cc_start: 0.7557 (p90) cc_final: 0.7151 (p90) REVERT: N 28 THR cc_start: 0.8477 (p) cc_final: 0.8252 (p) REVERT: N 72 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7380 (ttm170) REVERT: A 207 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6350 (mt) REVERT: A 292 MET cc_start: 0.6773 (mmt) cc_final: 0.6102 (mmm) REVERT: D 32 ASN cc_start: 0.8156 (t0) cc_final: 0.7917 (t0) outliers start: 27 outliers final: 15 residues processed: 174 average time/residue: 0.2920 time to fit residues: 63.5575 Evaluate side-chains 165 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 197 ARG 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 150 THR 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 24 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.0040 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 A 283 HIS D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125517 restraints weight = 12120.443| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.49 r_work: 0.3461 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8258 Z= 0.185 Angle : 0.525 6.997 11207 Z= 0.277 Chirality : 0.041 0.218 1309 Planarity : 0.004 0.071 1419 Dihedral : 5.423 49.868 1155 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.82 % Allowed : 13.16 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 1032 helix: 2.21 (0.29), residues: 341 sheet: -0.36 (0.32), residues: 249 loop : -1.95 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.005 0.001 HIS C 225 PHE 0.011 0.001 PHE C 235 TYR 0.013 0.001 TYR N 60 ARG 0.004 0.000 ARG B 342 *********************** 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 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8692 (t) cc_final: 0.8437 (t) REVERT: B 265 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7278 (mtt180) REVERT: B 283 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7403 (tpp80) REVERT: B 390 GLN cc_start: 0.8373 (tp40) cc_final: 0.8078 (tp-100) REVERT: C 59 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8133 (t80) REVERT: C 118 ASP cc_start: 0.7655 (t70) cc_final: 0.7039 (t0) REVERT: C 214 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7054 (mtt180) REVERT: C 217 MET cc_start: 0.7120 (mmm) cc_final: 0.6782 (mmm) REVERT: C 226 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 247 ASP cc_start: 0.7154 (t0) cc_final: 0.6784 (t0) REVERT: C 273 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8097 (mp) REVERT: N 28 THR cc_start: 0.8519 (p) cc_final: 0.8190 (p) REVERT: N 72 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7548 (ttm170) REVERT: A 207 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6397 (mt) REVERT: A 257 CYS cc_start: 0.8086 (m) cc_final: 0.7836 (p) REVERT: D 32 ASN cc_start: 0.8157 (t0) cc_final: 0.7890 (t0) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 0.2891 time to fit residues: 61.0888 Evaluate side-chains 168 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 N residue 58 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.143929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126585 restraints weight = 12180.577| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.53 r_work: 0.3488 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8258 Z= 0.146 Angle : 0.498 7.703 11207 Z= 0.263 Chirality : 0.040 0.147 1309 Planarity : 0.004 0.070 1419 Dihedral : 5.315 49.474 1155 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.94 % Allowed : 13.75 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.27), residues: 1032 helix: 2.41 (0.30), residues: 341 sheet: -0.18 (0.33), residues: 249 loop : -1.92 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.009 0.001 HIS B 362 PHE 0.009 0.001 PHE B 212 TYR 0.011 0.001 TYR N 60 ARG 0.004 0.000 ARG B 342 *********************** 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 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8557 (t) cc_final: 0.8293 (t) REVERT: B 265 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6997 (mtt180) REVERT: B 283 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7199 (tpp80) REVERT: B 390 GLN cc_start: 0.8104 (tp40) cc_final: 0.7891 (tp-100) REVERT: C 59 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7966 (t80) REVERT: C 98 SER cc_start: 0.8725 (m) cc_final: 0.8367 (p) REVERT: C 118 ASP cc_start: 0.7462 (t70) cc_final: 0.6881 (t0) REVERT: C 214 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6747 (mtt180) REVERT: C 217 MET cc_start: 0.6749 (mmm) cc_final: 0.6459 (mmm) REVERT: C 226 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7163 (mt-10) REVERT: C 247 ASP cc_start: 0.6857 (t0) cc_final: 0.6519 (t0) REVERT: C 251 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7592 (mmm-85) REVERT: N 28 THR cc_start: 0.8396 (p) cc_final: 0.8058 (p) REVERT: A 292 MET cc_start: 0.6408 (mmt) cc_final: 0.6043 (mmt) REVERT: D 32 ASN cc_start: 0.8076 (t0) cc_final: 0.7782 (t0) outliers start: 25 outliers final: 17 residues processed: 173 average time/residue: 0.2937 time to fit residues: 63.6508 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 125 ILE Chi-restraints excluded: chain A residue 149 PHE 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 22 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120676 