Starting phenix.real_space_refine on Tue Dec 31 13:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz5_37947/12_2024/8wz5_37947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz5_37947/12_2024/8wz5_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_37947/12_2024/8wz5_37947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz5_37947/12_2024/8wz5_37947.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz5_37947/12_2024/8wz5_37947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz5_37947/12_2024/8wz5_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-5532/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: 9.78, 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: 3.67 Conformation dependent library (CDL) restraints added in 2.1 seconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 25.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.067A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 207 removed outlier: 4.784A pdb=" N LEU A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 230 " --> pdb=" O MET A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 516 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.958A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.067A pdb=" N ASN B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 207 removed outlier: 4.784A pdb=" N LEU B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 477 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 516 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.957A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 99 removed outlier: 4.066A pdb=" N ASN C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 207 removed outlier: 4.783A pdb=" N LEU C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.604A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 230 " --> pdb=" O MET C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.548A pdb=" N ASN C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.247A pdb=" N ASN C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.853A pdb=" N ASN C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 477 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 516 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.958A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.653A pdb=" N ASP A 344 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 3.573A pdb=" N ALA A 177 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 192 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A 51 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 303 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 291 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 416 removed outlier: 3.862A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.795A pdb=" N ILE A 432 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.021A pdb=" N GLN L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.497A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.652A pdb=" N ASP B 344 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 176 through 180 removed outlier: 3.573A pdb=" N ALA B 177 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 192 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 51 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 303 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 291 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AC2, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AC3, first strand: chain 'B' and resid 411 through 416 removed outlier: 3.863A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.795A pdb=" N ILE B 432 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU D 10 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.022A pdb=" N GLN F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.496A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 31 through 33 removed outlier: 5.798A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AD4, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.653A pdb=" N ASP C 344 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.574A pdb=" N ALA C 177 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 10.815A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 192 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY C 51 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 303 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 291 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AD7, first strand: chain 'C' and resid 359 through 361 Processing sheet with id=AD8, first strand: chain 'C' and resid 411 through 416 removed outlier: 3.862A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.796A pdb=" N ILE C 432 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU E 10 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.314A pdb=" N GLU E 10 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 110 " --> pdb=" O TYR E 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.022A pdb=" N GLN G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.497A pdb=" N THR G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 4.22 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' 