Starting phenix.real_space_refine on Mon Jan 20 20:46:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz5_37947/01_2025/8wz5_37947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz5_37947/01_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_37947/01_2025/8wz5_37947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz5_37947/01_2025/8wz5_37947.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz5_37947/01_2025/8wz5_37947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz5_37947/01_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-5571/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: 9.85, per 1000 atoms: 0.63 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=10, 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 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 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 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: 3.68 Conformation dependent library (CDL) restraints added in 2.3 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: 2.00 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: 5.38 Time building geometry restraints manager: 4.15 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: 8438 17.59 - 35.18: 858 35.18 - 52.76: 229 52.76 - 70.35: 54 70.35 - 87.94: 15 Dihedral angle restraints: 9594 sinusoidal: 3738 harmonic: 5856 Sorted by residual: dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 143.00 -50.00 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual -86.00 -134.53 48.53 1 1.00e+01 1.00e-02 3.24e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual -86.00 -134.02 48.02 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 9591 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: 40 2.29 - 2.94: 7066 2.94 - 3.59: 22054 3.59 - 4.25: 33836 4.25 - 4.90: 58189 Nonbonded interactions: 121185 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 B 416 " pdb=" SG CYS B 422 " model vdw 1.882 3.760 nonbonded pdb=" SG CYS C 416 " pdb=" SG CYS C 422 " model vdw 1.882 3.760 nonbonded pdb=" SG CYS A 458 " pdb=" SG CYS B 149 " model vdw 1.910 3.760 ... (remaining 121180 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- 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 : 0.004 0.062 15942 Z= 0.272 Angle : 0.871 13.801 21615 Z= 0.510 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 *********************** 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 : 2.154 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: 0.3242 time to fit residues: 164.1538 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 : 2.016 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.0070 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.198115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162729 restraints weight = 21575.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162275 restraints weight = 15943.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164011 restraints weight = 16319.242| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15942 Z= 0.183 Angle : 0.579 9.973 21615 Z= 0.300 Chirality : 0.042 0.178 2502 Planarity : 0.003 0.023 2727 Dihedral : 4.586 41.916 2160 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.45 % Allowed : 23.43 % Favored : 72.12 % 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: -1.20 (0.19), residues: 1989 helix: 1.82 (0.25), residues: 435 sheet: -1.40 (0.21), residues: 666 loop : -1.60 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 314 HIS 0.002 0.001 HIS B 317 PHE 0.019 0.001 PHE G 46 TYR 0.019 0.001 TYR B 417 ARG 0.005 0.001 ARG B 235 *********************** 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 398 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7603 (t0) cc_final: 0.7287 (t0) REVERT: A 222 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7153 (tp30) REVERT: H 48 MET cc_start: 0.7263 (mmt) cc_final: 0.6607 (mmp) REVERT: B 289 MET cc_start: 0.8086 (tpp) cc_final: 0.7636 (tpt) REVERT: B 410 LEU cc_start: 0.7380 (mt) cc_final: 0.6828 (tt) REVERT: B 439 CYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6342 (p) REVERT: C 222 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: C 433 LYS cc_start: 0.7678 (tptm) cc_final: 0.7432 (tttp) REVERT: C 439 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6296 (p) REVERT: E 48 MET cc_start: 0.7274 (mmt) cc_final: 0.7061 (mmt) outliers start: 80 outliers final: 43 residues processed: 371 average time/residue: 0.3101 time to fit residues: 164.7733 Evaluate side-chains 333 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 439 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 70 PHE 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 402 ILE Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 439 CYS 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: 6.9990 chunk 140 optimal weight: 0.0570 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 185 optimal weight: 0.0060 overall best weight: 0.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.202108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.165233 restraints weight = 21721.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.163138 restraints weight = 16303.