Starting phenix.real_space_refine on Sat May 17 13:29:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz5_37947/05_2025/8wz5_37947.cif" } resolution = 3.51 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= 0.016 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 99 5.16 5 C 9903 2.51 5 N 2583 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15645 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3476 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 435} Chain breaks: 1 Chain: "E" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 909 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Restraints were copied for chains: C, B, D, H, F, L Time building chain proxies: 8.12, per 1000 atoms: 0.52 Number of scatterers: 15645 At special positions: 0 Unit cell: (144.708, 147.042, 122.924, 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 99 16.00 O 3060 8.00 N 2583 7.00 C 9903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS C 458 " distance=1.91 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.10 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=1.88 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS B 149 " distance=1.91 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=1.64 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS B 458 " distance=1.91 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.10 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.10 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=1.88 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=1.88 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: 3.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 25.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.067A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 207 removed outlier: 4.784A pdb=" N LEU A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 230 " --> pdb=" O MET A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 516 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.958A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.067A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 207 removed outlier: 4.784A pdb=" N LEU B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 477 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 516 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.957A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 99 removed outlier: 4.066A pdb=" N ASN C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 207 removed outlier: 4.783A pdb=" N LEU C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 230 " --> pdb=" O MET C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 477 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 516 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.958A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.653A pdb=" N ASP A 344 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 3.573A pdb=" N ALA A 177 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A 51 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 303 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 291 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 416 removed outlier: 3.862A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.795A pdb=" N ILE A 432 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.021A pdb=" N GLN L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.497A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.652A pdb=" N ASP B 344 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 180 removed outlier: 3.573A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 51 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 303 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 291 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AC2, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AC3, first strand: chain 'B' and resid 411 through 416 removed outlier: 3.863A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.795A pdb=" N ILE B 432 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.022A pdb=" N GLN F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.496A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AD4, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.653A pdb=" N ASP C 344 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.574A pdb=" N ALA C 177 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY C 51 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 303 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 291 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AD7, first strand: chain 'C' and resid 359 through 361 Processing sheet with id=AD8, first strand: chain 'C' and resid 411 through 416 removed outlier: 