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: 3.400 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.830 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.750 ------------------------------------------------------------------------------- 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 : 1.731 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: 0.3155 time to fit residues: 158.9902 Evaluate side-chains 281 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 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 : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8078 (t0) cc_final: 0.7766 (t0) REVERT: A 189 THR cc_start: 0.8547 (m) cc_final: 0.8277 (p) REVERT: A 222 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: A 232 GLU cc_start: 0.7402 (mp0) cc_final: 0.7138 (mp0) REVERT: A 465 GLN cc_start: 0.7125 (mt0) cc_final: 0.6448 (tp40) REVERT: H 12 LYS cc_start: 0.7868 (mttt) cc_final: 0.7661 (ptmt) REVERT: H 48 MET cc_start: 0.7202 (mmt) cc_final: 0.5882 (mmp) REVERT: L 87 TYR cc_start: 0.8047 (m-80) cc_final: 0.7648 (m-80) REVERT: B 232 GLU cc_start: 0.7445 (mp0) cc_final: 0.7154 (mp0) REVERT: B 410 LEU cc_start: 0.7183 (mt) cc_final: 0.6253 (tt) REVERT: B 439 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6293 (p) REVERT: F 87 TYR cc_start: 0.8091 (m-80) cc_final: 0.7699 (m-80) REVERT: C 194 ASP cc_start: 0.7293 (p0) cc_final: 0.7069 (p0) REVERT: C 222 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: C 232 GLU cc_start: 0.7455 (mp0) cc_final: 0.7159 (mp0) REVERT: C 439 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6181 (p) REVERT: C 461 LYS cc_start: 0.7944 (tptt) cc_final: 0.7655 (pttp) REVERT: C 465 GLN cc_start: 0.7185 (mt0) cc_final: 0.6555 (tp40) REVERT: E 48 MET cc_start: 0.7084 (mmt) cc_final: 0.6497 (mmt) REVERT: G 4 MET cc_start: 0.7707 (ttm) cc_final: 0.7262 (ttm) outliers start: 80 outliers final: 43 residues processed: 371 average time/residue: 0.3164 time to fit residues: 169.6283 Evaluate side-chains 338 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 277 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15942 Z= 0.227 Angle : 0.584 11.911 21615 Z= 0.301 Chirality : 0.043 0.189 2502 Planarity : 0.003 0.027 2727 Dihedral : 4.376 21.377 2154 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.06 % Allowed : 24.71 % Favored : 71.23 % 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: -1.41 (0.19), residues: 1989 helix: 1.69 (0.24), residues: 432 sheet: -1.57 (0.21), residues: 645 loop : -1.71 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 314 HIS 0.020 0.002 HIS B 159 PHE 0.020 0.002 PHE H 70 TYR 0.020 0.001 TYR C 299 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 373 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: A 92 ASP cc_start: 0.8074 (t0) cc_final: 0.7759 (t0) REVERT: A 194 ASP cc_start: 0.7382 (p0) cc_final: 0.7168 (p0) REVERT: A 465 GLN cc_start: 0.7049 (mt0) cc_final: 0.6381 (tp40) REVERT: H 48 MET cc_start: 0.7376 (mmt) cc_final: 0.5956 (mmp) REVERT: L 87 TYR cc_start: 0.7950 (m-80) cc_final: 0.7612 (m-80) REVERT: B 232 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: B 260 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6439 (tt) REVERT: B 429 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7428 (mpt180) REVERT: D 34 MET cc_start: 0.8285 (mmm) cc_final: 0.8083 (mmt) REVERT: D 87 LYS cc_start: 0.6438 (mmtm) cc_final: 0.6175 (mptt) REVERT: D 105 TYR cc_start: 0.7220 (t80) cc_final: 0.6961 (t80) REVERT: F 87 TYR cc_start: 0.8005 (m-80) cc_final: 0.7559 (m-80) REVERT: C 60 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 81 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: C 232 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: C 260 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6429 (tt) REVERT: C 461 LYS cc_start: 0.7963 (tptt) cc_final: 0.7606 (pttp) REVERT: C 465 GLN cc_start: 0.7009 (mt0) cc_final: 0.6333 (tp40) REVERT: E 48 MET cc_start: 0.7328 (mmt) cc_final: 0.5939 (mmp) outliers start: 73 outliers final: 43 residues processed: 347 average time/residue: 0.2965 time to fit residues: 149.7550 Evaluate side-chains 336 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 159 HIS 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 442 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 93 VAL 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 159 HIS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 232 GLU 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 432 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 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 214 ILE 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 402 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.0670 chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 168 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15942 Z= 0.160 Angle : 0.544 11.821 21615 Z= 0.277 Chirality : 0.042 0.162 2502 Planarity : 0.003 0.026 2727 Dihedral : 4.108 19.387 2154 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.73 % Allowed : 25.54 % Favored : 70.73 % 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: -1.31 (0.19), residues: 1989 helix: 1.86 (0.24), residues: 432 sheet: -1.54 (0.21), residues: 639 loop : -1.68 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS B 159 PHE 0.017 0.001 PHE E 70 TYR 0.015 0.001 TYR G 87 ARG 0.005 0.001 ARG A 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 357 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7548 (ttpt) REVERT: A 81 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 92 ASP cc_start: 0.8098 (t0) cc_final: 0.7677 (t0) REVERT: A 194 ASP cc_start: 0.7480 (p0) cc_final: 0.7255 (p0) REVERT: A 222 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: A 433 LYS cc_start: 0.6185 (tptm) cc_final: 0.5828 (tptm) REVERT: A 465 GLN cc_start: 0.7111 (mt0) cc_final: 0.6493 (tp40) REVERT: H 46 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7874 (mmtt) REVERT: H 48 MET cc_start: 0.7196 (mmt) cc_final: 0.5757 (mmp) REVERT: L 87 TYR cc_start: 0.7923 (m-80) cc_final: 0.7623 (m-80) REVERT: B 227 ASN cc_start: 0.8370 (t0) cc_final: 0.8152 (t0) REVERT: B 232 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: B 429 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7482 (mpt180) REVERT: B 439 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.6586 (p) REVERT: D 34 MET cc_start: 0.8152 (mmm) cc_final: 0.7941 (mmt) REVERT: D 87 LYS cc_start: 0.6481 (mmtm) cc_final: 0.6254 (mptt) REVERT: D 105 TYR cc_start: 0.7221 (t80) cc_final: 0.7014 (t80) REVERT: F 87 TYR cc_start: 0.8105 (m-80) cc_final: 0.7656 (m-80) REVERT: C 60 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 194 ASP cc_start: 0.7266 (p0) cc_final: 0.7010 (p0) REVERT: C 222 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: C 232 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: C 260 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6377 (tt) REVERT: C 439 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6502 (p) REVERT: C 461 LYS cc_start: 0.7962 (tptt) cc_final: 0.7617 (pttp) REVERT: C 465 GLN cc_start: 0.6964 (mt0) cc_final: 0.6273 (tp40) REVERT: C 503 LEU cc_start: 0.9585 (tt) cc_final: 0.9221 (tt) REVERT: E 34 MET cc_start: 0.8230 (mmm) cc_final: 0.7140 (mmm) REVERT: E 48 MET cc_start: 0.7244 (mmt) cc_final: 0.6520 (mmt) outliers start: 67 outliers final: 45 residues processed: 331 average time/residue: 0.3127 time to fit residues: 150.4633 Evaluate side-chains 328 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 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 70 PHE Chi-restraints excluded: chain H residue 80 TYR 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 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 248 SER 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 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 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 159 HIS Chi-restraints excluded: chain C residue 160 LEU 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 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 108 GLN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 0.0770 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- 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** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN E 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15942 Z= 0.378 Angle : 0.683 13.302 21615 Z= 0.349 Chirality : 0.045 0.192 2502 Planarity : 0.004 0.044 2727 Dihedral : 4.774 22.532 2154 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.06 % Allowed : 25.54 % Favored : 69.39 % 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: -1.77 (0.19), residues: 1989 helix: 0.94 (0.24), residues: 474 sheet: -1.73 (0.20), residues: 669 loop : -1.85 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 106 HIS 0.004 0.002 HIS G 30 PHE 0.030 0.002 PHE E 70 TYR 0.036 0.002 TYR C 441 ARG 0.010 0.001 ARG C 507 *********************** 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 380 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 289 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: A 81 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: A 92 ASP cc_start: 0.8180 (t0) cc_final: 0.7798 (t0) REVERT: A 194 ASP cc_start: 0.7506 (p0) cc_final: 0.7247 (p0) REVERT: A 222 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: A 465 GLN cc_start: 0.7202 (mt0) cc_final: 0.6550 (tp40) REVERT: H 48 MET cc_start: 0.7275 (mmt) cc_final: 0.6341 (mpp) REVERT: H 87 LYS cc_start: 0.6457 (mptt) cc_final: 0.6217 (mptt) REVERT: L 87 TYR cc_start: 0.7811 (m-80) cc_final: 0.7534 (m-80) REVERT: B 98 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6656 (mm-40) REVERT: B 222 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: B 275 SER cc_start: 0.7748 (t) cc_final: 0.7144 (p) REVERT: B 429 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7505 (mpt180) REVERT: B 503 LEU cc_start: 0.9612 (tt) cc_final: 0.9350 (tt) REVERT: D 48 MET cc_start: 0.7495 (mmp) cc_final: 0.6727 (mmp) REVERT: D 71 SER cc_start: 0.8213 (t) cc_final: 0.7952 (p) REVERT: D 87 LYS cc_start: 0.6723 (mmtm) cc_final: 0.6460 (mptt) REVERT: F 87 TYR cc_start: 0.8071 (m-80) cc_final: 0.7536 (m-80) REVERT: C 30 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: C 81 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: C 149 CYS cc_start: 0.8140 (t) cc_final: 0.7228 (p) REVERT: C 194 ASP cc_start: 0.7483 (p0) cc_final: 0.7239 (p0) REVERT: C 222 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: C 260 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6511 (tt) REVERT: C 275 SER cc_start: 0.7874 (t) cc_final: 0.7277 (p) REVERT: C 429 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7297 (mpt180) REVERT: C 461 LYS cc_start: 0.7951 (tptt) cc_final: 0.7596 (pttp) REVERT: C 465 GLN cc_start: 0.6975 (mt0) cc_final: 0.5826 (tm-30) REVERT: E 48 MET cc_start: 0.7526 (mmt) cc_final: 0.6661 (mpp) REVERT: E 87 LYS cc_start: 0.6620 (mmtm) cc_final: 0.6304 (mptt) outliers start: 91 outliers final: 57 residues processed: 343 average time/residue: 0.2890 time to fit residues: 145.2890 Evaluate side-chains 341 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 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 222 GLU 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 432 ILE 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 F residue 23 CYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 30 GLU 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 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 248 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP 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 63 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 0.0980 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN D 108 GLN C 496 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15942 Z= 0.195 Angle : 0.587 12.006 21615 Z= 0.297 Chirality : 0.042 0.161 2502 Planarity : 0.003 0.032 2727 Dihedral : 4.360 20.458 2154 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.56 % Allowed : 25.49 % 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: -1.54 (0.19), residues: 1989 helix: 1.47 (0.24), residues: 450 sheet: -1.69 (0.20), residues: 723 loop : -1.70 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 106 HIS 0.002 0.001 HIS B 317 PHE 0.023 0.001 PHE H 70 TYR 0.024 0.001 TYR C 441 ARG 0.005 0.001 ARG C 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 374 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 292 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 81 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 92 ASP cc_start: 0.8138 (t0) cc_final: 0.7743 (t0) REVERT: A 194 ASP cc_start: 0.7446 (p0) cc_final: 0.7240 (p0) REVERT: A 222 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: A 232 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 429 ARG cc_start: 0.7273 (mmp80) cc_final: 0.7020 (mmp80) REVERT: A 433 LYS cc_start: 0.6094 (tptm) cc_final: 0.5763 (tptm) REVERT: A 465 GLN cc_start: 0.7184 (mt0) cc_final: 0.6561 (tp40) REVERT: H 48 MET cc_start: 0.7248 (mmt) cc_final: 0.6313 (mpp) REVERT: L 87 TYR cc_start: 0.7831 (m-80) cc_final: 0.7423 (m-80) REVERT: B 30 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 222 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: B 275 SER cc_start: 0.7572 (t) cc_final: 0.6947 (p) REVERT: B 429 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7560 (mpt180) REVERT: D 87 LYS cc_start: 0.6665 (mmtm) cc_final: 0.6412 (mptt) REVERT: F 87 TYR cc_start: 0.8162 (m-80) cc_final: 0.7648 (m-80) REVERT: C 30 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: C 60 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 194 ASP cc_start: 0.7464 (p0) cc_final: 0.7241 (p0) REVERT: C 222 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: C 260 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6366 (tt) REVERT: C 429 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7366 (mpt180) REVERT: C 461 LYS cc_start: 0.7932 (tptt) cc_final: 0.7528 (pttp) REVERT: C 465 GLN cc_start: 0.6980 (mt0) cc_final: 0.5897 (tm-30) REVERT: E 48 MET cc_start: 0.7345 (mmt) cc_final: 0.6536 (mpp) REVERT: E 65 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7044 (mtpp) REVERT: E 87 LYS cc_start: 0.6602 (mmtm) cc_final: 0.6268 (mptt) outliers start: 82 outliers final: 54 residues processed: 343 average time/residue: 0.2909 time to fit residues: 145.8852 Evaluate side-chains 344 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 158 LEU 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 232 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 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 H residue 108 GLN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 222 GLU 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 432 ILE 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 30 GLU 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 337 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15942 Z= 0.300 Angle : 0.632 13.852 21615 Z= 0.324 Chirality : 0.044 0.174 2502 Planarity : 0.004 0.035 2727 Dihedral : 4.571 22.182 2154 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.18 % Allowed : 24.82 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1989 helix: 1.24 (0.24), residues: 456 sheet: -1.81 (0.20), residues: 723 loop : -1.68 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 106 HIS 