Starting phenix.real_space_refine on Sun May 11 13:05:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qj2_18442/05_2025/8qj2_18442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qj2_18442/05_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_18442/05_2025/8qj2_18442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qj2_18442/05_2025/8qj2_18442.map" model { file = "/net/cci-nas-00/data/ceres_data/8qj2_18442/05_2025/8qj2_18442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qj2_18442/05_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-5687/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: 4.85, per 1000 atoms: 0.60 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: 1.90 Conformation dependent library (CDL) restraints added in 1.1 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: 1.00 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: 2.10 Time building geometry restraints manager: 2.24 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: 0.340 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.090 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8262 Z= 0.121 Angle : 0.491 6.031 11215 Z= 0.269 Chirality : 0.040 0.131 1309 Planarity : 0.003 0.060 1419 Dihedral : 10.541 88.457 2883 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.27 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 Details of bonding type rmsd hydrogen bonds : bond 0.16054 ( 365) hydrogen bonds : angle 6.16862 ( 1044) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.70887 ( 8) covalent geometry : bond 0.00248 ( 8258) covalent geometry : angle 0.49044 (11207) *********************** 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 : 0.864 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: 0.2694 time to fit residues: 65.5754 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 : 0.902 ------------------------------------------------------------------------------- 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: 0.2980 chunk 60 optimal weight: 0.0000 chunk 93 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.143945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126765 restraints weight = 11910.109| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.35 r_work: 0.3486 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8262 Z= 0.129 Angle : 0.536 14.547 11215 Z= 0.281 Chirality : 0.041 0.180 1309 Planarity : 0.004 0.067 1419 Dihedral : 5.804 49.774 1165 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.94 % Allowed : 11.75 % 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: -0.20 (0.27), residues: 1032 helix: 2.15 (0.29), residues: 340 sheet: -0.38 (0.32), residues: 246 loop : -1.87 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS A 283 PHE 0.012 0.001 PHE C 241 TYR 0.013 0.001 TYR N 60 ARG 0.005 0.000 ARG C 283 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 365) hydrogen bonds : angle 4.76070 ( 1044) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.69913 ( 8) covalent geometry : bond 0.00276 ( 8258) covalent geometry : angle 0.53615 (11207) *********************** 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 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8650 (t) cc_final: 0.8422 (t) REVERT: B 265 ARG cc_start: 0.7512 (mtt180) cc_final: 0.7278 (mtt180) REVERT: B 283 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7359 (tpp80) REVERT: C 59 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 98 SER cc_start: 0.8816 (m) cc_final: 0.8478 (p) REVERT: C 118 ASP cc_start: 0.7588 (t70) cc_final: 0.7062 (t0) REVERT: C 214 ARG cc_start: 0.7669 (mtt180) cc_final: 0.7022 (mtt180) REVERT: C 217 MET cc_start: 0.7032 (mmm) cc_final: 0.6709 (mmm) REVERT: C 226 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7363 (mt-10) REVERT: C 247 ASP cc_start: 0.7167 (t0) cc_final: 0.6668 (t0) REVERT: C 251 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8018 (mtt90) REVERT: N 27 PHE cc_start: 0.7560 (p90) cc_final: 0.7155 (p90) REVERT: N 28 THR cc_start: 0.8491 (p) cc_final: 0.8253 (p) REVERT: N 72 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7363 (ttm170) REVERT: A 103 VAL cc_start: 0.7536 (m) cc_final: 0.7325 (t) REVERT: A 207 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6332 (mt) REVERT: A 292 MET cc_start: 0.6737 (mmt) cc_final: 0.6089 (mmm) REVERT: D 32 ASN cc_start: 0.8159 (t0) cc_final: 0.7919 (t0) outliers start: 25 outliers final: 15 residues processed: 176 average time/residue: 0.2827 time to fit residues: 62.3509 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 : 0.885 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123295 restraints weight = 12164.744| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.45 r_work: 0.3424 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8262 Z= 0.215 Angle : 0.600 7.854 11215 Z= 0.319 Chirality : 0.044 0.262 1309 Planarity : 0.004 0.077 1419 Dihedral : 5.771 51.640 1155 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.53 % Allowed : 12.57 % Favored : 83.90 % 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: -0.44 (0.27), residues: 1032 helix: 1.96 (0.29), residues: 334 sheet: -0.39 (0.32), residues: 251 loop : -2.08 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.011 0.002 HIS B 362 PHE 0.020 0.002 PHE C 235 TYR 0.019 0.002 TYR N 60 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.05739 ( 365) hydrogen bonds : angle 4.86154 ( 1044) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.76876 ( 8) covalent geometry : bond 0.00486 ( 8258) covalent geometry : angle 0.60035 (11207) *********************** 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 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7936 (tp) cc_final: 0.7684 (tt) REVERT: B 224 VAL cc_start: 0.8033 (t) cc_final: 0.7611 (m) REVERT: B 250 SER cc_start: 0.8711 (t) cc_final: 0.8471 (t) REVERT: B 265 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7414 (mtt180) REVERT: B 283 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7440 (tpp80) REVERT: B 390 GLN cc_start: 0.8321 (tp40) cc_final: 0.8093 (tp-100) REVERT: C 59 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 118 ASP cc_start: 0.7657 (t70) cc_final: 0.7082 (t0) REVERT: C 214 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7011 (mtt180) REVERT: C 217 MET cc_start: 0.7077 (mmm) cc_final: 0.6775 (mmm) REVERT: C 247 ASP cc_start: 0.7219 (t0) cc_final: 0.6773 (t0) REVERT: C 251 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8053 (mtt90) REVERT: N 28 THR cc_start: 0.8499 (p) cc_final: 0.8271 (p) REVERT: A 207 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6503 (mt) REVERT: A 218 MET cc_start: 0.8378 (tpp) cc_final: 0.8160 (tpp) REVERT: A 257 CYS cc_start: 0.8090 (m) cc_final: 0.7873 (p) REVERT: D 32 ASN cc_start: 0.8218 (t0) cc_final: 0.7946 (t0) outliers start: 30 outliers final: 20 residues processed: 174 average time/residue: 0.3011 time to fit residues: 65.4116 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 : 0.793 ------------------------------------------------------------------------------- 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 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 G residue 38 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 37 optimal weight: 0.0570 chunk 52 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124251 restraints weight = 12152.927| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.61 r_work: 0.3457 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.120 Angle : 0.519 6.384 11215 Z= 0.276 Chirality : 0.041 0.153 1309 Planarity : 0.004 0.073 1419 Dihedral : 5.360 51.488 1151 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.94 % Allowed : 14.34 % Favored : 82.73 % 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: -0.19 (0.27), residues: 1032 helix: 2.33 (0.29), residues: 333 sheet: -0.38 (0.32), residues: 256 loop : -1.99 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.007 0.001 HIS B 362 PHE 0.011 0.001 PHE B 212 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 365) hydrogen bonds : angle 4.54677 ( 1044) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.59402 ( 8) covalent geometry : bond 0.00256 ( 8258) covalent geometry : angle 0.51848 (11207) *********************** 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 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7798 (tp) cc_final: 0.7580 (tt) REVERT: B 224 VAL cc_start: 0.7827 (t) cc_final: 0.7309 (m) REVERT: B 250 SER cc_start: 0.8609 (t) cc_final: 0.8355 (t) REVERT: B 265 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6966 (mtt180) REVERT: B 283 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7276 (tpp80) REVERT: B 390 GLN cc_start: 0.8140 (tp40) cc_final: 0.7938 (tp-100) REVERT: C 59 