Starting phenix.real_space_refine on Thu Feb 13 15:48:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.map" model { file = "/net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lbh_0869/02_2025/6lbh_0869.cif" } resolution = 3.7 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= 0.000 sd= 0.003 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 34 5.16 5 C 5907 2.51 5 N 1507 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9219 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1352 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1618 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1637 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1612 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1644 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 6.14, per 1000 atoms: 0.67 Number of scatterers: 9219 At special positions: 0 Unit cell: (113.98, 122.18, 125.46, 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 34 16.00 O 1771 8.00 N 1507 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 22 sheets defined 30.7% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 277 through 306 removed outlier: 4.020A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.855A pdb=" N LEU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 343 removed outlier: 4.230A pdb=" N ASN A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 382 removed outlier: 3.879A pdb=" N LEU A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 416 removed outlier: 3.755A pdb=" N VAL A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.920A pdb=" N VAL A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.717A pdb=" N ALA A 428 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 306 removed outlier: 4.376A pdb=" N ILE B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.587A pdb=" N LEU B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 344 removed outlier: 3.572A pdb=" N ASN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 382 removed outlier: 3.744A pdb=" N VAL B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 401 removed outlier: 3.699A pdb=" N VAL B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.748A pdb=" N ALA B 428 " --> pdb=" O ASN B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.691A pdb=" N THR D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.661A pdb=" N HIS D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.625A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 126 through 131 removed outlier: 3.639A pdb=" N THR F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 removed outlier: 3.625A pdb=" N HIS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.670A pdb=" N LYS E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.531A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.585A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP D 75 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 72 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.029A pdb=" N GLU D 110 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 53 removed outlier: 5.455A pdb=" N LEU D 51 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.665A pdb=" N ASN D 142 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR D 178 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 165 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.729A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.698A pdb=" N ILE C 121 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.698A pdb=" N ILE C 121 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.550A pdb=" N SER C 131 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 186 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.550A pdb=" N SER C 131 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 186 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 180 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.607A pdb=" N THR C 162 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 207 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.569A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 75 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 72 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 12 through 13 removed outlier: 5.959A pdb=" N GLU F 110 " --> pdb=" O VAL F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 50 through 53 removed outlier: 5.429A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.764A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 165 " --> pdb=" O THR F 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.727A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.570A pdb=" N ILE E 121 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.570A pdb=" N ILE E 121 " --> pdb=" O GLU E 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AC3, first strand: chain 'E' and resid 131 through 133 removed outlier: 3.690A pdb=" N VAL E 180 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.522A pdb=" N THR E 162 " --> pdb=" O ALA E 209 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1185 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: 2.91 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 2284 1.46 - 1.58: 4205 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 9435 Sorted by residual: bond pdb=" CB VAL B 398 " pdb=" CG2 VAL B 398 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" N TYR E 109E" pdb=" CA TYR E 109E" ideal model delta sigma weight residual 1.459 1.446 0.013 9.10e-03 1.21e+04 2.06e+00 bond pdb=" CG1 ILE B 339 " pdb=" CD1 ILE B 339 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" N