Starting phenix.real_space_refine on Sun Aug 24 00:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz5_37947/08_2025/8wz5_37947.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: "H" 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: "L" 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: B, C, D, E, F, G Time building chain proxies: 3.72, per 1000 atoms: 0.24 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=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS C 458 " distance=1.91 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.10 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=1.88 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS B 149 " distance=1.91 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=1.64 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS B 458 " distance=1.91 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.10 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.10 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=1.88 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=1.88 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=1.64 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 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: 1.34 Conformation dependent library (CDL) restraints added in 767.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.75 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: 2.97 Time building geometry restraints manager: 1.82 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: 8458 17.59 - 35.18: 885 35.18 - 52.76: 248 52.76 - 70.35: 57 70.35 - 87.94: 15 Dihedral angle restraints: 9663 sinusoidal: 3807 harmonic: 5856 Sorted by residual: dihedral pdb=" CB CYS B 458 " pdb=" SG CYS B 458 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 151.80 -58.80 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS A 149 " pdb=" SG CYS A 149 " pdb=" SG CYS C 458 " pdb=" CB CYS C 458 " ideal model delta sinusoidal sigma weight residual 93.00 151.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 151.78 -58.78 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 9660 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: 2.16 - 2.70: 486 2.70 - 3.25: 15301 3.25 - 3.80: 23939 3.80 - 4.35: 30003 4.35 - 4.90: 51387 Nonbonded interactions: 121116 Sorted by model distance: nonbonded pdb=" SG CYS B 458 " pdb=" CA CYS C 149 " model vdw 2.156 3.064 nonbonded pdb=" SG CYS A 458 " pdb=" CA CYS B 149 " model vdw 2.156 3.064 nonbonded pdb=" CA CYS A 149 " pdb=" SG CYS C 458 " model vdw 2.157 3.064 nonbonded pdb=" O ARG C 49 " pdb=" OG1 THR C 369 " model vdw 2.201 3.040 nonbonded pdb=" O ARG A 49 " pdb=" OG1 THR A 369 " model vdw 2.201 3.040 ... (remaining 121111 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'L' selection = chain 'F' selection = chain 'G' } 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: 4.090 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.930 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- 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 : 0.007 0.394 15975 Z= 0.395 Angle : 1.117 34.147 21681 Z= 0.608 Chirality : 0.051 0.312 2502 Planarity : 0.006 0.085 2727 Dihedral : 15.773 87.940 5802 Min Nonbonded Distance : 2.156 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG B 202 TYR 0.019 0.001 TYR A 457 PHE 0.020 0.001 PHE F 46 TRP 0.012 0.001 TRP D 106 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00412 (15942) covalent geometry : angle 0.87121 (21615) SS BOND : bond 0.13390 ( 33) SS BOND : angle 12.70257 ( 66) hydrogen bonds : bond 0.21285 ( 615) hydrogen bonds : angle 8.43952 ( 1665) *********************** 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 : 0.668 Fit side-chains 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: A 503 LEU cc_start: 0.9614 (tt) cc_final: 0.9404 (tt) 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: 0.6851 (mmtt) outliers start: 15 outliers final: 9 residues processed: 352 average time/residue: 0.1475 time to fit residues: 74.6543 Evaluate side-chains 280 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 271 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 277 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 277 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 494 GLN E 82 GLN E 108 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.191393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154887 restraints weight = 21618.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.153484 restraints weight = 16103.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154940 restraints weight = 19688.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155976 restraints weight = 12205.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156713 restraints weight = 10631.871| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15975 Z= 0.211 Angle : 0.658 10.070 21681 Z= 0.342 Chirality : 0.045 0.194 2502 Planarity : 0.004 0.031 2727 Dihedral : 4.996 43.728 2160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.84 % Allowed : 22.48 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.19), residues: 1989 helix: 1.51 (0.25), residues: 435 sheet: -1.57 (0.21), residues: 681 loop : -1.66 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 235 TYR 0.023 0.002 TYR C 299 PHE 0.025 0.002 PHE H 70 TRP 0.018 0.002 TRP C 314 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00499 (15942) covalent geometry : angle 0.65116 (21615) SS BOND : bond 0.00312 ( 33) SS BOND : angle 1.79702 ( 66) hydrogen bonds : bond 0.04172 ( 615) hydrogen bonds : angle 5.72101 ( 1665) *********************** 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 410 