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165301 restraints weight = 15207.940| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15942 Z= 0.155 Angle : 0.548 11.664 21615 Z= 0.281 Chirality : 0.042 0.166 2502 Planarity : 0.003 0.024 2727 Dihedral : 4.110 18.852 2154 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.39 % Allowed : 25.10 % Favored : 71.51 % 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: -1.14 (0.19), residues: 1989 helix: 1.76 (0.25), residues: 447 sheet: -1.38 (0.21), residues: 660 loop : -1.54 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 50 HIS 0.020 0.001 HIS B 159 PHE 0.020 0.001 PHE D 64 TYR 0.014 0.001 TYR G 87 ARG 0.005 0.001 ARG B 429 *********************** 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 372 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7710 (t0) cc_final: 0.7268 (t0) REVERT: A 148 ILE cc_start: 0.7378 (pt) cc_final: 0.7129 (pt) REVERT: A 260 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 289 MET cc_start: 0.8190 (tpt) cc_final: 0.7894 (tpt) REVERT: H 48 MET cc_start: 0.7192 (mmt) cc_final: 0.6500 (mmp) REVERT: B 92 ASP cc_start: 0.7643 (t0) cc_final: 0.7290 (t0) REVERT: B 260 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 410 LEU cc_start: 0.7318 (mt) cc_final: 0.6842 (tt) REVERT: C 189 THR cc_start: 0.8595 (m) cc_final: 0.8380 (p) REVERT: C 260 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 410 LEU cc_start: 0.7212 (mt) cc_final: 0.6705 (tt) REVERT: C 433 LYS cc_start: 0.7585 (tptm) cc_final: 0.7306 (tttp) REVERT: E 48 MET cc_start: 0.7076 (mmt) cc_final: 0.6387 (mmp) outliers start: 61 outliers final: 33 residues processed: 354 average time/residue: 0.2947 time to fit residues: 152.5691 Evaluate side-chains 313 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 260 LEU 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 70 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 48 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 248 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU 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 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 260 LEU 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: 7.9990 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156103 restraints weight = 21988.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155127 restraints weight = 16429.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156809 restraints weight = 18115.084| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15942 Z= 0.288 Angle : 0.618 12.252 21615 Z= 0.318 Chirality : 0.044 0.189 2502 Planarity : 0.004 0.031 2727 Dihedral : 4.535 21.977 2154 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.34 % Allowed : 26.10 % Favored : 69.56 % 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: -1.44 (0.19), residues: 1989 helix: 1.40 (0.24), residues: 453 sheet: -1.63 (0.21), residues: 645 loop : -1.60 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 106 HIS 0.003 0.001 HIS B 317 PHE 0.023 0.002 PHE D 70 TYR 0.023 0.002 TYR C 299 ARG 0.004 0.001 ARG C 235 *********************** 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 358 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 280 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7763 (t0) cc_final: 0.7288 (t0) REVERT: A 222 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: A 232 GLU cc_start: 0.6887 (mp0) cc_final: 0.6627 (mp0) REVERT: A 260 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 260 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 275 SER cc_start: 0.8213 (t) cc_final: 0.7925 (p) REVERT: B 439 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.6579 (p) REVERT: C 222 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: C 260 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7649 (tt) REVERT: C 275 SER cc_start: 0.8267 (t) cc_final: 0.7969 (p) REVERT: C 433 LYS cc_start: 0.7633 (tptm) cc_final: 0.7350 (tttp) REVERT: C 439 CYS cc_start: 0.8286 (OUTLIER) cc_final: 0.6892 (p) REVERT: C 503 LEU cc_start: 0.9069 (tt) cc_final: 0.7935 (tt) REVERT: E 48 MET cc_start: 0.7345 (mmt) cc_final: 0.6736 (mmp) outliers start: 78 outliers final: 53 residues processed: 326 average time/residue: 0.2939 time to fit residues: 140.0537 Evaluate side-chains 331 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 260 LEU 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 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 68 PHE 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 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE 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 260 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 334 LEU 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 439 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 148 ILE 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 260 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 439 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 G residue 47 LEU 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: 2.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 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 = 0.4347 r_free = 0.4347 target = 0.193814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155696 restraints weight = 22252.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154994 restraints weight = 16176.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156830 restraints weight = 17684.537| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15942 Z= 0.256 Angle : 0.600 12.925 21615 Z= 0.309 Chirality : 0.043 0.211 2502 Planarity : 0.003 0.031 2727 Dihedral : 4.454 21.757 2154 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.84 % Allowed : 25.21 % Favored : 69.95 % 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: -1.50 (0.19), residues: 1989 helix: 1.46 (0.24), residues: 447 sheet: -1.69 (0.21), residues: 645 loop : -1.67 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.002 0.001 HIS B 317 PHE 0.027 0.002 PHE H 70 TYR 0.018 0.002 TYR C 299 ARG 0.005 0.001 ARG A 235 *********************** 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 369 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7839 (t0) cc_final: 0.7388 (t0) REVERT: A 222 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: A 260 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7770 (tt) REVERT: H 87 LYS cc_start: 0.7180 (mptt) cc_final: 0.6943 (mptt) REVERT: B 260 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7659 (tt) REVERT: B 275 SER cc_start: 