Starting phenix.real_space_refine on Thu Mar 13 18:34:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lbh_0869/03_2025/6lbh_0869.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lbh_0869/03_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_0869/03_2025/6lbh_0869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2025/6lbh_0869.map" model { file = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_2025/6lbh_0869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lbh_0869/03_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-5624/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: 6.12, per 1000 atoms: 0.66 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: 2.55 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: 1.30 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: 3.01 Time building geometry restraints manager: 2.96 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.690 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- 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 : 1.033 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: 0.2058 time to fit residues: 72.7101 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 : 1.037 ------------------------------------------------------------------------------- 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 = 0.153273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115303 restraints weight = 13608.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115611 restraints weight = 11992.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116282 restraints weight = 9431.703| |-----------------------------------------------------------------------------| 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 : 1.053 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: 0.7668 (ttt) cc_final: 0.7463 (ttt) REVERT: F 172 ASP cc_start: 0.7078 (t70) cc_final: 0.6793 (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: 0.8258 (m170) outliers start: 23 outliers final: 15 residues processed: 255 average time/residue: 0.1997 time to fit residues: 71.5753 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 : 1.024 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116636 restraints weight = 13849.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115016 restraints weight = 12913.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116864 restraints weight = 14662.112| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9435 Z= 0.261 Angle : 0.690 12.583 12908 Z= 0.348 Chirality : 0.045 0.171 1539 Planarity : 0.004 0.036 1612 Dihedral : 5.433 40.886 1322 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.57 % Allowed : 13.60 % Favored : 82.82 % 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: -2.33 (0.24), residues: 1224 helix: -0.93 (0.28), residues: 326 sheet: -1.67 (0.25), residues: 410 loop : -1.63 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 168 HIS 0.003 0.001 HIS D 39 PHE 0.013 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 271 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 288 TRP cc_start: 0.7082 (t-100) cc_final: 0.6694 (t60) REVERT: A 292 LEU cc_start: 0.8453 (tt) cc_final: 0.8131 (mt) REVERT: A 307 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 381 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7168 (m-30) REVERT: B 303 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8943 (tt) REVERT: D 128 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7586 (tm-30) REVERT: D 194 HIS cc_start: 0.7109 (m170) cc_final: 0.6837 (m170) REVERT: F 175 ASP cc_start: 0.8088 (p0) cc_final: 0.7849 (p0) outliers start: 36 outliers final: 25 residues processed: 249 average time/residue: 0.2052 time to fit residues: 71.3616 Evaluate side-chains 250 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 18 VAL Chi-restraints excluded: chain E residue 37 VAL 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 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** 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 = 0.3787 r_free = 0.3787 target = 0.151202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116392 restraints weight = 13689.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112950 restraints weight = 13849.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114974 restraints weight = 12955.710| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9435 Z= 0.294 Angle : 0.680 9.350 12908 Z= 0.346 Chirality : 0.045 0.171 1539 Planarity : 0.004 0.035 1612 Dihedral : 5.353 40.587 1322 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.97 % Allowed : 15.69 % 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: -2.25 (0.24), residues: 1224 helix: -0.91 (0.28), residues: 328 sheet: -1.60 (0.24), residues: 410 loop : -1.56 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 168 HIS 0.003 0.001 HIS F 194 PHE 0.013 0.001 PHE E 177 TYR 0.021 0.002 TYR D 145 ARG 0.003 0.000 ARG B 354 *********************** 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 269 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.105 Fit side-chains REVERT: A 292 LEU cc_start: 0.8538 (tt) cc_final: 0.8077 (mp) REVERT: A 307 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 381 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: B 303 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8983 (tt) REVERT: D 128 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7571 (tm-30) outliers start: 40 outliers final: 31 residues processed: 249 average time/residue: 0.2573 time to fit residues: 89.6425 Evaluate side-chains 254 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 356 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 303 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 102 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 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 102 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 37 VAL 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 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: 0.7980 chunk 70 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN F 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117104 restraints weight = 13674.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115223 restraints weight = 13306.