3.862A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.796A pdb=" N ILE C 432 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU E 10 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU E 10 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.022A pdb=" N GLN G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.497A pdb=" N THR G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1665 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: 6.43 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2574 1.30 - 1.44: 4239 1.44 - 1.57: 8997 1.57 - 1.70: 0 1.70 - 1.83: 132 Bond restraints: 15942 Sorted by residual: bond pdb=" C THR C 335 " pdb=" O THR C 335 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.36e-02 5.41e+03 2.08e+01 bond pdb=" C THR A 335 " pdb=" O THR A 335 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.36e-02 5.41e+03 2.08e+01 bond pdb=" C THR B 335 " pdb=" O THR B 335 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.36e-02 5.41e+03 2.07e+01 bond pdb=" C ILE A 148 " pdb=" O ILE A 148 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.19e-02 7.06e+03 2.07e+01 bond pdb=" C ILE C 148 " pdb=" O ILE C 148 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.19e-02 7.06e+03 2.06e+01 ... (remaining 15937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 21221 2.76 - 5.52: 312 5.52 - 8.28: 47 8.28 - 11.04: 26 11.04 - 13.80: 9 Bond angle restraints: 21615 Sorted by residual: angle pdb=" O CYS C 333 " pdb=" C CYS C 333 " pdb=" N LEU C 334 " ideal model delta sigma weight residual 123.42 112.54 10.88 1.07e+00 8.73e-01 1.03e+02 angle pdb=" O CYS B 333 " pdb=" C CYS B 333 " pdb=" N LEU B 334 " ideal model delta sigma weight residual 123.42 112.55 10.87 1.07e+00 8.73e-01 1.03e+02 angle pdb=" O CYS A 333 " pdb=" C CYS A 333 " pdb=" N LEU A 334 " ideal model delta sigma weight residual 123.42 112.56 10.86 1.07e+00 8.73e-01 1.03e+02 angle pdb=" N SER A 146 " pdb=" CA SER A 146 " pdb=" C SER A 146 " ideal model delta sigma weight residual 113.19 105.48 7.71 1.19e+00 7.06e-01 4.19e+01 angle pdb=" N SER B 146 " pdb=" CA SER B 146 " pdb=" C SER B 146 " ideal model delta sigma weight residual 113.19 105.49 7.70 1.19e+00 7.06e-01 4.19e+01 ... (remaining 21610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 8452 17.59 - 35.18: 883 35.18 - 52.76: 244 52.76 - 70.35: 57 70.35 - 87.94: 15 Dihedral angle restraints: 9651 sinusoidal: 3795 harmonic: 5856 Sorted by residual: dihedral pdb=" CB CYS B 458 " pdb=" SG CYS B 458 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 151.80 -58.80 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 149 " pdb=" SG CYS A 149 " pdb=" SG CYS C 458 " pdb=" CB CYS C 458 " ideal model delta sinusoidal sigma weight residual 93.00 151.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 151.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2115 0.062 - 0.125: 331 0.125 - 0.187: 35 0.187 - 0.250: 9 0.250 - 0.312: 12 Chirality restraints: 2502 Sorted by residual: chirality pdb=" CA ILE B 395 " pdb=" N ILE B 395 " pdb=" C ILE B 395 " pdb=" CB ILE B 395 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE C 395 " pdb=" N ILE C 395 " pdb=" C ILE C 395 " pdb=" CB ILE C 395 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2499 not shown) Planarity restraints: 2727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 333 " 0.040 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C CYS C 333 " -0.127 2.00e-02 2.50e+03 pdb=" O CYS C 333 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU C 334 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 333 " 0.040 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C CYS B 333 " -0.127 2.00e-02 2.50e+03 pdb=" O CYS B 333 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU B 334 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 333 " 0.040 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C CYS A 333 " -0.127 2.00e-02 2.50e+03 pdb=" O CYS A 333 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU A 334 " 0.042 2.00e-02 2.50e+03 ... (remaining 2724 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 16 2.29 - 2.94: 7063 2.94 - 3.59: 22024 3.59 - 4.25: 33836 4.25 - 4.90: 58189 Nonbonded interactions: 121128 Sorted by model distance: nonbonded pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " model vdw 1.637 3.760 nonbonded pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " model vdw 1.638 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS B 458 " pdb=" CA CYS C 149 " model vdw 2.156 3.064 ... (remaining 121123 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'L' } 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: 10.