TYR C 109E" pdb=" CA TYR C 109E" ideal model delta sigma weight residual 1.459 1.447 0.012 9.10e-03 1.21e+04 1.85e+00 bond pdb=" CB VAL E 37 " pdb=" CG1 VAL E 37 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 9430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12285 1.64 - 3.29: 489 3.29 - 4.93: 98 4.93 - 6.57: 22 6.57 - 8.22: 14 Bond angle restraints: 12908 Sorted by residual: angle pdb=" N MET E 111G" pdb=" CA MET E 111G" pdb=" C MET E 111G" ideal model delta sigma weight residual 110.06 117.32 -7.26 1.43e+00 4.89e-01 2.58e+01 angle pdb=" N ALA C 110F" pdb=" CA ALA C 110F" pdb=" C ALA C 110F" ideal model delta sigma weight residual 111.34 118.66 -7.32 1.49e+00 4.50e-01 2.42e+01 angle pdb=" N ALA E 110F" pdb=" CA ALA E 110F" pdb=" C ALA E 110F" ideal model delta sigma weight residual 112.12 118.67 -6.55 1.34e+00 5.57e-01 2.39e+01 angle pdb=" C TYR C 109E" pdb=" N ALA C 110F" pdb=" CA ALA C 110F" ideal model delta sigma weight residual 121.90 116.05 5.85 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N MET C 111G" pdb=" CA MET C 111G" pdb=" C MET C 111G" ideal model delta sigma weight residual 109.83 116.94 -7.11 1.55e+00 4.16e-01 2.10e+01 ... (remaining 12903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5008 17.34 - 34.69: 418 34.69 - 52.03: 88 52.03 - 69.37: 7 69.37 - 86.72: 7 Dihedral angle restraints: 5528 sinusoidal: 1968 harmonic: 3560 Sorted by residual: dihedral pdb=" CA LYS F 55 " pdb=" C LYS F 55 " pdb=" N VAL F 56 " pdb=" CA VAL F 56 " ideal model delta harmonic sigma weight residual -180.00 -139.17 -40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CA LYS D 55 " pdb=" C LYS D 55 " pdb=" N VAL D 56 " pdb=" CA VAL D 56 " ideal model delta harmonic sigma weight residual -180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASN D 35E" pdb=" C ASN D 35E" pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta harmonic sigma weight residual 180.00 141.92 38.08 0 5.00e+00 4.00e-02 5.80e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 956 0.037 - 0.073: 414 0.073 - 0.110: 131 0.110 - 0.147: 32 0.147 - 0.183: 6 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA THR F 36 " pdb=" N THR F 36 " pdb=" C THR F 36 " pdb=" CB THR F 36 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA THR D 36 " pdb=" N THR D 36 " pdb=" C THR D 36 " pdb=" CB THR D 36 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA ALA E 110F" pdb=" N ALA E 110F" pdb=" C ALA E 110F" pdb=" CB ALA E 110F" both_signs ideal model delta sigma weight residual False 2.48 2.31 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1536 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 331 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLY B 331 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY B 331 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 332 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 331 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLY A 331 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 331 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 332 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 145 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 146 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.020 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 179 2.64 - 3.21: 9089 3.21 - 3.77: 14396 3.77 - 4.34: 20067 4.34 - 4.90: 33017 Nonbonded interactions: 76748 Sorted by model distance: nonbonded pdb=" O GLN F 129 " pdb=" NZ LYS F 188 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR A 273 " pdb=" OE2 GLU B 359 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN F 150 " pdb=" OG1 THR F 202 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 359 " pdb=" OH TYR B 273 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN D 150 " pdb=" OG1 THR D 202 " model vdw 2.171 3.040 ... (remaining 76743 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 271 through 339 or (resid 340 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or resid 341 through 448)) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 121 or (resid 122 through 126 and ( \ name N or name CA or name C or name O or name CB )) or resid 127 through 224)) } ncs_group { reference = (chain 'D' and (resid 1 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 216)) selection = chain 'F' } 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 group one per residue 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: 1.160 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.006 0.056 9435 Z= 0.380 Angle : 0.825 8.217 12908 Z= 0.450 Chirality : 0.046 0.183 1539 Planarity : 0.005 0.040 1612 Dihedral : 13.616 86.716 3228 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.87 (0.23), residues: 1224 helix: -1.18 (0.29), residues: 310 sheet: -2.12 (0.23), residues: 418 loop : -1.95 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.011 0.001 HIS F 39 PHE 0.024 0.002 PHE E 177 TYR 0.026 0.002 TYR E 133 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 LYS cc_start: 0.8128 (tppt) cc_final: 0.7892 (mmmt) REVERT: F 188 LYS cc_start: 0.6456 (mmtt) cc_final: 0.6156 (mmtt) REVERT: E 109 TYR cc_start: 0.7789 (t80) cc_final: 0.7515 (t80) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.2102 time to fit residues: 73.7223 Evaluate side-chains 215 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 HIS F 6 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 58 ASN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS E 39 GLN E 104 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115300 restraints weight = 13608.