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8004 (t80) REVERT: C 98 SER cc_start: 0.8749 (m) cc_final: 0.8419 (p) REVERT: C 118 ASP cc_start: 0.7487 (t70) cc_final: 0.6896 (t0) REVERT: C 214 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6717 (mtt180) REVERT: C 217 MET cc_start: 0.6804 (mmm) cc_final: 0.6550 (mmm) REVERT: C 226 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7214 (mt-10) REVERT: C 247 ASP cc_start: 0.6879 (t0) cc_final: 0.6468 (t0) REVERT: G 48 ASP cc_start: 0.7697 (t0) cc_final: 0.7309 (t0) REVERT: G 49 PRO cc_start: 0.8292 (Cg_exo) cc_final: 0.8009 (Cg_endo) REVERT: N 28 THR cc_start: 0.8428 (p) cc_final: 0.8082 (p) REVERT: A 292 MET cc_start: 0.6678 (mmt) cc_final: 0.6417 (mmt) REVERT: A 297 ILE cc_start: 0.7442 (tp) cc_final: 0.7016 (tt) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.2866 time to fit residues: 61.0439 Evaluate side-chains 164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 221 MET 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 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: 0.8980 chunk 48 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN G 59 ASN N 31 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122744 restraints weight = 11966.329| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.44 r_work: 0.3474 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8262 Z= 0.120 Angle : 0.518 7.591 11215 Z= 0.275 Chirality : 0.041 0.152 1309 Planarity : 0.004 0.064 1419 Dihedral : 5.326 51.666 1151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.70 % Allowed : 14.92 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.29), residues: 340 sheet: -0.34 (0.32), residues: 255 loop : -1.95 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.006 0.001 HIS B 362 PHE 0.011 0.001 PHE C 151 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 365) hydrogen bonds : angle 4.48369 ( 1044) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.58825 ( 8) covalent geometry : bond 0.00260 ( 8258) covalent geometry : angle 0.51787 (11207) *********************** 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 183 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.7874 (tp) cc_final: 0.7645 (tt) REVERT: B 224 VAL cc_start: 0.7974 (t) cc_final: 0.7459 (m) REVERT: B 250 SER cc_start: 0.8684 (t) cc_final: 0.8423 (t) REVERT: B 265 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7240 (mtt180) REVERT: B 283 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7457 (tpp80) REVERT: B 342 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7264 (tmm-80) REVERT: C 59 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8164 (t80) REVERT: C 98 SER cc_start: 0.8805 (m) cc_final: 0.8475 (p) REVERT: C 118 ASP cc_start: 0.7670 (t70) cc_final: 0.7057 (t0) REVERT: C 214 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7368 (mtt180) REVERT: C 217 MET cc_start: 0.7072 (mmm) cc_final: 0.6775 (mmm) REVERT: C 226 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7339 (mt-10) REVERT: C 247 ASP cc_start: 0.7063 (t0) cc_final: 0.6653 (t0) REVERT: C 251 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7849 (mmm-85) REVERT: N 28 THR cc_start: 0.8528 (p) cc_final: 0.8184 (p) REVERT: A 218 MET cc_start: 0.8471 (tpp) cc_final: 0.8264 (tpp) REVERT: A 292 MET cc_start: 0.6745 (mmt) cc_final: 0.6518 (mmt) REVERT: D 32 ASN cc_start: 0.8155 (t0) cc_final: 0.7914 (t0) outliers start: 23 outliers final: 19 residues processed: 169 average time/residue: 0.2720 time to fit residues: 57.7007 Evaluate side-chains 174 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 221 MET 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 197 ARG 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 140 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123517 restraints weight = 12109.356| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.47 r_work: 0.3486 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.107 Angle : 0.500 6.905 11215 Z= 0.266 Chirality : 0.040 0.145 1309 Planarity : 0.003 0.047 1419 Dihedral : 5.090 51.604 1149 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.41 % Allowed : 15.04 % Favored : 81.55 % 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: -0.08 (0.27), residues: 1032 helix: 2.42 (0.29), residues: 341 sheet: -0.25 (0.32), residues: 255 loop : -2.