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.470 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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 0.394 15971 Z= 0.328 Angle : 1.064 34.147 21673 Z= 0.587 Chirality : 0.051 0.312 2502 Planarity : 0.006 0.085 2727 Dihedral : 15.773 87.940 5802 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.83 % Allowed : 22.37 % Favored : 76.79 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1989 helix: 1.60 (0.26), residues: 429 sheet: -1.13 (0.22), residues: 618 loop : -1.91 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.002 0.001 HIS C 317 PHE 0.020 0.001 PHE F 46 TYR 0.019 0.001 TYR A 457 ARG 0.018 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.21285 ( 615) hydrogen bonds : angle 8.43952 ( 1665) SS BOND : bond 0.09851 ( 29) SS BOND : angle 11.84262 ( 58) covalent geometry : bond 0.00412 (15942) covalent geometry : angle 0.87121 (21615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 346 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6930 (mmt90) REVERT: A 451 SER cc_start: 0.8555 (t) cc_final: 0.7791 (p) REVERT: A 465 GLN cc_start: 0.6702 (mt0) cc_final: 0.6426 (tp40) REVERT: H 12 LYS cc_start: 0.7942 (mttt) cc_final: 0.7699 (ptmt) REVERT: L 46 PHE cc_start: 0.7301 (p90) cc_final: 0.7042 (p90) REVERT: B 42 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6794 (mmt90) REVERT: B 76 VAL cc_start: 0.8825 (t) cc_final: 0.8582 (p) REVERT: B 202 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6682 (mmm-85) REVERT: B 510 ASP cc_start: 0.9235 (m-30) cc_final: 0.9018 (p0) REVERT: F 46 PHE cc_start: 0.7335 (p90) cc_final: 0.7076 (p90) REVERT: C 42 ARG cc_start: 0.7164 (mmm-85) cc_final: 0.6910 (mmt90) REVERT: C 465 GLN cc_start: 0.6676 (mt0) cc_final: 0.6431 (tp40) REVERT: C 510 ASP cc_start: 0.9180 (m-30) cc_final: 0.8963 (p0) REVERT: E 38 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6942 (mmtt) outliers start: 15 outliers final: 9 residues processed: 352 average time/residue: 0.2960 time to fit residues: 149.0516 Evaluate side-chains 281 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 0.0970 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN E 82 GLN E 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.196380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160139 restraints weight = 21616.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160321 restraints weight = 14827.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161299 restraints weight = 17227.308| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15971 Z= 0.134 Angle : 0.590 9.849 21673 Z= 0.306 Chirality : 0.043 0.188 2502 Planarity : 0.003 0.024 2727 Dihedral : 4.634 42.571 2160 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.79 % Allowed : 23.21 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1989 helix: 1.86 (0.25), residues: 435 sheet: -1.42 (0.21), residues: 666 loop : -1.62 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.002 0.001 HIS B 317 PHE 0.019 0.001 PHE H 70 TYR 0.016 0.001 TYR C 299 ARG 0.005 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 615) hydrogen bonds : angle 5.58608 ( 1665) SS BOND : bond 0.00225 ( 29) SS BOND : angle 1.65021 ( 58) covalent geometry : bond 0.00315 (15942) covalent geometry : angle 0.58497 (21615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 305 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7632 (t0) cc_final: 0.7329 (t0) REVERT: A 222 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7181 (tp30) REVERT: H 48 MET cc_start: 0.7322 (mmt) cc_final: 0.6614 (mmp) REVERT: H 108 GLN cc_start: 0.7265 (pm20) cc_final: 0.7042 (pm20) REVERT: D 38 LYS cc_start: 0.7409 (mmtt) cc_final: 0.6219 (mmtt) REVERT: C 222 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: C 260 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 289 MET cc_start: 0.7983 (tpp) cc_final: 0.7075 (tpt) REVERT: C 410 LEU cc_start: 0.7368 (mt) cc_final: 0.6782 (tt) REVERT: C 433 LYS cc_start: 0.7664 (tptm) cc_final: 0.7421 (tttp) REVERT: E 48 MET cc_start: 0.7336 (mmt) cc_final: 0.7061 (mmt) REVERT: G 4 MET cc_start: 0.7687 (ttm) cc_final: 0.7480 (ttm) outliers start: 86 outliers final: 45 residues processed: 361 average time/residue: 0.2922 time to fit residues: 152.2175 Evaluate side-chains 326 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 108 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 277 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153793 restraints weight = 21865.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152726 restraints weight = 16337.