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115606 restraints weight = 11992.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116266 restraints weight = 9426.493| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9435 Z= 0.229 Angle : 0.703 9.674 12908 Z= 0.361 Chirality : 0.045 0.171 1539 Planarity : 0.005 0.036 1612 Dihedral : 5.626 43.405 1322 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.28 % Allowed : 11.72 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.52 (0.24), residues: 1224 helix: -1.05 (0.28), residues: 328 sheet: -1.84 (0.25), residues: 390 loop : -1.75 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 288 HIS 0.003 0.001 HIS F 39 PHE 0.013 0.001 PHE E 177 TYR 0.015 0.001 TYR E 109E ARG 0.005 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 297 MET cc_start: 0.6958 (ttp) cc_final: 0.6681 (ttm) REVERT: D 128 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 180 MET cc_start: 0.7666 (ttt) cc_final: 0.7464 (ttt) REVERT: F 172 ASP cc_start: 0.7078 (t70) cc_final: 0.6792 (t0) REVERT: F 175 ASP cc_start: 0.8113 (p0) cc_final: 0.7768 (p0) REVERT: E 175 HIS cc_start: 0.8470 (m-70) cc_final: 0.8260 (m170) outliers start: 23 outliers final: 15 residues processed: 255 average time/residue: 0.2074 time to fit residues: 73.9868 Evaluate side-chains 245 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 83 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119921 restraints weight = 13739.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120929 restraints weight = 11730.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122137 restraints weight = 10505.033| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9435 Z= 0.187 Angle : 0.668 14.338 12908 Z= 0.335 Chirality : 0.044 0.169 1539 Planarity : 0.004 0.035 1612 Dihedral : 5.328 40.329 1322 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.38 % Allowed : 14.10 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.15 (0.24), residues: 1224 helix: -0.79 (0.29), residues: 312 sheet: -1.60 (0.25), residues: 410 loop : -1.48 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 40 HIS 0.003 0.001 HIS D 39 PHE 0.010 0.001 PHE E 177 TYR 0.018 0.001 TYR F 145 ARG 0.004 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 288 TRP cc_start: 0.7014 (t-100) cc_final: 0.6536 (t60) REVERT: A 307 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 381 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: D 128 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7580 (tm-30) REVERT: D 194 HIS cc_start: 0.7043 (m170) cc_final: 0.6732 (m-70) REVERT: F 175 ASP cc_start: 0.8032 (p0) cc_final: 0.7776 (p0) REVERT: F 212 LYS cc_start: 0.8637 (tptt) cc_final: 0.8370 (tppt) outliers start: 34 outliers final: 24 residues processed: 250 average time/residue: 0.2069 time to fit residues: 71.9415 Evaluate side-chains 246 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 14 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3839 r_free = 0.3839 target = 0.155970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121619 restraints weight = 13600.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118804 restraints weight = 13191.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121281 restraints weight = 12676.397| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9435 Z= 0.216 Angle : 0.662 14.574 12908 Z= 0.330 Chirality : 0.044 0.170 1539 Planarity : 0.004 0.034 1612 Dihedral : 5.150 40.135 1322 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.67 % Allowed : 15.99 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.01 (0.24), residues: 1224 helix: -0.66 (0.29), residues: 312 sheet: -1.49 (0.25), residues: 410 loop : -1.43 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 36 HIS 0.003 0.001 HIS E 175 PHE 0.011 0.001 PHE E 177 TYR 0.020 0.001 TYR D 145 ARG 0.004 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 381 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: B 303 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8894 (tt) REVERT: D 128 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7601 (tm-30) REVERT: D 153 TRP cc_start: 0.7201 (m100) cc_final: 0.6860 (m100) REVERT: F 92 PHE cc_start: 0.9046 (m-80) cc_final: 0.8709 (m-10) outliers start: 37 outliers final: 26 residues processed: 252 average time/residue: 0.2029 time to fit residues: 71.5962 Evaluate side-chains 242 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3857 r_free = 0.3857 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120704 restraints weight = 13556.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120755 restraints weight = 11221.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122027 restraints weight = 11288.437| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9435 Z= 0.197 Angle : 0.639 10.815 12908 Z= 0.323 Chirality : 0.044 0.231 1539 Planarity : 0.004 0.034 1612 Dihedral : 4.991 39.388 1322 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.27 % Allowed : 16.78 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.81 (0.24), residues: 1224 helix: -0.58 (0.29), residues: 312 sheet: -1.24 (0.25), residues: 400 loop : -1.37 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 36 HIS 0.003 0.001 HIS F 194 PHE 0.009 0.001 PHE E 177 TYR 0.021 0.001 TYR D 145 ARG 0.005 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 354 ARG cc_start: 0.8097 (tmm-80) cc_final: 0.7542 (ttp80) REVERT: A 381 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: B 292 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7636 (mt) REVERT: B 303 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 351 ASP cc_start: 0.7953 (t0) cc_final: 0.7751 (t0) REVERT: B 354 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7886 (tmm-80) REVERT: D 128 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7634 (tm-30) REVERT: F 193 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7369 (ptt180) outliers start: 43 outliers final: 31 residues processed: 241 average time/residue: 0.2139 time to fit residues: 71.8016 Evaluate side-chains 245 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.158953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122559 restraints weight = 13442.