0.8227 (t) cc_final: 0.7921 (p) REVERT: B 439 CYS cc_start: 0.8193 (OUTLIER) cc_final: 0.6699 (p) REVERT: D 48 MET cc_start: 0.7619 (mmp) cc_final: 0.6924 (mmp) REVERT: C 222 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: C 232 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 260 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7658 (tt) REVERT: C 433 LYS cc_start: 0.7564 (tptm) cc_final: 0.7251 (tttp) REVERT: C 439 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 503 LEU cc_start: 0.9300 (tt) cc_final: 0.8897 (tt) outliers start: 87 outliers final: 59 residues processed: 329 average time/residue: 0.2989 time to fit residues: 144.0192 Evaluate side-chains 337 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 189 THR 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 260 LEU 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 442 VAL Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 503 LEU 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 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 260 LEU 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 410 LEU Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 494 GLN 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 108 GLN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 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 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 439 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 106 TRP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN C 227 ASN C 496 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.195292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157422 restraints weight = 22084.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.156650 restraints weight = 15713.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158452 restraints weight = 16264.940| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15942 Z= 0.209 Angle : 0.578 12.931 21615 Z= 0.297 Chirality : 0.042 0.164 2502 Planarity : 0.003 0.028 2727 Dihedral : 4.317 20.837 2154 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.51 % Allowed : 25.21 % Favored : 70.28 % 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: -1.46 (0.19), residues: 1989 helix: 1.50 (0.24), residues: 447 sheet: -1.61 (0.20), residues: 717 loop : -1.66 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.002 0.001 HIS B 317 PHE 0.022 0.001 PHE H 70 TYR 0.018 0.001 TYR E 105 ARG 0.005 0.000 ARG A 235 *********************** 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 369 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7814 (t0) cc_final: 0.7342 (t0) REVERT: A 222 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: A 260 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7706 (tt) REVERT: H 34 MET cc_start: 0.7989 (mmm) cc_final: 0.7757 (mmt) REVERT: H 87 LYS cc_start: 0.7291 (mptt) cc_final: 0.7058 (mptt) REVERT: B 92 ASP cc_start: 0.7695 (t0) cc_final: 0.7399 (t0) REVERT: B 260 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7595 (tt) REVERT: B 275 SER cc_start: 0.8228 (t) cc_final: 0.7918 (p) REVERT: D 48 MET cc_start: 0.7586 (mmp) cc_final: 0.6897 (mmp) REVERT: C 222 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: C 232 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: C 260 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7633 (tt) REVERT: C 417 TYR cc_start: 0.5916 (m-80) cc_final: 0.5519 (m-80) REVERT: C 433 LYS cc_start: 0.7530 (tptm) cc_final: 0.7219 (tttp) REVERT: C 439 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.6761 (p) REVERT: E 65 LYS cc_start: 0.6977 (mtpp) cc_final: 0.6774 (mtpp) outliers start: 81 outliers final: 53 residues processed: 334 average time/residue: 0.3057 time to fit residues: 149.6257 Evaluate side-chains 332 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 260 LEU 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 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 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 260 LEU 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 442 VAL Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain D residue 70 PHE 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 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL 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 232 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 402 ILE Chi-restraints excluded: chain C residue 439 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 106 TRP 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: 0.7980 chunk 136 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 126 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN D 108 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.194596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156522 restraints weight = 22108.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155860 restraints weight = 15731.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157552 restraints weight = 16426.299| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15942 Z= 0.231 Angle : 0.592 13.682 21615 Z= 0.303 Chirality : 0.043 0.181 2502 Planarity : 0.003 0.029 2727 Dihedral : 4.317 21.195 2154 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.40 % Allowed : 25.15 % Favored : 70.45 % 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: 1.52 (0.24), residues: 447 sheet: -1.59 (0.20), residues: 711 loop : -1.65 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.003 0.001 HIS A 317 PHE 0.021 0.001 PHE H 70 TYR 0.018 0.001 TYR C 299 ARG 0.009 0.001 ARG C 429 *********************** 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 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 275 time to evaluate : 2.297 Fit side-chains REVERT: A 77 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8381 (ttpt) REVERT: A 92 ASP cc_start: 0.7846 (t0) cc_final: 0.7357 (t0) REVERT: A 222 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: A 433 LYS cc_start: 0.7557 (tptm) cc_final: 0.7333 (tptm) REVERT: H 34 MET cc_start: 0.8004 (mmm) cc_final: 0.7778 (mmt) REVERT: B 260 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7600 (tt) REVERT: B 275 SER cc_start: 0.8245 (t) cc_final: 0.7930 (p) REVERT: B 463 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6362 (mm-30) REVERT: D 48 MET cc_start: 0.7553 (mmp) cc_final: 0.6847 (mmp) REVERT: F 87 TYR cc_start: 0.8145 (m-80) cc_final: 0.7866 (m-80) REVERT: C 222 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: C 232 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: C 260 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7618 (tt) REVERT: C 433 LYS cc_start: 0.7521 (tptm) cc_final: 0.7209 (tttp) REVERT: C 507 ARG cc_start: 0.8184 (ptt180) cc_final: 0.7923 (mtm180) outliers start: 79 outliers final: 58 residues processed: 321 average time/residue: 0.3151 time to fit residues: 148.2361 Evaluate side-chains 325 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 148 ILE 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 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 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE 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 260 LEU 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 442 VAL Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL 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 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 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 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 442 VAL 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 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: 4.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.191768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.153932 restraints weight = 22024.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153346 restraints weight = 16147.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154683 restraints weight = 18981.885| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15942 Z= 0.311 Angle : 0.644 13.856 21615 Z= 0.330 Chirality : 0.044 0.174 2502 Planarity : 0.004 0.036 2727 Dihedral : 4.588 22.179 2154 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.51 % Allowed : 24.82 % Favored : 70.67 % 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: -1.61 (0.19), residues: 1989 helix: 1.29 (0.24), residues: 450 sheet: -1.77 (0.20), residues: 732 loop : -1.62 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 106 HIS 0.003 0.001 HIS A 317 PHE 0.023 0.002 PHE H 70 TYR 0.023 0.002 TYR C 299 ARG 0.009 0.001 ARG B 429 *********************** 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 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 273 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: A 92 ASP cc_start: 0.7818 (t0) cc_final: 0.7350 (t0) REVERT: A 222 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: H 34 MET cc_start: 0.8007 (mmm) cc_final: 0.7779 (mmt) REVERT: B 260 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 275 SER cc_start: 0.8267 (t) cc_final: 0.7992 (p) REVERT: B 503 LEU cc_start: 0.8890 (tt) cc_final: 0.8484 (mm) REVERT: D 38 LYS cc_start: 0.7506 (tptp) cc_final: 0.7304 (tppt) REVERT: D 48 MET cc_start: 0.7589 (mmp) cc_final: 0.6927 (mmp) REVERT: D 64 PHE cc_start: 0.7617 (m-80) cc_final: 0.7258 (m-80) REVERT: F 87 TYR cc_start: 0.8149 (m-80) cc_final: 0.7900 (m-80) REVERT: C 87 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (mtmp) REVERT: C 222 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: C 232 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: C 260 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7657 (tt) REVERT: C 433 LYS cc_start: 0.7562 (tptm) cc_final: 0.7253 (tttp) outliers start: 81 outliers final: 65 residues processed: 322 average time/residue: 0.3213 time to fit residues: 150.6808 Evaluate side-chains 338 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 266 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 148 ILE 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 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 416 CYS Chi-restraints excluded: chain A residue 432 ILE 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 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 260 LEU 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 410 LEU 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 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 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 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 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 45 LEU 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 106 TRP 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: 0.9980 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.194024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156111 restraints weight = 22102.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155177 restraints weight = 16243.