0.003 0.001 HIS A 317 PHE 0.024 0.002 PHE H 70 TYR 0.026 0.002 TYR C 441 ARG 0.006 0.001 ARG C 235 *********************** 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 375 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 282 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: A 81 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7242 (mp10) REVERT: A 92 ASP cc_start: 0.8184 (t0) cc_final: 0.7809 (t0) REVERT: A 194 ASP cc_start: 0.7572 (p0) cc_final: 0.7330 (p0) REVERT: A 222 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: A 433 LYS cc_start: 0.6102 (tptm) cc_final: 0.5762 (tptm) REVERT: A 465 GLN cc_start: 0.7157 (mt0) cc_final: 0.6563 (tp40) REVERT: H 38 LYS cc_start: 0.7479 (mmtt) cc_final: 0.6269 (mmmt) REVERT: H 48 MET cc_start: 0.7323 (mmt) cc_final: 0.6325 (mpp) REVERT: H 87 LYS cc_start: 0.6511 (mptt) cc_final: 0.6286 (mptt) REVERT: L 87 TYR cc_start: 0.7775 (m-80) cc_final: 0.7385 (m-80) REVERT: B 30 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: B 92 ASP cc_start: 0.8173 (t0) cc_final: 0.7943 (t0) REVERT: B 222 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: B 275 SER cc_start: 0.7638 (t) cc_final: 0.7018 (p) REVERT: B 429 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7572 (mpt180) REVERT: D 48 MET cc_start: 0.7467 (mmp) cc_final: 0.6634 (mmp) REVERT: F 87 TYR cc_start: 0.8089 (m-80) cc_final: 0.7533 (m-80) REVERT: C 30 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: C 60 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8064 (mm-30) REVERT: C 194 ASP cc_start: 0.7496 (p0) cc_final: 0.7262 (p0) REVERT: C 222 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: C 260 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6395 (tt) REVERT: C 275 SER cc_start: 0.7881 (t) cc_final: 0.7258 (p) REVERT: C 429 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7426 (mpt180) REVERT: C 461 LYS cc_start: 0.7909 (tptt) cc_final: 0.7478 (pttp) REVERT: C 465 GLN cc_start: 0.6981 (mt0) cc_final: 0.5866 (tm-30) REVERT: E 38 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7052 (tppt) REVERT: E 48 MET cc_start: 0.7472 (mmt) cc_final: 0.6605 (mpp) REVERT: E 65 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7038 (mtpp) outliers start: 93 outliers final: 67 residues processed: 342 average time/residue: 0.2996 time to fit residues: 152.4137 Evaluate side-chains 353 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 278 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 81 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 LEU 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 291 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 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 30 GLU 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 222 GLU 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 432 ILE Chi-restraints excluded: chain B residue 440 ASP 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 30 GLU 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 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 402 ILE Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** L 38 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15942 Z= 0.240 Angle : 0.615 13.535 21615 Z= 0.311 Chirality : 0.043 0.164 2502 Planarity : 0.003 0.043 2727 Dihedral : 4.464 21.393 2154 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.45 % Allowed : 25.93 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 1989 helix: 1.37 (0.25), residues: 450 sheet: -1.80 (0.19), residues: 726 loop : -1.66 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 106 HIS 0.003 0.001 HIS B 317 PHE 0.023 0.001 PHE H 70 TYR 0.022 0.002 TYR C 441 ARG 0.012 0.001 ARG A 507 *********************** 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 357 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 277 time to evaluate : 1.800 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: A 81 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: A 92 ASP cc_start: 0.8166 (t0) cc_final: 0.7788 (t0) REVERT: A 222 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: A 433 LYS cc_start: 0.6124 (tptm) cc_final: 0.5795 (tptm) REVERT: A 465 GLN cc_start: 0.7157 (mt0) cc_final: 0.6554 (tp40) REVERT: H 38 LYS cc_start: 0.7489 (mmtt) cc_final: 0.6329 (mmmt) REVERT: H 48 MET cc_start: 0.7296 (mmt) cc_final: 0.6271 (mpp) REVERT: H 87 LYS cc_start: 0.6563 (mptt) cc_final: 0.6332 (mptt) REVERT: L 87 TYR cc_start: 0.7804 (m-80) cc_final: 0.7441 (m-80) REVERT: B 30 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 222 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: B 275 SER cc_start: 0.7638 (t) cc_final: 0.7004 (p) REVERT: B 429 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7551 (mpt180) REVERT: F 87 TYR cc_start: 0.8138 (m-80) cc_final: 0.7586 (m-80) REVERT: C 30 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: C 60 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 81 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7351 (pm20) REVERT: C 222 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: C 260 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6407 (tt) REVERT: C 429 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7408 (mpt180) REVERT: C 461 LYS cc_start: 0.7832 (tptt) cc_final: 0.7394 (pttp) REVERT: C 465 GLN cc_start: 0.6981 (mt0) cc_final: 0.5879 (tm-30) REVERT: E 38 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7165 (tptt) REVERT: E 48 MET cc_start: 0.7447 (mmt) cc_final: 0.6597 (mpp) REVERT: E 65 LYS cc_start: 0.7332 (mtpp) cc_final: 0.7041 (mtpp) outliers start: 80 outliers final: 65 residues processed: 328 average time/residue: 0.2944 time to fit residues: 141.6744 Evaluate side-chains 351 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 GLU 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 158 LEU 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 291 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 492 ILE 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 H residue 108 GLN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 GLU 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 222 GLU 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 432 ILE 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 29 THR Chi-restraints excluded: chain C residue 30 GLU 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 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 402 ILE Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL 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 104 PHE 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 180 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 105 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 15942 Z= 0.341 Angle : 0.671 14.003 21615 Z= 0.343 Chirality : 0.045 0.172 2502 Planarity : 0.004 0.045 2727 Dihedral : 4.689 22.497 2154 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.18 % Allowed : 25.32 % Favored : 69.50 % 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: -1.87 (0.19), residues: 1989 helix: 0.92 (0.24), residues: 471 sheet: -1.88 (0.19), residues: 735 loop : -1.80 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 106 HIS 0.003 0.001 HIS B 317 PHE 0.025 0.002 PHE H 70 TYR 0.023 0.002 TYR C 299 ARG 0.008 0.001 ARG A 508 *********************** 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 367 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 274 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: A 92 ASP cc_start: 0.8186 (t0) cc_final: 0.7793 (t0) REVERT: A 172 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7615 (tt) REVERT: A 222 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: A 465 GLN cc_start: 0.7129 (mt0) cc_final: 0.6562 (tp40) REVERT: H 48 MET cc_start: 0.7344 (mmt) cc_final: 0.6335 (mpp) REVERT: L 87 TYR cc_start: 0.7774 (m-80) cc_final: 0.7288 (m-80) REVERT: B 30 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: B 222 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: B 232 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 275 SER cc_start: 0.7661 (t) cc_final: 0.7018 (p) REVERT: D 22 CYS cc_start: 0.5711 (t) cc_final: 0.5489 (t) REVERT: D 48 MET cc_start: 0.7503 (mmp) cc_final: 0.6768 (mmp) REVERT: F 87 TYR cc_start: 0.8108 (m-80) cc_final: 0.7550 (m-80) REVERT: C 30 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 60 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8091 (mm-30) REVERT: C 87 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7240 (mtmt) REVERT: C 172 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7726 (tt) REVERT: C 222 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: C 260 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6401 (tt) REVERT: C 429 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7420 (mpt180) REVERT: C 461 LYS cc_start: 0.7764 (tptt) cc_final: 0.7309 (pttp) REVERT: C 465 GLN cc_start: 0.6926 (mt0) cc_final: 0.5823 (tm-30) REVERT: E 48 MET cc_start: 0.7551 (mmt) cc_final: 0.6612 (mpp) REVERT: E 65 LYS cc_start: 0.7332 (mtpp) cc_final: 0.7046 (mtpp) outliers start: 93 outliers final: 74 residues processed: 334 average time/residue: 0.2933 time to fit residues: 142.8580 Evaluate side-chains 354 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 269 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 76 VAL 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 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 172 LEU 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 291 ILE Chi-restraints excluded: chain A residue 296 VAL 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 429 ARG 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 6 GLN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 GLU 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 222 GLU Chi-restraints excluded: chain B residue 232 GLU 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 432 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 459 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 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 29 THR Chi-restraints excluded: chain C residue 30 GLU 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 172 LEU 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 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 432 