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154012 restraints weight = 19938.099| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15971 Z= 0.259 Angle : 0.693 12.489 21673 Z= 0.358 Chirality : 0.046 0.221 2502 Planarity : 0.004 0.039 2727 Dihedral : 4.861 22.939 2154 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.34 % Allowed : 23.87 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1989 helix: 1.04 (0.24), residues: 474 sheet: -1.74 (0.20), residues: 678 loop : -1.78 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 106 HIS 0.014 0.002 HIS B 159 PHE 0.026 0.002 PHE E 70 TYR 0.023 0.002 TYR C 299 ARG 0.004 0.001 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 615) hydrogen bonds : angle 5.60224 ( 1665) SS BOND : bond 0.00556 ( 29) SS BOND : angle 1.66725 ( 58) covalent geometry : bond 0.00611 (15942) covalent geometry : angle 0.68853 (21615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7800 (t0) cc_final: 0.7391 (t0) REVERT: A 222 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: H 38 LYS cc_start: 0.7483 (mmtt) cc_final: 0.7241 (mmtt) REVERT: H 48 MET cc_start: 0.7460 (mmt) cc_final: 0.7218 (mpp) REVERT: B 275 SER cc_start: 0.8296 (t) cc_final: 0.7984 (p) REVERT: C 87 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8413 (mtmp) REVERT: C 222 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: C 260 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 266 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5805 (pt) REVERT: C 275 SER cc_start: 0.8326 (t) cc_final: 0.8044 (p) REVERT: C 433 LYS cc_start: 0.7666 (tptm) cc_final: 0.7418 (tttp) REVERT: E 38 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7199 (mmtt) REVERT: E 48 MET cc_start: 0.7539 (mmt) cc_final: 0.7328 (mmt) outliers start: 96 outliers final: 60 residues processed: 345 average time/residue: 0.2708 time to fit residues: 136.3862 Evaluate side-chains 328 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.195929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158060 restraints weight = 22011.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155657 restraints weight = 18273.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.158055 restraints weight = 16408.277| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15971 Z= 0.129 Angle : 0.586 12.086 21673 Z= 0.300 Chirality : 0.043 0.167 2502 Planarity : 0.003 0.031 2727 Dihedral : 4.415 20.396 2154 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.17 % Allowed : 25.21 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1989 helix: 1.46 (0.24), residues: 459 sheet: -1.75 (0.21), residues: 642 loop : -1.67 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 106 HIS 0.002 0.001 HIS B 317 PHE 0.024 0.002 PHE H 70 TYR 0.015 0.001 TYR G 87 ARG 0.006 0.001 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 615) hydrogen bonds : angle 5.11312 ( 1665) SS BOND : bond 0.00274 ( 29) SS BOND : angle 1.14910 ( 58) covalent geometry : bond 0.00311 (15942) covalent geometry : angle 0.58387 (21615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 294 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7833 (t0) cc_final: 0.7364 (t0) REVERT: H 38 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7263 (mmtt) REVERT: B 275 SER cc_start: 0.8261 (t) cc_final: 0.7903 (p) REVERT: D 38 LYS cc_start: 0.7660 (tptp) cc_final: 0.7221 (tptp) REVERT: F 87 TYR cc_start: 0.8141 (m-80) cc_final: 0.7857 (m-80) REVERT: C 266 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5605 (pt) REVERT: C 433 LYS cc_start: 0.7553 (tptm) cc_final: 0.7295 (tttp) outliers start: 75 outliers final: 55 residues processed: 341 average time/residue: 0.2689 time to fit residues: 135.3652 Evaluate side-chains 333 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 174 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN G 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.194930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157473 restraints weight = 22240.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158114 restraints weight = 15949.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159323 restraints weight = 17652.950| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15971 Z= 0.145 Angle : 0.604 13.371 21673 Z= 0.309 Chirality : 0.043 0.172 2502 Planarity : 0.003 0.031 2727 Dihedral : 4.430 20.812 2154 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.84 % Allowed : 25.38 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1989 helix: 1.55 (0.25), residues: 453 sheet: -1.80 (0.20), residues: 666 loop : -1.67 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 106 HIS 0.002 0.001 HIS A 317 PHE 0.023 0.001 PHE D 70 TYR 0.018 0.001 TYR C 299 ARG 0.005 0.000 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 615) hydrogen bonds : angle 5.04300 ( 1665) SS BOND : bond 0.00254 ( 29) SS BOND : angle 1.16249 ( 58) covalent geometry : bond 0.00352 (15942) covalent geometry : angle 0.60213 (21615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 286 