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.005 0.001 HIS B 362 PHE 0.010 0.001 PHE B 212 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 365) hydrogen bonds : angle 4.39208 ( 1044) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.54627 ( 8) covalent geometry : bond 0.00229 ( 8258) covalent geometry : angle 0.50028 (11207) *********************** 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 186 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8666 (t) cc_final: 0.8385 (t) REVERT: B 265 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7214 (mtt180) REVERT: B 283 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7446 (tpp80) REVERT: B 342 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7133 (tmm-80) REVERT: C 59 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7995 (t80) REVERT: C 98 SER cc_start: 0.8767 (m) cc_final: 0.8448 (p) REVERT: C 118 ASP cc_start: 0.7549 (t70) cc_final: 0.7053 (t0) REVERT: C 214 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7385 (mtt180) REVERT: C 217 MET cc_start: 0.7056 (mmm) cc_final: 0.6754 (mmm) REVERT: C 247 ASP cc_start: 0.7053 (t0) cc_final: 0.6669 (t0) REVERT: C 251 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7868 (mmm-85) REVERT: N 27 PHE cc_start: 0.7553 (p90) cc_final: 0.7157 (p90) REVERT: N 28 THR cc_start: 0.8520 (p) cc_final: 0.8251 (p) REVERT: A 146 ASP cc_start: 0.8716 (t70) cc_final: 0.8419 (t0) REVERT: A 292 MET cc_start: 0.6706 (mmt) cc_final: 0.6485 (mmt) REVERT: A 297 ILE cc_start: 0.7576 (tp) cc_final: 0.7159 (tt) REVERT: D 32 ASN cc_start: 0.8152 (t0) cc_final: 0.7912 (t0) outliers start: 29 outliers final: 20 residues processed: 173 average time/residue: 0.2854 time to fit residues: 61.9684 Evaluate side-chains 175 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 N residue 70 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 204 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 HIS 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: 0.9980 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124374 restraints weight = 12106.283| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.49 r_work: 0.3448 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8262 Z= 0.164 Angle : 0.564 9.198 11215 Z= 0.296 Chirality : 0.042 0.150 1309 Planarity : 0.004 0.051 1419 Dihedral : 5.357 53.138 1149 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.94 % Allowed : 15.63 % 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: -0.24 (0.27), residues: 1032 helix: 2.25 (0.29), residues: 335 sheet: -0.38 (0.32), residues: 257 loop : -2.02 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.006 0.001 HIS B 362 PHE 0.016 0.002 PHE C 241 TYR 0.016 0.002 TYR N 60 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 365) hydrogen bonds : angle 4.55656 ( 1044) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.69821 ( 8) covalent geometry : bond 0.00368 ( 8258) covalent geometry : angle 0.56382 (11207) *********************** 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 176 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7189 (pp20) REVERT: B 224 VAL cc_start: 0.8013 (t) cc_final: 0.7525 (m) REVERT: B 250 SER cc_start: 0.8682 (t) cc_final: 0.8403 (t) REVERT: B 265 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7290 (mtt180) REVERT: B 283 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7480 (tpp80) REVERT: B 342 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7262 (tmm-80) REVERT: B 390 GLN cc_start: 0.8259 (tp40) cc_final: 0.7984 (tp-100) REVERT: C 59 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8077 (t80) REVERT: C 118 ASP cc_start: 0.7607 (t70) cc_final: 0.7099 (t0) REVERT: C 214 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7369 (mtt180) REVERT: C 217 MET cc_start: 0.7078 (mmm) cc_final: 0.6729 (mmm) REVERT: C 247 ASP cc_start: 0.7082 (t0) cc_final: 0.6581 (t0) REVERT: C 251 ARG cc_start: 0.8310 (mtt90) cc_final: 0.7945 (mmm-85) REVERT: A 297 ILE cc_start: 0.7631 (tp) cc_final: 0.7191 (tt) REVERT: D 32 ASN cc_start: 0.8140 (t0) cc_final: 0.7891 (t0) outliers start: 25 outliers final: 21 residues processed: 163 average time/residue: 0.2704 time to fit residues: 55.2885 Evaluate side-chains 171 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU 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: 1.