restraints weight = 12062.985| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.42 r_work: 0.3449 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8258 Z= 0.278 Angle : 0.572 7.706 11207 Z= 0.303 Chirality : 0.043 0.166 1309 Planarity : 0.004 0.054 1419 Dihedral : 5.630 50.839 1155 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.53 % Allowed : 14.34 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 1032 helix: 2.11 (0.29), residues: 336 sheet: -0.34 (0.32), residues: 255 loop : -2.05 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.005 0.001 HIS A 264 PHE 0.018 0.002 PHE C 241 TYR 0.019 0.002 TYR N 60 ARG 0.005 0.000 ARG N 98 *********************** 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: 30 poor density : 160 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 VAL cc_start: 0.8023 (t) cc_final: 0.7593 (m) REVERT: B 250 SER cc_start: 0.8717 (t) cc_final: 0.8457 (t) REVERT: B 265 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7312 (mtt180) REVERT: B 283 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7621 (tpp80) REVERT: B 342 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7359 (tmm-80) REVERT: B 390 GLN cc_start: 0.8321 (tp40) cc_final: 0.8101 (tp-100) REVERT: C 59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8147 (t80) REVERT: C 118 ASP cc_start: 0.7662 (t70) cc_final: 0.7066 (t0) REVERT: C 214 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7319 (mtt180) REVERT: C 217 MET cc_start: 0.7074 (mmm) cc_final: 0.6793 (mmm) REVERT: C 226 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 247 ASP cc_start: 0.7207 (t0) cc_final: 0.6697 (t0) REVERT: C 251 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7949 (mmm-85) REVERT: N 28 THR cc_start: 0.8522 (p) cc_final: 0.8217 (p) REVERT: A 207 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6521 (mt) REVERT: A 292 MET cc_start: 0.6464 (mmt) cc_final: 0.5683 (mmm) REVERT: A 297 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7328 (tt) REVERT: D 32 ASN cc_start: 0.8226 (t0) cc_final: 0.7954 (t0) outliers start: 30 outliers final: 18 residues processed: 175 average time/residue: 0.3914 time to fit residues: 88.8891 Evaluate side-chains 173 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 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 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain A residue 125 ILE 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 297 ILE Chi-restraints excluded: chain D residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN N 31 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123774 restraints weight = 12116.554| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.49 r_work: 0.3462 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: 0.7298 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8258 Z= 0.199 Angle : 0.541 9.742 11207 Z= 0.285 Chirality : 0.042 0.236 1309 Planarity : 0.004 0.056 1419 Dihedral : 5.392 51.409 1151 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.29 % Allowed : 15.28 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 1032 helix: 2.27 (0.29), residues: 336 sheet: -0.38 (0.32), residues: 257 loop : -2.01 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.003 0.001 HIS A 214 PHE 0.012 0.001 PHE C 241 TYR 0.013 0.001 TYR N 60 ARG 0.004 0.000 ARG N 98 *********************** 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 181 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7198 (pp20) REVERT: B 224 VAL cc_start: 0.8005 (t) cc_final: 0.7498 (m) REVERT: B 250 SER cc_start: 0.8706 (t) cc_final: 0.8435 (t) REVERT: B 265 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7252 (mtt180) REVERT: B 283 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7583 (tpp80) REVERT: B 342 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (mmm-85) REVERT: B 390 GLN cc_start: 0.8275 (tp40) cc_final: 0.8059 (tp-100) REVERT: C 59 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 98 SER cc_start: 0.8780 (m) cc_final: 0.8472 (p) REVERT: C 118 ASP cc_start: 0.7615 (t70) cc_final: 0.7065 (t0) REVERT: C 214 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7316 (mtt180) REVERT: C 217 MET cc_start: 0.7069 (mmm) cc_final: 0.6756 (mmm) REVERT: C 226 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 247 ASP cc_start: 0.7172 (t0) cc_final: 0.6674 (t0) REVERT: C 251 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7914 (mmm-85) REVERT: N 28 THR cc_start: 0.8483 (p) cc_final: 0.8147 (p) REVERT: A 207 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6447 (mt) REVERT: A 297 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7222 (tt) REVERT: D 32 ASN cc_start: 0.8127 (t0) cc_final: 0.7849 (t0) outliers start: 28 outliers final: 22 residues processed: 168 average time/residue: 0.2764 time to fit residues: 58.2859 Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain C residue 197 ARG 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 C residue 316 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 PHE 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 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 8 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.137437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120698 restraints weight = 12133.960| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.43 r_work: 0.3443 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8258 Z= 0.259 Angle : 0.575 9.337 11207 Z= 0.303 Chirality : 0.043 0.198 1309 Planarity : 0.004 0.060 1419 Dihedral : 5.568 52.675 1151 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.64 % Allowed : 15.