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117521 restraints weight = 12239.977| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9435 Z= 0.257 Angle : 0.667 8.976 12908 Z= 0.337 Chirality : 0.045 0.175 1539 Planarity : 0.004 0.035 1612 Dihedral : 5.240 40.244 1322 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.37 % Allowed : 16.88 % Favored : 78.75 % 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: -2.07 (0.24), residues: 1224 helix: -0.82 (0.29), residues: 314 sheet: -1.53 (0.25), residues: 406 loop : -1.38 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 168 HIS 0.003 0.001 HIS D 194 PHE 0.009 0.001 PHE E 177 TYR 0.021 0.001 TYR F 145 ARG 0.006 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 275 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 354 ARG cc_start: 0.8173 (tmm-80) cc_final: 0.7957 (tmm-80) REVERT: A 381 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: D 128 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 44 outliers final: 31 residues processed: 256 average time/residue: 0.2441 time to fit residues: 88.6072 Evaluate side-chains 247 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 356 PHE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 313 VAL 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 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 18 VAL 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 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- 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 6 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN E 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118321 restraints weight = 13642.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114624 restraints weight = 16052.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116375 restraints weight = 14725.140| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9435 Z= 0.298 Angle : 0.678 9.440 12908 Z= 0.345 Chirality : 0.045 0.180 1539 Planarity : 0.004 0.034 1612 Dihedral : 5.208 39.871 1322 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.06 % Allowed : 17.97 % Favored : 76.96 % 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: -2.04 (0.24), residues: 1224 helix: -0.81 (0.28), residues: 326 sheet: -1.42 (0.25), residues: 406 loop : -1.46 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 36 HIS 0.003 0.001 HIS F 194 PHE 0.011 0.001 PHE E 177 TYR 0.022 0.001 TYR D 145 ARG 0.006 0.000 ARG D 113 *********************** 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 277 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 381 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: D 128 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 219 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7681 (mtmm) outliers start: 51 outliers final: 37 residues processed: 257 average time/residue: 0.2013 time to fit residues: 72.7546 Evaluate side-chains 250 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 298 VAL 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 297 MET Chi-restraints excluded: chain B residue 313 VAL 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 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 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 63 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 CYS 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 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: 20.0000 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 116 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118568 restraints weight = 13809.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115643 restraints weight = 12898.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117126 restraints weight = 12171.791| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9435 Z= 0.259 Angle : 0.673 9.166 12908 Z= 0.340 Chirality : 0.045 0.187 1539 Planarity : 0.004 0.036 1612 Dihedral : 5.180 39.974 1322 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.67 % Allowed : 19.27 % Favored : 76.07 % 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: -1.85 (0.24), residues: 1224 helix: -0.69 (0.29), residues: 312 sheet: -1.18 (0.25), residues: 396 loop : -1.43 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 36 HIS 0.003 0.001 HIS F 39 PHE 0.035 0.001 PHE F 140 TYR 0.020 0.001 TYR F 145 ARG 0.005 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 263 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 354 ARG cc_start: 0.8141 (tmm-80) cc_final: 0.7926 (tmm-80) REVERT: A 381 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: D 128 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 104 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8979 (t0) REVERT: E 219 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (mtmm) outliers start: 47 outliers final: 35 residues processed: 243 average time/residue: 0.1945 time to fit residues: 66.9426 Evaluate side-chains 248 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 298 VAL 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 297 MET Chi-restraints excluded: chain B residue 313 VAL 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 63 VAL 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 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 104 ASN 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 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: 0.8980 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119835 restraints weight = 13931.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116829 restraints weight = 12569.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118663 restraints weight = 14464.417| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9435 Z= 0.237 Angle : 0.655 8.999 12908 Z= 0.332 Chirality : 0.044 0.193 1539 Planarity : 0.004 0.035 1612 Dihedral : 5.082 39.417 1322 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.97 % Allowed : 19.66 % Favored : 75.37 % 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: -1.69 (0.25), residues: 1224 helix: -0.62 (0.29), residues: 312 sheet: -1.07 (0.25), residues: 400 loop : -1.31 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 36 HIS 0.003 0.001 HIS F 39 PHE 0.023 0.001 PHE F 140 TYR 0.021 0.001 TYR F 145 ARG 0.005 0.000 ARG B 354 *********************** 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 269 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7898 (tmm-80) REVERT: A 381 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: D 128 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7771 (tm-30) REVERT: D 172 ASP cc_start: 0.6481 (t70) cc_final: 0.6252 (t0) REVERT: D 175 ASP cc_start: 0.8415 (p0) cc_final: 0.8135 (p0) REVERT: F 175 ASP cc_start: 0.8278 (p0) cc_final: 0.7956 (p0) REVERT: E 219 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7749 (ptpp) outliers start: 50 outliers final: 39 residues processed: 249 average time/residue: 0.2302 time to fit residues: 80.8639 Evaluate side-chains 255 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 298 VAL 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 336 THR Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 369 THR 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 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 63 VAL 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 112 ASP 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 63 VAL 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 72 VAL Chi-restraints excluded: chain E residue 112 ASP 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 192 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: 3.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.0570 chunk 41 optimal weight: 0.0060 overall best weight: 0.5114 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN E 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122338 restraints weight = 13635.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121267 restraints weight = 13699.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123163 restraints weight = 11862.109| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3091 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= 0.196 Angle : 0.659 10.408 12908 Z= 0.332 Chirality : 0.044 0.316 1539 Planarity : 0.004 0.033 1612 Dihedral : 4.977 39.121 1322 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.47 % Allowed : 20.85 % Favored : 74.68 % 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: -1.52 (0.25), residues: 1224 helix: -0.45 (0.29), residues: 312 sheet: -0.94 (0.26), residues: 400 loop : -1.25 (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 39 PHE 0.018 0.001 PHE F 140 TYR 0.022 0.001 TYR D 91 ARG 0.005 0.001 ARG B 354 *********************** 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 259 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8561 (mp) REVERT: D 128 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7776 (tm-30) REVERT: D 172 ASP cc_start: 0.6368 (t70) cc_final: 0.6124 (t0) REVERT: D 175 ASP cc_start: 0.8326 (p0) cc_final: 0.8095 (p0) REVERT: E 219 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7805 (ptpp) outliers start: 45 outliers final: 32 residues processed: 242 average time/residue: 0.2780 time to fit residues: 96.2091 Evaluate side-chains 238 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 298 VAL 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 337 LEU Chi-restraints excluded: chain A residue 369 THR 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 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 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 63 VAL Chi-restraints excluded: chain F residue 155 ILE 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 192 VAL 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: 6.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 99 optimal weight: 0.0000 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN E 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121883 restraints weight = 13809.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120764 restraints weight = 12266.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122480 restraints weight = 12532.501| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3268 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= 0.209 Angle : 0.654 9.535 12908 Z= 0.328 Chirality : 0.045 0.281 1539 Planarity : 0.004 0.034 1612 Dihedral : 4.891 38.477 1322 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.67 % Allowed : 22.05 % Favored : 74.28 % 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: -1.38 (0.25), residues: 1224 helix: -0.41 (0.29), residues: 312 sheet: -0.73 (0.26), residues: 400 loop : -1.23 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 36 HIS 0.006 0.001 HIS F 194 PHE 0.019 0.001 PHE F 140 TYR 0.022 0.001 TYR F 145 ARG 0.005 0.000 ARG A 354 ********************** 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 245 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8660 (mp) REVERT: D 128 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 212 LYS cc_start: 0.8675 (tppt) cc_final: 0.8392 (tppt) REVERT: E 219 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7660 (mtmm) outliers start: 37 outliers final: 33 residues processed: 233 average time/residue: 0.2495 time to fit residues: 82.9422 Evaluate side-chains 240 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 298 VAL 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 337 LEU Chi-restraints excluded: chain A residue 369 THR 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 63 VAL 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 63 VAL Chi-restraints excluded: chain F residue 155 ILE 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 192 VAL 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: 7.9990 chunk 84 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.0030 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN E 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123125 restraints weight = 13738.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119893 restraints weight = 12729.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121924 restraints weight = 12155.414| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3319 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= 0.220 Angle : 0.665 9.374 12908 Z= 0.335 Chirality : 0.045 0.277 1539 Planarity : 0.004 0.034 1612 Dihedral : 4.896 38.478 1322 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.07 % Allowed : 21.25 % Favored : 74.68 % 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: -1.26 (0.25), residues: 1224 helix: -0.32 (0.29), residues: 312 sheet: -0.60 (0.26), residues: 400 loop : -1.21 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 36 HIS 0.007 0.001 HIS F 194 PHE 0.019 0.001 PHE F 140 TYR 0.022 0.001 TYR F 145 ARG 0.007 0.001 ARG A 354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.68 seconds wall clock time: 67 minutes 37.18 seconds (4057.18 seconds total)