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 23 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 ** 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 = 0.3846 r_free = 0.3846 target = 0.144509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127240 restraints weight = 12149.794| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.52 r_work: 0.3497 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.102 Angle : 0.516 11.592 11215 Z= 0.268 Chirality : 0.040 0.140 1309 Planarity : 0.003 0.040 1419 Dihedral : 5.040 52.324 1149 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.23 % Allowed : 16.92 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1032 helix: 2.47 (0.29), residues: 341 sheet: -0.26 (0.32), residues: 255 loop : -2.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 297 HIS 0.003 0.001 HIS B 362 PHE 0.009 0.001 PHE B 212 TYR 0.010 0.001 TYR N 60 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 365) hydrogen bonds : angle 4.35245 ( 1044) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.53524 ( 8) covalent geometry : bond 0.00214 ( 8258) covalent geometry : angle 0.51584 (11207) *********************** 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 172 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 250 SER cc_start: 0.8636 (t) cc_final: 0.8344 (t) REVERT: B 283 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7435 (tpp80) REVERT: B 342 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7024 (tmm-80) REVERT: B 390 GLN cc_start: 0.8237 (tp40) cc_final: 0.7993 (tp-100) REVERT: C 59 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 98 SER cc_start: 0.8758 (m) cc_final: 0.8406 (p) REVERT: C 118 ASP cc_start: 0.7591 (t70) cc_final: 0.7017 (t0) REVERT: C 165 THR cc_start: 0.7405 (m) cc_final: 0.7194 (p) REVERT: C 214 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7425 (mtt180) REVERT: C 217 MET cc_start: 0.7061 (mmm) cc_final: 0.6702 (mmm) REVERT: C 247 ASP cc_start: 0.6853 (t0) cc_final: 0.6415 (t0) REVERT: N 28 THR cc_start: 0.8573 (p) cc_final: 0.8263 (p) REVERT: A 146 ASP cc_start: 0.8666 (t70) cc_final: 0.8387 (t0) REVERT: A 297 ILE cc_start: 0.7407 (tp) cc_final: 0.7044 (tt) REVERT: D 32 ASN cc_start: 0.8090 (t0) cc_final: 0.7847 (t0) outliers start: 19 outliers final: 17 residues processed: 162 average time/residue: 0.2872 time to fit residues: 58.5173 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 : 0.955 ------------------------------------------------------------------------------- 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 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124481 restraints weight = 12248.420| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.52 r_work: 0.3471 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8262 Z= 0.130 Angle : 0.545 11.318 11215 Z= 0.283 Chirality : 0.041 0.158 1309 Planarity : 0.003 0.042 1419 Dihedral : 5.170 52.841 1149 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.59 % Allowed : 17.39 % Favored : 80.02 % 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: -0.14 (0.27), residues: 1032 helix: 2.23 (0.29), residues: 348 sheet: -0.29 (0.32), residues: 257 loop : -2.03 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.002 0.001 HIS A 264 PHE 0.012 0.001 PHE C 241 TYR 0.011 0.001 TYR N 60 ARG 0.006 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 365) hydrogen bonds : angle 4.43145 ( 1044) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.64202 ( 8) covalent geometry : bond 0.00288 ( 8258) covalent geometry : angle 0.54445 (11207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 VAL cc_start: 0.7952 (t) cc_final: 0.7454 (m) REVERT: B 250 SER cc_start: 0.8652 (t) cc_final: 0.8372 (t) REVERT: B 283 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7456 (tpp80) REVERT: B 342 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7063 (tmm-80) REVERT: B 390 GLN cc_start: 0.8247 (tp40) cc_final: 0.8015 (tp-100) REVERT: C 59 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8082 (t80) REVERT: C 98 SER cc_start: 0.8755 (m) cc_final: 0.8417 (p) REVERT: C 118 ASP cc_start: 0.7657 (t70) cc_final: 0.7064 (t0) REVERT: C 165 THR cc_start: 0.7412 (m) cc_final: 0.7193 (p) REVERT: C 214 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7407 (mtt180) REVERT: C 217 MET cc_start: 0.7053 (mmm) cc_final: 0.6712 (mmm) REVERT: C 247 ASP cc_start: 0.6938 (t0) cc_final: 0.6432 (t0) REVERT: C 251 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7785 (mmm-85) REVERT: C 262 