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 305 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7285 (t0) REVERT: A 222 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: H 38 LYS cc_start: 0.7522 (tptt) cc_final: 0.7266 (tppt) REVERT: L 61 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7380 (mtm-85) REVERT: L 87 TYR cc_start: 0.8222 (m-80) cc_final: 0.8008 (m-80) REVERT: B 222 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: B 275 SER cc_start: 0.8261 (t) cc_final: 0.7928 (p) REVERT: D 38 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6335 (mmtt) REVERT: C 87 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8497 (mtmp) REVERT: C 222 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: C 289 MET cc_start: 0.7904 (tpp) cc_final: 0.7087 (tpt) REVERT: C 433 LYS cc_start: 0.7676 (tptm) cc_final: 0.7421 (tttp) REVERT: G 61 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7323 (mtm-85) outliers start: 105 outliers final: 58 residues processed: 371 average time/residue: 0.1420 time to fit residues: 76.1507 Evaluate side-chains 350 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 149 CYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 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 432 ILE 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 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 149 CYS 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 232 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 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 D residue 106 TRP Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 291 ILE 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 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 Chi-restraints excluded: chain G residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.0000 chunk 122 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.157817 restraints weight = 22016.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155729 restraints weight = 18376.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157888 restraints weight = 16450.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158638 restraints weight = 11457.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159064 restraints weight = 10527.351| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15975 Z= 0.145 Angle : 0.592 12.090 21681 Z= 0.305 Chirality : 0.044 0.183 2502 Planarity : 0.003 0.030 2727 Dihedral : 4.458 21.576 2154 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.28 % Allowed : 24.60 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1989 helix: 1.65 (0.24), residues: 435 sheet: -1.57 (0.21), residues: 645 loop : -1.76 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.018 0.001 TYR B 299 PHE 0.021 0.001 PHE E 70 TRP 0.013 0.002 TRP D 106 HIS 0.015 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00344 (15942) covalent geometry : angle 0.58832 (21615) SS BOND : bond 0.00294 ( 33) SS BOND : angle 1.28458 ( 66) hydrogen bonds : bond 0.03413 ( 615) hydrogen bonds : angle 5.27607 ( 1665) *********************** 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 370 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 293 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7825 (t0) cc_final: 0.7441 (t0) REVERT: B 275 SER cc_start: 0.8250 (t) cc_final: 0.7879 (p) REVERT: C 266 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5757 (pt) REVERT: C 433 LYS cc_start: 0.7554 (tptm) cc_final: 0.7320 (tttp) REVERT: E 48 MET cc_start: 0.7724 (mmt) cc_final: 0.7444 (mmp) outliers start: 77 outliers final: 56 residues processed: 343 average time/residue: 0.1411 time to fit residues: 70.3926 Evaluate side-chains 334 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS 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 362 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 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 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 158 LEU 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 253 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 130 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.189789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153755 restraints weight = 21733.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152825 restraints weight = 17046.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154500 restraints weight = 19242.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155401 restraints weight = 12245.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156064 restraints weight = 10898.746| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15975 Z= 0.193 Angle : 0.624 12.091 21681 Z= 0.322 Chirality : 0.044 0.188 2502 Planarity : 0.004 0.035 2727 Dihedral : 4.656 22.348 2154 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.56 % Allowed : 23.98 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.19), residues: 1989 helix: 1.14 (0.24), residues: 474 sheet: -1.73 (0.20), residues: 672 loop : -1.77 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.022 0.002 TYR C 299 PHE 0.027 0.002 PHE H 70 TRP 0.015 0.002 TRP H 106 HIS 0.003 0.001 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00459 (15942) covalent geometry : angle 0.62044 (21615) SS BOND : bond 0.00293 ( 33) SS BOND : angle 1.33493 ( 66) hydrogen bonds : bond 0.03479 ( 615) hydrogen bonds : angle 5.24404 ( 1665) *********************** 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 386 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 286 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7773 (t0) cc_final: 0.7341 (t0) REVERT: A 222 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: A 232 GLU