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8396 (ttpt) REVERT: A 92 ASP cc_start: 0.7874 (t0) cc_final: 0.7391 (t0) REVERT: A 222 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7088 (tp30) REVERT: A 232 GLU cc_start: 0.6922 (mp0) cc_final: 0.6700 (mm-30) REVERT: A 316 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7329 (tt) REVERT: B 275 SER cc_start: 0.8257 (t) cc_final: 0.7940 (p) REVERT: D 38 LYS cc_start: 0.7588 (tptp) cc_final: 0.7205 (tptp) REVERT: F 87 TYR cc_start: 0.8046 (m-80) cc_final: 0.7830 (m-80) REVERT: C 222 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: C 260 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7674 (tt) REVERT: C 266 ILE cc_start: 0.5748 (OUTLIER) cc_final: 0.5467 (pt) REVERT: C 433 LYS cc_start: 0.7578 (tptm) cc_final: 0.7295 (tttp) REVERT: C 503 LEU cc_start: 0.8972 (tt) cc_final: 0.7818 (tt) outliers start: 87 outliers final: 63 residues processed: 342 average time/residue: 0.2705 time to fit residues: 135.9014 Evaluate side-chains 345 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 143 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN D 108 GLN F 38 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN E 108 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.194302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158398 restraints weight = 21844.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.158133 restraints weight = 15591.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.159677 restraints weight = 17673.315| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15971 Z= 0.116 Angle : 0.574 13.000 21673 Z= 0.295 Chirality : 0.042 0.164 2502 Planarity : 0.003 0.030 2727 Dihedral : 4.285 19.845 2154 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.79 % Allowed : 25.10 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1989 helix: 1.66 (0.25), residues: 453 sheet: -1.76 (0.20), residues: 666 loop : -1.61 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 106 HIS 0.002 0.001 HIS B 317 PHE 0.021 0.001 PHE D 70 TYR 0.014 0.001 TYR C 299 ARG 0.006 0.000 ARG C 507 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 615) hydrogen bonds : angle 4.87421 ( 1665) SS BOND : bond 0.00253 ( 29) SS BOND : angle 1.36710 ( 58) covalent geometry : bond 0.00285 (15942) covalent geometry : angle 0.57073 (21615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 288 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 92 ASP cc_start: 0.7752 (t0) cc_final: 0.7275 (t0) REVERT: A 222 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: A 232 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: A 316 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7142 (tt) REVERT: B 232 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: B 275 SER cc_start: 0.8255 (t) cc_final: 0.7942 (p) REVERT: D 38 LYS cc_start: 0.7529 (tptp) cc_final: 0.7091 (tptp) REVERT: D 106 TRP cc_start: 0.6713 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: C 222 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: C 260 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7655 (tt) REVERT: C 266 ILE cc_start: 0.5670 (OUTLIER) cc_final: 0.5403 (pt) REVERT: C 433 LYS cc_start: 0.7556 (tptm) cc_final: 0.7266 (tttp) REVERT: C 503 LEU cc_start: 0.9150 (tt) cc_final: 0.8915 (tt) outliers start: 86 outliers final: 53 residues processed: 343 average time/residue: 0.2742 time to fit residues: 137.1671 Evaluate side-chains 333 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 271 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 0.0070 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 181 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.199363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161572 restraints weight = 22100.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.159116 restraints weight = 16989.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161966 restraints weight = 16424.138| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 15971 Z= 0.110 Angle : 0.606 15.052 21673 Z= 0.306 Chirality : 0.042 0.154 2502 Planarity : 0.003 0.045 2727 Dihedral : 4.302 42.759 2154 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.90 % Allowed : 25.99 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.28 (0.19), residues: 1989 helix: 1.79 (0.25), residues: 450 sheet: -1.63 (0.21), residues: 660 loop : -1.55 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 106 HIS 0.002 0.001 HIS B 317 PHE 0.020 0.001 PHE G 46 TYR 0.014 0.001 TYR H 105 ARG 0.009 0.001 ARG C 429 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 615) hydrogen bonds : angle 4.80329 ( 1665) SS BOND : bond 0.00280 ( 29) SS BOND : angle 1.82176 ( 58) covalent geometry : bond 0.00277 (15942) covalent geometry : angle 