MET cc_start: 0.7931 (mtm) cc_final: 0.7555 (mmm) REVERT: N 7 SER cc_start: 0.7116 (t) cc_final: 0.6900 (p) REVERT: N 28 THR cc_start: 0.8549 (p) cc_final: 0.8339 (p) REVERT: A 146 ASP cc_start: 0.8676 (t70) cc_final: 0.8382 (t0) REVERT: A 297 ILE cc_start: 0.7508 (tp) cc_final: 0.7248 (tt) REVERT: D 32 ASN cc_start: 0.8130 (t0) cc_final: 0.7873 (t0) outliers start: 22 outliers final: 19 residues processed: 168 average time/residue: 0.2801 time to fit residues: 59.2852 Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 342 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 82 TRP Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121008 restraints weight = 12068.281| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.44 r_work: 0.3452 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8262 Z= 0.176 Angle : 0.600 13.119 11215 Z= 0.312 Chirality : 0.043 0.168 1309 Planarity : 0.004 0.044 1419 Dihedral : 5.463 54.624 1149 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.82 % Allowed : 17.04 % Favored : 80.14 % 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: -0.29 (0.27), residues: 1032 helix: 2.18 (0.29), residues: 339 sheet: -0.36 (0.32), residues: 258 loop : -2.10 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.006 0.001 HIS A 214 PHE 0.018 0.002 PHE C 241 TYR 0.018 0.002 TYR N 60 ARG 0.008 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 365) hydrogen bonds : angle 4.59718 ( 1044) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.68388 ( 8) covalent geometry : bond 0.00398 ( 8258) covalent geometry : angle 0.60024 (11207) ********************** 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 182 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 VAL cc_start: 0.8021 (t) cc_final: 0.7544 (m) REVERT: B 250 SER cc_start: 0.8691 (t) cc_final: 0.8420 (t) REVERT: B 265 ARG cc_start: 0.7382 (mtm110) cc_final: 0.7125 (mtm110) REVERT: B 283 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7395 (tpp80) REVERT: B 342 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7245 (tmm-80) REVERT: B 390 GLN cc_start: 0.8285 (tp40) cc_final: 0.8008 (tp-100) REVERT: C 59 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8058 (t80) REVERT: C 118 ASP cc_start: 0.7669 (t70) cc_final: 0.7070 (t0) REVERT: C 214 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7394 (mtt180) REVERT: C 217 MET cc_start: 0.7119 (mmm) cc_final: 0.6787 (mmm) REVERT: C 247 ASP cc_start: 0.7013 (t0) cc_final: 0.6579 (t0) REVERT: C 251 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7871 (mmm-85) REVERT: N 7 SER cc_start: 0.7088 (t) cc_final: 0.6857 (p) REVERT: N 28 THR cc_start: 0.8605 (p) cc_final: 0.8383 (p) REVERT: A 160 ILE cc_start: 0.7954 (pt) cc_final: 0.7683 (mm) REVERT: A 297 ILE cc_start: 0.7756 (tp) cc_final: 0.7471 (tt) REVERT: D 32 ASN cc_start: 0.8254 (t0) cc_final: 0.8020 (t0) outliers start: 24 outliers final: 20 residues processed: 170 average time/residue: 0.2687 time to fit residues: 57.5132 Evaluate side-chains 181 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 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 N residue 70 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 140 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 5 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 88 ASN N 31 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124866 restraints weight = 12111.648| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.40 r_work: 0.3500 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.104 Angle : 0.540 12.611 11215 Z= 0.278 Chirality : 0.040 0.162 1309 Planarity : 0.003 0.037 1419 Dihedral : 5.127 53.704 1149 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.23 % Allowed : 17.98 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.27), residues: 1032 helix: 2.45 (0.29), residues: 341 sheet: -0.18 (0.32), residues: 254 loop : -2.09 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 297 HIS 0.004 0.001 HIS A 214 PHE 0.009 0.001 PHE B 212 TYR 0.011 0.001 TYR N 60 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 365) hydrogen bonds : angle 4.38184 ( 1044) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.51218 ( 8) covalent geometry : bond 0.00219 ( 8258) covalent geometry : angle 0.53979 (11207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.89 seconds wall clock time: 76 minutes 33.90 seconds (4593.90 seconds total)