cc_start: 0.6932 (mp0) cc_final: 0.6722 (mm-30) REVERT: A 275 SER cc_start: 0.8341 (t) cc_final: 0.8095 (p) REVERT: B 222 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: B 275 SER cc_start: 0.8268 (t) cc_final: 0.7996 (p) REVERT: D 38 LYS cc_start: 0.7096 (mmmt) cc_final: 0.5996 (mptt) REVERT: D 64 PHE cc_start: 0.7495 (m-80) cc_final: 0.7191 (m-80) REVERT: C 87 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8459 (mtmp) REVERT: C 222 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7312 (tp30) REVERT: C 266 ILE cc_start: 0.5905 (OUTLIER) cc_final: 0.5578 (pt) REVERT: C 275 SER cc_start: 0.8373 (t) cc_final: 0.8085 (p) REVERT: C 433 LYS cc_start: 0.7659 (tptm) cc_final: 0.7400 (tttp) outliers start: 100 outliers final: 68 residues processed: 354 average time/residue: 0.1390 time to fit residues: 72.0483 Evaluate side-chains 346 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 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 416 CYS Chi-restraints excluded: chain A residue 442 VAL 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 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 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 222 GLU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 18 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 D residue 106 TRP Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 147 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN L 38 GLN D 108 GLN F 38 GLN E 108 GLN G 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155112 restraints weight = 22171.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154769 restraints weight = 16617.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156530 restraints weight = 17777.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156994 restraints weight = 11789.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.157700 restraints weight = 10701.852| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15975 Z= 0.178 Angle : 0.630 13.489 21681 Z= 0.321 Chirality : 0.044 0.214 2502 Planarity : 0.004 0.036 2727 Dihedral : 4.613 21.647 2154 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.95 % Allowed : 24.26 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.19), residues: 1989 helix: 1.12 (0.24), residues: 477 sheet: -1.77 (0.20), residues: 672 loop : -1.76 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.019 0.002 TYR C 299 PHE 0.025 0.002 PHE H 70 TRP 0.017 0.002 TRP D 106 HIS 0.002 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00426 (15942) covalent geometry : angle 0.62686 (21615) SS BOND : bond 0.00241 ( 33) SS BOND : angle 1.22553 ( 66) hydrogen bonds : bond 0.03293 ( 615) hydrogen bonds : angle 5.14413 ( 1665) *********************** 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 393 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 286 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7406 (t0) REVERT: A 222 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7090 (tp30) REVERT: A 260 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 275 SER cc_start: 0.8357 (t) cc_final: 0.8099 (p) REVERT: B 222 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: B 260 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 275 SER cc_start: 0.8313 (t) cc_final: 0.7990 (p) REVERT: D 38 LYS cc_start: 0.7151 (mmmt) cc_final: 0.5985 (mptt) REVERT: D 64 PHE cc_start: 0.7565 (m-80) cc_final: 0.7233 (m-80) REVERT: C 222 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: C 266 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5608 (pt) REVERT: C 275 SER cc_start: 0.8395 (t) cc_final: 0.8093 (p) REVERT: C 433 LYS cc_start: 0.7607 (tptm) cc_final: 0.7352 (tttp) REVERT: C 503 LEU cc_start: 0.9029 (tt) cc_final: 0.7862 (tt) outliers start: 107 outliers final: 75 residues processed: 359 average time/residue: 0.1347 time to fit residues: 70.9864 Evaluate side-chains 353 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 272 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 260 LEU 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 442 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 149 CYS 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 260 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.190474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154608 restraints weight = 21818.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153891 restraints weight = 16935.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.155237 restraints weight = 19737.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156213 restraints weight = 12569.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156728 restraints weight = 11053.033| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15975 Z= 0.163 Angle : 0.620 13.259 21681 Z= 0.317 Chirality : 0.044 0.162 2502 Planarity : 0.003 0.035 2727 Dihedral : 4.613 21.360 2154 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.84 % Allowed : 24.71 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.19), residues: 1989 helix: 1.15 (0.24), residues: 477 sheet: -1.73 (0.21), residues: 648 loop : -1.80 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.019 0.002 TYR E 105 PHE 0.026 0.002 PHE E 64 TRP 0.016 0.002 TRP H 106 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00394 (15942) covalent geometry : angle 0.61538 (21615) SS BOND : bond 0.00261 ( 33) SS BOND : angle 1.47941 ( 66) hydrogen bonds : bond 0.03183 ( 615) hydrogen bonds : angle 5.06958 ( 1665) *********************** 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 394 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 289 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 92 ASP cc_start: 