0.59975 (21615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: A 92 ASP cc_start: 0.7895 (t0) cc_final: 0.7457 (t0) REVERT: A 232 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: A 433 LYS cc_start: 0.7323 (tptm) cc_final: 0.6970 (tttm) REVERT: L 87 TYR cc_start: 0.8205 (m-80) cc_final: 0.7873 (m-80) REVERT: B 92 ASP cc_start: 0.7650 (t0) cc_final: 0.7337 (t0) REVERT: B 232 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 275 SER cc_start: 0.8215 (t) cc_final: 0.7849 (p) REVERT: B 503 LEU cc_start: 0.9140 (tt) cc_final: 0.8844 (mm) REVERT: D 34 MET cc_start: 0.8120 (mmm) cc_final: 0.7712 (mmt) REVERT: D 106 TRP cc_start: 0.6628 (OUTLIER) cc_final: 0.6428 (m-90) REVERT: C 92 ASP cc_start: 0.7695 (t0) cc_final: 0.7380 (t0) REVERT: C 222 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: C 260 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7522 (tt) REVERT: C 289 MET cc_start: 0.8108 (tpp) cc_final: 0.7365 (tpt) REVERT: C 433 LYS cc_start: 0.7465 (tptm) cc_final: 0.7165 (tttp) REVERT: C 507 ARG cc_start: 0.8081 (ptp-170) cc_final: 0.7876 (mtm180) REVERT: E 48 MET cc_start: 0.7165 (mpp) cc_final: 0.6849 (mpp) outliers start: 70 outliers final: 47 residues processed: 326 average time/residue: 0.2884 time to fit residues: 137.7040 Evaluate side-chains 320 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.194530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158041 restraints weight = 21655.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157966 restraints weight = 15368.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159446 restraints weight = 17245.946| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 15971 Z= 0.135 Angle : 0.634 13.120 21673 Z= 0.320 Chirality : 0.043 0.262 2502 Planarity : 0.003 0.039 2727 Dihedral : 4.397 43.228 2154 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.01 % Allowed : 26.60 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.32 (0.19), residues: 1989 helix: 1.68 (0.25), residues: 453 sheet: -1.62 (0.21), residues: 654 loop : -1.59 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 50 HIS 0.002 0.001 HIS B 317 PHE 0.020 0.001 PHE G 46 TYR 0.034 0.001 TYR C 441 ARG 0.009 0.001 ARG C 429 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 615) hydrogen bonds : angle 4.87435 ( 1665) SS BOND : bond 0.00276 ( 29) SS BOND : angle 2.11947 ( 58) covalent geometry : bond 0.00343 (15942) covalent geometry : angle 0.62501 (21615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 1.769 Fit side-chains REVERT: A 81 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6929 (pm20) REVERT: A 92 ASP cc_start: 0.7798 (t0) cc_final: 0.7359 (t0) REVERT: A 222 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: A 433 LYS cc_start: 0.7450 (tptm) cc_final: 0.7075 (tttm) REVERT: L 87 TYR cc_start: 0.8126 (m-80) cc_final: 0.7856 (m-80) REVERT: B 92 ASP cc_start: 0.7575 (t0) cc_final: 0.7253 (t0) REVERT: B 232 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: B 275 SER cc_start: 0.8232 (t) cc_final: 0.7925 (p) REVERT: D 34 MET cc_start: 0.8055 (mmm) cc_final: 0.7669 (mmt) REVERT: D 106 TRP cc_start: 0.6762 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: C 222 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: C 260 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7590 (tt) REVERT: C 433 LYS cc_start: 0.7527 (tptm) cc_final: 0.7222 (tttp) outliers start: 72 outliers final: 53 residues processed: 317 average time/residue: 0.2947 time to fit residues: 135.8345 Evaluate side-chains 324 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 265 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 155 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 20 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 30.0000 overall best weight: 0.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.195247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159698 restraints weight = 21751.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.159083 restraints weight = 15821.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160545 restraints weight = 18280.217| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 15971 Z= 0.132 Angle : 0.652 14.052 21673 Z= 0.332 Chirality : 0.043 0.158 2502 Planarity : 0.004 0.062 2727 Dihedral : 4.540 44.644 2154 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.78 % Allowed : 26.82 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.31 (0.19), residues: 1989 helix: 1.77 (0.25), residues: 447 sheet: -1.63 (0.20), residues: 714 loop : -1.55 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS C 317 PHE 0.021 0.001 PHE G 46 TYR 0.030 0.001 TYR C 441 ARG 0.011 0.001 ARG A 429 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 