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.27), residues: 1032 helix: 2.09 (0.29), residues: 336 sheet: -0.41 (0.32), residues: 255 loop : -2.07 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS A 214 PHE 0.017 0.002 PHE C 241 TYR 0.018 0.002 TYR N 60 ARG 0.005 0.000 ARG N 98 *********************** 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: 31 poor density : 154 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7346 (pp20) REVERT: B 224 VAL cc_start: 0.8017 (t) cc_final: 0.7579 (m) REVERT: B 250 SER cc_start: 0.8724 (t) cc_final: 0.8464 (t) REVERT: B 265 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7258 (mtt180) REVERT: B 283 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7619 (tpp80) REVERT: B 342 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7539 (mmm-85) REVERT: B 390 GLN cc_start: 0.8289 (tp40) cc_final: 0.8058 (tp-100) REVERT: C 59 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 118 ASP cc_start: 0.7632 (t70) cc_final: 0.7114 (t0) REVERT: C 214 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7344 (mtt180) REVERT: C 217 MET cc_start: 0.7101 (mmm) cc_final: 0.6777 (mmm) REVERT: C 226 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 247 ASP cc_start: 0.7190 (t0) cc_final: 0.6708 (t0) REVERT: C 251 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7983 (mmm-85) REVERT: N 28 THR cc_start: 0.8512 (p) cc_final: 0.8204 (p) REVERT: A 207 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6532 (mt) REVERT: D 32 ASN cc_start: 0.8152 (t0) cc_final: 0.7899 (t0) outliers start: 31 outliers final: 22 residues processed: 172 average time/residue: 0.2801 time to fit residues: 60.6162 Evaluate side-chains 176 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 143 THR Chi-restraints excluded: chain C residue 177 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 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU 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 222 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3808 r_free = 0.3808 target = 0.141786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124836 restraints weight = 12179.296| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.50 r_work: 0.3459 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8258 Z= 0.208 Angle : 0.541 8.697 11207 Z= 0.286 Chirality : 0.042 0.157 1309 Planarity : 0.004 0.044 1419 Dihedral : 5.459 53.151 1151 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.17 % Allowed : 15.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 1032 helix: 2.17 (0.29), residues: 336 sheet: -0.42 (0.32), residues: 257 loop : -2.09 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS A 214 PHE 0.013 0.001 PHE C 241 TYR 0.014 0.001 TYR N 60 ARG 0.005 0.000 ARG N 98 *********************** 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 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7316 (pp20) REVERT: B 224 VAL cc_start: 0.8038 (t) cc_final: 0.7543 (m) REVERT: B 250 SER cc_start: 0.8689 (t) cc_final: 0.8418 (t) REVERT: B 265 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7242 (mtt180) REVERT: B 283 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7427 (tpp80) REVERT: B 342 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7532 (mmm-85) REVERT: B 390 GLN cc_start: 0.8258 (tp40) cc_final: 0.8040 (tp-100) REVERT: C 59 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8113 (t80) REVERT: C 98 SER cc_start: 0.8800 (m) cc_final: 0.8486 (p) REVERT: C 118 ASP cc_start: 0.7633 (t70) cc_final: 0.7079 (t0) REVERT: C 214 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7375 (mtt180) REVERT: C 217 MET cc_start: 0.7079 (mmm) cc_final: 0.6751 (mmm) REVERT: C 226 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 247 ASP cc_start: 0.7195 (t0) cc_final: 0.6696 (t0) REVERT: C 251 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7930 (mmm-85) REVERT: C 289 TYR cc_start: 0.8394 (m-80) cc_final: 0.8155 (m-80) REVERT: N 28 THR cc_start: 0.8482 (p) cc_final: 0.8154 (p) REVERT: A 218 MET cc_start: 0.8478 (tpp) cc_final: 0.8270 (tpp) REVERT: A 297 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7252 (tt) REVERT: D 32 ASN cc_start: 0.8131 (t0) cc_final: 0.7865 (t0) outliers start: 27 outliers final: 23 residues processed: 168 average time/residue: 0.2826 time to fit residues: 59.4576 Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 177 THR 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 C residue 316 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 PHE 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 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126634 restraints weight = 12238.338| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.52 r_work: 0.3476 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8258 Z= 0.156 Angle : 0.518 10.310 11207 Z= 0.272 Chirality : 0.041 0.145 