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122291 restraints weight = 11613.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124083 restraints weight = 10486.165| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9435 Z= 0.187 Angle : 0.626 9.834 12908 Z= 0.315 Chirality : 0.044 0.196 1539 Planarity : 0.004 0.033 1612 Dihedral : 4.865 39.103 1322 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.57 % Allowed : 17.38 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.60 (0.24), residues: 1224 helix: -0.42 (0.29), residues: 312 sheet: -0.98 (0.26), residues: 396 loop : -1.38 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 352 HIS 0.003 0.001 HIS F 194 PHE 0.008 0.001 PHE E 177 TYR 0.022 0.001 TYR F 145 ARG 0.005 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 354 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7554 (ttp80) REVERT: A 381 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: B 292 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7578 (mt) REVERT: B 342 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 351 ASP cc_start: 0.8031 (t0) cc_final: 0.7753 (t0) REVERT: B 354 ARG cc_start: 0.8161 (tmm-80) cc_final: 0.7816 (tmm-80) REVERT: D 128 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7701 (tm-30) REVERT: F 92 PHE cc_start: 0.9024 (m-80) cc_final: 0.8717 (m-10) REVERT: F 95 GLN cc_start: 0.9026 (pp30) cc_final: 0.8717 (pp30) REVERT: F 193 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7414 (ptt180) REVERT: E 219 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7522 (mtmm) outliers start: 46 outliers final: 31 residues processed: 240 average time/residue: 0.2226 time to fit residues: 75.4559 Evaluate side-chains 244 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 219 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 55 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 171 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3868 r_free = 0.3868 target = 0.158467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122089 restraints weight = 13612.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121874 restraints weight = 11293.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123418 restraints weight = 10967.906| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9435 Z= 0.201 Angle : 0.629 9.234 12908 Z= 0.318 Chirality : 0.044 0.181 1539 Planarity : 0.004 0.033 1612 Dihedral : 4.816 38.589 1322 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.47 % Allowed : 18.47 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.46 (0.25), residues: 1224 helix: -0.33 (0.29), residues: 312 sheet: -0.94 (0.26), residues: 410 loop : -1.23 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 352 HIS 0.003 0.001 HIS F 194 PHE 0.008 0.001 PHE E 177 TYR 0.023 0.001 TYR D 145 ARG 0.003 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 354 ARG cc_start: 0.8096 (tmm-80) cc_final: 0.7602 (ttp80) REVERT: A 381 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: B 342 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 351 ASP cc_start: 0.8049 (t0) cc_final: 0.7734 (t0) REVERT: B 354 ARG cc_start: 0.8160 (tmm-80) cc_final: 0.7805 (tmm-80) REVERT: D 128 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7734 (tm-30) REVERT: F 153 TRP cc_start: 0.7153 (m100) cc_final: 0.6697 (m100) REVERT: F 193 ARG cc_start: 0.7739 (mtm180) cc_final: 0.7523 (ptt180) REVERT: F 194 HIS cc_start: 0.6064 (m-70) cc_final: 0.5787 (m170) REVERT: E 219 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7569 (mtmm) outliers start: 45 outliers final: 31 residues processed: 248 average time/residue: 0.2022 time to fit residues: 70.3581 Evaluate side-chains 247 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 219 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 83 optimal weight: 0.0000 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 116 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 194 HIS ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123467 restraints weight = 13721.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123617 restraints weight = 11547.