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 493 SER 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 104 PHE 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 185 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 ** L 38 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 15942 Z= 0.218 Angle : 0.623 14.233 21615 Z= 0.313 Chirality : 0.043 0.155 2502 Planarity : 0.003 0.040 2727 Dihedral : 4.383 20.608 2154 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.78 % Allowed : 26.88 % Favored : 69.34 % 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: -1.58 (0.19), residues: 1989 helix: 1.29 (0.25), residues: 456 sheet: -1.76 (0.19), residues: 729 loop : -1.60 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.002 0.001 HIS A 317 PHE 0.020 0.001 PHE H 70 TYR 0.019 0.001 TYR C 441 ARG 0.007 0.001 ARG A 508 ********************** 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 350 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: A 92 ASP cc_start: 0.8161 (t0) cc_final: 0.7803 (t0) REVERT: A 98 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6696 (mm-40) REVERT: A 172 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7545 (tt) REVERT: A 222 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: A 429 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6956 (mmp80) REVERT: A 433 LYS cc_start: 0.6135 (tptm) cc_final: 0.5800 (tptm) REVERT: A 465 GLN cc_start: 0.7142 (mt0) cc_final: 0.6574 (tp40) REVERT: H 48 MET cc_start: 0.7235 (mmt) cc_final: 0.6226 (mpp) REVERT: L 87 TYR cc_start: 0.7822 (m-80) cc_final: 0.7422 (m-80) REVERT: B 30 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 60 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8169 (mm-30) REVERT: B 92 ASP cc_start: 0.8159 (t0) cc_final: 0.7953 (t0) REVERT: B 222 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: B 275 SER cc_start: 0.7631 (t) cc_final: 0.6994 (p) REVERT: D 38 LYS cc_start: 0.7267 (mmtt) cc_final: 0.7054 (tppt) REVERT: D 48 MET cc_start: 0.7344 (mmp) cc_final: 0.6429 (mmp) REVERT: D 64 PHE cc_start: 0.7359 (m-80) cc_final: 0.7071 (m-80) REVERT: F 87 TYR cc_start: 0.8139 (m-80) cc_final: 0.7675 (m-80) REVERT: C 30 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: C 60 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8077 (mm-30) REVERT: C 92 ASP cc_start: 0.8102 (t0) cc_final: 0.7902 (t0) REVERT: C 172 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7625 (tt) REVERT: C 194 ASP cc_start: 0.7613 (m-30) cc_final: 0.7408 (p0) REVERT: C 222 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: C 260 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6614 (tt) REVERT: C 289 MET cc_start: 0.8225 (tpp) cc_final: 0.7533 (tpt) REVERT: C 429 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7444 (mpt180) REVERT: C 461 LYS cc_start: 0.7750 (tptt) cc_final: 0.7292 (pttp) REVERT: C 465 GLN cc_start: 0.6967 (mt0) cc_final: 0.5869 (tm-30) REVERT: E 48 MET cc_start: 0.7376 (mmt) cc_final: 0.6494 (mpp) REVERT: E 65 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6972 (mtpp) outliers start: 68 outliers final: 50 residues processed: 325 average time/residue: 0.2959 time to fit residues: 140.8506 Evaluate side-chains 339 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 172 LEU 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 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 429 ARG 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 H residue 108 GLN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 GLU 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 222 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 402 ILE 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 48 VAL Chi-restraints excluded: chain C residue 30 GLU 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 172 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 212 CYS 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 432 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 G residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** L 38 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 = 0.4357 r_free = 0.4357 target = 0.194661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156577 restraints weight = 22060.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157069 restraints weight = 15834.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158896 restraints weight = 15894.730| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 15942 Z= 0.292 Angle : 0.847 59.176 21615 Z= 0.467 Chirality : 0.043 0.245 2502 Planarity : 0.004 0.129 2727 Dihedral : 4.382 20.604 2154 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.67 % Allowed : 27.16 % Favored : 69.17 % 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: -1.58 (0.19), residues: 1989 helix: 1.30 (0.25), residues: 456 sheet: -1.75 (0.19), residues: 729 loop : -1.61 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.002 0.001 HIS A 317 PHE 0.020 0.001 PHE B 32 TYR 0.026 0.001 TYR B 441 ARG 0.008 0.001 ARG B 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3685.04 seconds wall clock time: 69 minutes 55.27 seconds (4195.27 seconds total)