615) hydrogen bonds : angle 4.94875 ( 1665) SS BOND : bond 0.00278 ( 29) SS BOND : angle 2.64167 ( 58) covalent geometry : bond 0.00341 (15942) covalent geometry : angle 0.63852 (21615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: A 92 ASP cc_start: 0.7787 (t0) cc_final: 0.7347 (t0) REVERT: A 222 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: A 433 LYS cc_start: 0.7407 (tptm) cc_final: 0.7027 (tttm) REVERT: A 503 LEU cc_start: 0.8876 (tt) cc_final: 0.8397 (mm) REVERT: L 87 TYR cc_start: 0.8098 (m-80) cc_final: 0.7854 (m-80) REVERT: B 92 ASP cc_start: 0.7667 (t0) cc_final: 0.7331 (t0) REVERT: B 232 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: B 275 SER cc_start: 0.8240 (t) cc_final: 0.7942 (p) REVERT: B 289 MET cc_start: 0.7914 (tpp) cc_final: 0.7394 (tpt) REVERT: C 222 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: C 260 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7590 (tt) REVERT: C 433 LYS cc_start: 0.7493 (tptm) cc_final: 0.7175 (tttp) REVERT: E 65 LYS cc_start: 0.6871 (mtpp) cc_final: 0.6666 (mtpp) outliers start: 68 outliers final: 53 residues processed: 319 average time/residue: 0.2828 time to fit residues: 131.5760 Evaluate side-chains 329 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 149 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN C 63 ASN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.194278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158111 restraints weight = 21804.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156538 restraints weight = 17148.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158695 restraints weight = 18518.793| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 15971 Z= 0.146 Angle : 0.693 24.277 21673 Z= 0.346 Chirality : 0.044 0.270 2502 Planarity : 0.004 0.061 2727 Dihedral : 4.592 41.242 2154 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.73 % Allowed : 27.38 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.36 (0.19), residues: 1989 helix: 1.67 (0.25), residues: 447 sheet: -1.63 (0.20), residues: 717 loop : -1.57 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 106 HIS 0.002 0.001 HIS A 317 PHE 0.019 0.001 PHE G 46 TYR 0.031 0.001 TYR C 441 ARG 0.012 0.001 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 615) hydrogen bonds : angle 5.03194 ( 1665) SS BOND : bond 0.00299 ( 29) SS BOND : angle 2.49731 ( 58) covalent geometry : bond 0.00378 (15942) covalent geometry : angle 0.68200 (21615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 1.629 Fit side-chains REVERT: A 81 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: A 92 ASP cc_start: 0.7828 (t0) cc_final: 0.7382 (t0) REVERT: A 222 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: A 433 LYS cc_start: 0.7466 (tptm) cc_final: 0.7076 (tttm) REVERT: L 87 TYR cc_start: 0.8153 (m-80) cc_final: 0.7875 (m-80) REVERT: B 92 ASP cc_start: 0.7686 (t0) cc_final: 0.7368 (t0) REVERT: B 232 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: B 275 SER cc_start: 0.8241 (t) cc_final: 0.7961 (p) REVERT: C 92 ASP cc_start: 0.7600 (t0) cc_final: 0.7354 (t0) REVERT: C 222 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: C 260 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7632 (tt) REVERT: C 507 ARG cc_start: 0.8084 (ptt180) cc_final: 0.7787 (mtm180) outliers start: 67 outliers final: 56 residues processed: 320 average time/residue: 0.2758 time to fit residues: 128.6391 Evaluate side-chains 332 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.192161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155874 restraints weight = 21802.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155512 restraints weight = 16947.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.156838 restraints weight = 19398.142| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 15971 Z= 0.173 Angle : 0.695 14.353 21673 Z= 0.354 Chirality : 0.045 0.196 2502 Planarity : 0.004 0.069 2727 Dihedral : 4.738 37.658 2154 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.73 % Allowed : 27.71 % Favored : 68.56 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.39 (0.19), residues: 1989 helix: 1.84 (0.25), residues: 426 sheet: -1.56 (0.21), residues: 651 loop : -1.76 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 106 HIS 0.003 0.001 HIS B 317 PHE 0.019 0.002 PHE G 46 TYR 0.034 0.002 TYR C 441 ARG 0.009 0.001 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 615) hydrogen bonds : angle 5.17037 ( 1665) SS BOND : bond 0.00362 ( 29) SS BOND : angle 2.50581 ( 58) covalent geometry : bond 0.00446 (15942) covalent geometry : angle 0.68367 (21615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5106.15 seconds wall clock time: 90 minutes 58.40 seconds (5458.40 seconds total)