1309 Planarity : 0.003 0.041 1419 Dihedral : 5.275 52.853 1151 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.47 % Allowed : 16.92 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1032 helix: 2.20 (0.29), residues: 347 sheet: -0.26 (0.32), residues: 255 loop : -2.04 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.002 0.001 HIS A 214 PHE 0.009 0.001 PHE C 241 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG B 342 *********************** 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 173 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7323 (pp20) REVERT: B 230 GLU cc_start: 0.7819 (tp30) cc_final: 0.7614 (tp30) REVERT: B 250 SER cc_start: 0.8660 (t) cc_final: 0.8372 (t) REVERT: B 265 ARG cc_start: 0.7456 (mtt180) cc_final: 0.7241 (mtt180) REVERT: B 283 ARG cc_start: 0.7852 (ttm110) cc_final: 0.7434 (tpp80) REVERT: C 59 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8012 (t80) REVERT: C 98 SER cc_start: 0.8772 (m) cc_final: 0.8453 (p) REVERT: C 118 ASP cc_start: 0.7603 (t70) cc_final: 0.7035 (t0) REVERT: C 165 THR cc_start: 0.7398 (m) cc_final: 0.7184 (p) REVERT: C 214 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7383 (mtt180) REVERT: C 217 MET cc_start: 0.7065 (mmm) cc_final: 0.6713 (mmm) REVERT: C 226 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 247 ASP cc_start: 0.7122 (t0) cc_final: 0.6565 (t0) REVERT: C 251 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7858 (mmm-85) REVERT: C 289 TYR cc_start: 0.8359 (m-80) cc_final: 0.8123 (m-80) REVERT: C 291 ASP cc_start: 0.7698 (m-30) cc_final: 0.7216 (m-30) REVERT: N 28 THR cc_start: 0.8499 (p) cc_final: 0.8158 (p) REVERT: A 146 ASP cc_start: 0.8681 (t70) cc_final: 0.8406 (t0) REVERT: A 297 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7255 (tt) REVERT: D 32 ASN cc_start: 0.8105 (t0) cc_final: 0.7849 (t0) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.2739 time to fit residues: 56.3756 Evaluate side-chains 170 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 204 MET 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 71 optimal weight: 0.0370 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3793 r_free = 0.3793 target = 0.141964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124875 restraints weight = 12003.445| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.45 r_work: 0.3454 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8258 Z= 0.232 Angle : 0.579 12.735 11207 Z= 0.300 Chirality : 0.042 0.157 1309 Planarity : 0.004 0.047 1419 Dihedral : 5.341 53.964 1149 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.23 % Allowed : 17.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 1032 helix: 2.15 (0.29), residues: 342 sheet: -0.36 (0.32), residues: 257 loop : -2.13 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.004 0.001 HIS A 214 PHE 0.015 0.002 PHE C 241 TYR 0.016 0.001 TYR N 60 ARG 0.003 0.000 ARG C 68 ********************** 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 170 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7209 (pp20) REVERT: B 224 VAL cc_start: 0.8031 (t) cc_final: 0.7535 (m) REVERT: B 250 SER cc_start: 0.8696 (t) cc_final: 0.8420 (t) REVERT: B 265 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7273 (mtt180) REVERT: B 283 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7620 (tpp80) REVERT: C 59 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 98 SER cc_start: 0.8800 (m) cc_final: 0.8494 (p) REVERT: C 118 ASP cc_start: 0.7603 (t70) cc_final: 0.7058 (t0) REVERT: C 165 THR cc_start: 0.7409 (m) cc_final: 0.7195 (p) REVERT: C 214 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7380 (mtt180) REVERT: C 217 MET cc_start: 0.7077 (mmm) cc_final: 0.6737 (mmm) REVERT: C 226 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 247 ASP cc_start: 0.7155 (t0) cc_final: 0.6762 (t0) REVERT: C 251 ARG cc_start: 0.8409 (mtt90) cc_final: 0.7978 (mmm-85) REVERT: C 289 TYR cc_start: 0.8346 (m-80) cc_final: 0.8113 (m-80) REVERT: N 28 THR cc_start: 0.8535 (p) cc_final: 0.8207 (p) REVERT: A 297 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7345 (tt) REVERT: D 32 ASN cc_start: 0.8160 (t0) cc_final: 0.7942 (t0) outliers start: 19 outliers final: 16 residues processed: 160 average time/residue: 0.2921 time to fit residues: 58.6136 Evaluate side-chains 168 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 12 VAL 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 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124753 restraints weight = 12136.695| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.50 r_work: 0.3474 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8258 Z= 0.175 Angle : 0.550 12.574 11207 Z= 0.284 Chirality : 0.041 0.156 1309 Planarity : 0.003 0.043 1419 Dihedral : 5.208 53.879 1149 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.59 % Allowed : 17.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1032 helix: 2.32 (0.29), residues: 341 sheet: -0.28 (0.32), residues: 255 loop : -2.11 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.004 0.001 HIS A 214 PHE 0.011 0.001 PHE C 241 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4257.68 seconds wall clock time: 74 minutes 38.42 seconds (4478.42 seconds total)