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156810 restraints weight = 18288.350| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 15942 Z= 0.250 Angle : 0.637 17.327 21615 Z= 0.321 Chirality : 0.044 0.233 2502 Planarity : 0.003 0.030 2727 Dihedral : 4.439 21.174 2154 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.17 % Allowed : 25.71 % 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: -1.52 (0.19), residues: 1989 helix: 1.40 (0.25), residues: 447 sheet: -1.70 (0.20), residues: 717 loop : -1.60 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 106 HIS 0.003 0.001 HIS A 317 PHE 0.021 0.001 PHE H 70 TYR 0.019 0.001 TYR C 299 ARG 0.010 0.001 ARG B 507 *********************** 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 347 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 1.881 Fit side-chains REVERT: A 81 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: A 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7415 (t0) REVERT: A 222 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7173 (tp30) REVERT: A 433 LYS cc_start: 0.7585 (tptm) cc_final: 0.7345 (tptm) REVERT: H 34 MET cc_start: 0.8023 (mmm) cc_final: 0.7821 (mmt) REVERT: B 92 ASP cc_start: 0.7783 (t0) cc_final: 0.7499 (t0) REVERT: B 260 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7597 (tt) REVERT: B 275 SER cc_start: 0.8271 (t) cc_final: 0.7933 (p) REVERT: F 87 TYR cc_start: 0.8195 (m-80) cc_final: 0.7859 (m-80) REVERT: C 92 ASP cc_start: 0.7783 (t0) cc_final: 0.7521 (t0) REVERT: C 222 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: C 232 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: C 260 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 433 LYS cc_start: 0.7485 (tptm) cc_final: 0.7215 (tttp) outliers start: 75 outliers final: 55 residues processed: 318 average time/residue: 0.2898 time to fit residues: 134.7089 Evaluate side-chains 328 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 174 THR 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 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 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 402 ILE 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 80 TYR 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 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 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 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 402 ILE Chi-restraints excluded: chain C residue 442 VAL 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 80 TYR 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 149 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 181 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN ** 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 = 0.4371 r_free = 0.4371 target = 0.195976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158493 restraints weight = 22185.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157447 restraints weight = 15942.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159489 restraints weight = 16443.067| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 15942 Z= 0.228 Angle : 0.620 13.837 21615 Z= 0.313 Chirality : 0.043 0.246 2502 Planarity : 0.003 0.044 2727 Dihedral : 4.247 20.389 2154 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.23 % Allowed : 26.66 % Favored : 70.12 % Cbeta Deviations : 0.05 % 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: -1.44 (0.19), residues: 1989 helix: 1.46 (0.25), residues: 447 sheet: -1.64 (0.20), residues: 717 loop : -1.55 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.002 0.001 HIS A 317 PHE 0.020 0.001 PHE G 46 TYR 0.018 0.001 TYR E 105 ARG 0.007 0.001 ARG C 429 ********************** 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 337 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 1.805 Fit side-chains REVERT: A 81 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: A 92 ASP cc_start: 0.7899 (t0) cc_final: 0.7500 (t0) REVERT: A 222 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7186 (tp30) REVERT: A 433 LYS cc_start: 0.7562 (tptm) cc_final: 0.7321 (tptm) REVERT: H 60 TYR cc_start: 0.6404 (m-80) cc_final: 0.6186 (m-80) REVERT: B 92 ASP cc_start: 0.7701 (t0) cc_final: 0.7425 (t0) REVERT: B 222 GLU cc_start: 0.7975 (tp30) cc_final: 0.7630 (tp30) REVERT: B 260 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7561 (tt) REVERT: B 275 SER cc_start: 0.8235 (t) cc_final: 0.7930 (p) REVERT: F 87 TYR cc_start: 0.8160 (m-80) cc_final: 0.7866 (m-80) REVERT: C 92 ASP cc_start: 0.7716 (t0) cc_final: 0.7456 (t0) REVERT: C 222 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7316 (tp30) REVERT: C 260 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7744 (tt) REVERT: C 289 MET cc_start: 0.8055 (tpp) cc_final: 0.7253 (tpt) REVERT: C 433 LYS cc_start: 0.7444 (tptm) cc_final: 0.7126 (tttp) outliers start: 58 outliers final: 44 residues processed: 313 average time/residue: 0.2970 time to fit residues: 135.2394 Evaluate side-chains 316 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 81 GLN 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 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 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 212 CYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 402 ILE 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 108 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL 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 260 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 442 VAL 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 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: 4.9990 chunk 136 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158053 restraints weight = 22116.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157066 restraints weight = 15510.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158985 restraints weight = 16825.458| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 15942 Z= 0.324 Angle : 0.840 59.062 21615 Z= 0.459 Chirality : 0.045 0.506 2502 Planarity : 0.004 0.060 2727 Dihedral : 4.244 20.510 2154 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.06 % Allowed : 27.49 % Favored : 69.45 % Cbeta Deviations : 0.05 % 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: -1.44 (0.19), residues: 1989 helix: 1.45 (0.25), residues: 447 sheet: -1.64 (0.20), residues: 717 loop : -1.56 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.002 0.001 HIS A 317 PHE 0.022 0.002 PHE A 32 TYR 0.018 0.002 TYR B 441 ARG 0.025 0.001 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.51 seconds wall clock time: 92 minutes 53.32 seconds (5573.32 seconds total)