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125455 restraints weight = 8447.220| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9435 Z= 0.193 Angle : 0.628 8.760 12908 Z= 0.317 Chirality : 0.044 0.196 1539 Planarity : 0.004 0.035 1612 Dihedral : 4.773 38.405 1322 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.77 % Allowed : 19.46 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.29 (0.25), residues: 1224 helix: -0.22 (0.29), residues: 312 sheet: -0.67 (0.26), residues: 400 loop : -1.27 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 352 HIS 0.003 0.001 HIS F 194 PHE 0.007 0.001 PHE E 177 TYR 0.023 0.001 TYR D 145 ARG 0.008 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8086 (tmm-80) cc_final: 0.7621 (ttp80) REVERT: A 381 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: B 342 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8676 (mp) REVERT: B 351 ASP cc_start: 0.8000 (t0) cc_final: 0.7701 (t0) REVERT: B 354 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7846 (tmm-80) REVERT: D 128 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7731 (tm-30) REVERT: F 95 GLN cc_start: 0.9084 (pp30) cc_final: 0.8764 (pp30) REVERT: F 153 TRP cc_start: 0.7132 (m100) cc_final: 0.6679 (m100) REVERT: F 194 HIS cc_start: 0.6100 (m-70) cc_final: 0.5846 (m170) REVERT: E 219 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7526 (mtmm) outliers start: 38 outliers final: 31 residues processed: 241 average time/residue: 0.2136 time to fit residues: 71.5149 Evaluate side-chains 248 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 219 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3869 r_free = 0.3869 target = 0.158685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121260 restraints weight = 13558.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120962 restraints weight = 11496.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123299 restraints weight = 9701.390| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9435 Z= 0.224 Angle : 0.640 8.003 12908 Z= 0.323 Chirality : 0.044 0.208 1539 Planarity : 0.004 0.037 1612 Dihedral : 4.778 37.820 1322 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.77 % Allowed : 20.06 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.21 (0.25), residues: 1224 helix: -0.20 (0.29), residues: 312 sheet: -0.65 (0.26), residues: 410 loop : -1.17 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 352 HIS 0.005 0.001 HIS F 194 PHE 0.010 0.001 PHE A 306 TYR 0.022 0.001 TYR D 145 ARG 0.010 0.001 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.8386 (mm) cc_final: 0.8000 (mt) REVERT: A 354 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7643 (ttp80) REVERT: A 381 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: B 351 ASP cc_start: 0.8041 (t0) cc_final: 0.7735 (t0) REVERT: B 354 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7802 (tmm-80) REVERT: D 128 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7719 (tm-30) REVERT: E 219 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7641 (mtmm) outliers start: 38 outliers final: 32 residues processed: 235 average time/residue: 0.2122 time to fit residues: 69.3723 Evaluate side-chains 244 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 219 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 85 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 99 optimal weight: 0.0870 chunk 68 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 171 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 171 GLN ** 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 = 0.3887 r_free = 0.3887 target = 0.160272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123646 restraints weight = 13626.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122886 restraints weight = 12132.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125321 restraints weight = 11131.133| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9435 Z= 0.196 Angle : 0.639 8.192 12908 Z= 0.324 Chirality : 0.044 0.200 1539 Planarity : 0.004 0.037 1612 Dihedral : 4.761 38.372 1322 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.18 % Allowed : 20.95 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.08 (0.25), residues: 1224 helix: -0.08 (0.29), residues: 312 sheet: -0.46 (0.27), residues: 400 loop : -1.19 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 352 HIS 0.004 0.001 HIS F 194 PHE 0.007 0.001 PHE E 177 TYR 0.021 0.001 TYR D 145 ARG 0.009 0.001 ARG D 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8105 (tmm-80) cc_final: 0.7619 (ttp80) REVERT: A 381 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 351 ASP cc_start: 0.8022 (t0) cc_final: 0.7727 (t0) REVERT: B 354 ARG cc_start: 0.8217 (tmm-80) cc_final: 0.7847 (tmm-80) REVERT: D 128 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 95 GLN cc_start: 0.9027 (pp30) cc_final: 0.8713 (pp30) REVERT: E 219 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7622 (mtmm) outliers start: 32 outliers final: 28 residues processed: 233 average time/residue: 0.2032 time to fit residues: 66.0298 Evaluate side-chains 237 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 160 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 219 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN F 58 ASN ** F 171 GLN ** 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 = 0.3894 r_free = 0.3894 target = 0.160828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123713 restraints weight = 13647.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123713 restraints weight = 11169.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125447 restraints weight = 9821.809| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9435 Z= 0.196 Angle : 0.635 8.027 12908 Z= 0.322 Chirality : 0.044 0.196 1539 Planarity : 0.004 0.038 1612 Dihedral : 4.731 37.579 1322 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.28 % Allowed : 21.25 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.01 (0.25), residues: 1224 helix: 0.03 (0.29), residues: 312 sheet: -0.51 (0.27), residues: 410 loop : -1.11 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 352 HIS 0.013 0.001 HIS F 194 PHE 0.007 0.001 PHE E 177 TYR 0.021 0.001 TYR D 145 ARG 0.009 0.001 ARG F 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.32 seconds wall clock time: 59 minutes 47.58 seconds (3587.58 seconds total)