0.7824 (t0) cc_final: 0.7372 (t0) REVERT: A 222 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: A 260 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7781 (tt) REVERT: A 275 SER cc_start: 0.8387 (t) cc_final: 0.8127 (p) REVERT: A 503 LEU cc_start: 0.9168 (tt) cc_final: 0.7743 (tt) REVERT: H 34 MET cc_start: 0.7967 (mmm) cc_final: 0.7733 (mmt) REVERT: H 48 MET cc_start: 0.7530 (mmm) cc_final: 0.7050 (mtt) REVERT: B 222 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: B 260 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7596 (tt) REVERT: B 275 SER cc_start: 0.8306 (t) cc_final: 0.7998 (p) REVERT: D 64 PHE cc_start: 0.7542 (m-80) cc_final: 0.7179 (m-80) REVERT: F 87 TYR cc_start: 0.8087 (m-80) cc_final: 0.7795 (m-80) REVERT: C 87 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8420 (mtmp) REVERT: C 222 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: C 260 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 266 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5576 (pt) REVERT: C 275 SER cc_start: 0.8416 (t) cc_final: 0.8124 (p) REVERT: C 433 LYS cc_start: 0.7588 (tptm) cc_final: 0.7315 (tttp) REVERT: E 38 LYS cc_start: 0.7366 (tptp) cc_final: 0.7148 (tppt) REVERT: E 48 MET cc_start: 0.7550 (mmp) cc_final: 0.7059 (mmp) outliers start: 105 outliers final: 78 residues processed: 362 average time/residue: 0.1357 time to fit residues: 71.8587 Evaluate side-chains 364 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 277 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 87 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 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 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 GLN 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 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 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 222 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 296 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 18 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 D residue 106 TRP Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 33 LEU 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 7 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.192234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154340 restraints weight = 21988.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154931 restraints weight = 16329.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156480 restraints weight = 16924.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156872 restraints weight = 11274.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157683 restraints weight = 10370.480| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15975 Z= 0.190 Angle : 0.670 15.857 21681 Z= 0.341 Chirality : 0.045 0.221 2502 Planarity : 0.004 0.036 2727 Dihedral : 4.827 44.184 2154 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.07 % Allowed : 24.32 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.19), residues: 1989 helix: 1.05 (0.24), residues: 480 sheet: -1.72 (0.21), residues: 636 loop : -1.80 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 429 TYR 0.020 0.002 TYR C 299 PHE 0.025 0.002 PHE E 64 TRP 0.017 0.002 TRP D 106 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00462 (15942) covalent geometry : angle 0.65861 (21615) SS BOND : bond 0.00321 ( 33) SS BOND : angle 2.27949 ( 66) hydrogen bonds : bond 0.03338 ( 615) hydrogen bonds : angle 5.14836 ( 1665) *********************** 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 389 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 280 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 92 ASP cc_start: 0.7915 (t0) cc_final: 0.7436 (t0) REVERT: A 222 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7106 (tp30) REVERT: A 256 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: A 260 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7745 (tt) REVERT: A 275 SER cc_start: 0.8413 (t) cc_final: 0.8147 (p) REVERT: A 507 ARG cc_start: 0.8019 (ptp-170) cc_final: 0.7613 (ptp-170) REVERT: H 34 MET cc_start: 0.8002 (mmm) cc_final: 0.7764 (mmt) REVERT: H 48 MET cc_start: 0.7623 (mmm) cc_final: 0.6992 (mtm) REVERT: B 222 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7545 (tp30) REVERT: B 232 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: B 260 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 275 SER cc_start: 0.8312 (t) cc_final: 0.8002 (p) REVERT: D 38 LYS cc_start: 0.6904 (mmmt) cc_final: 0.6092 (mmtt) REVERT: D 48 MET cc_start: 0.7431 (mmp) cc_final: 0.7098 (mmp) REVERT: D 64 PHE cc_start: 0.7585 (m-80) cc_final: 0.7112 (m-80) REVERT: F 87 TYR cc_start: 0.8106 (m-80) cc_final: 0.7893 (m-80) REVERT: C 87 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8357 (mtmp) REVERT: C 222 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: C 260 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7848 (tt) REVERT: C 266 ILE cc_start: 0.5896 (OUTLIER) cc_final: 0.5615 (pt) REVERT: C 433 LYS cc_start: 0.7544 (tptm) cc_final: 0.7279 (tttp) REVERT: E 65 LYS cc_start: 0.6702 (mtpp) cc_final: 0.6121 (tttm) outliers start: 109 outliers final: 81 residues processed: 360 average time/residue: 0.1388 time to fit residues: 73.1159 Evaluate side-chains 360 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 268 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 87 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 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 442 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain H residue 18 VAL 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 72 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 76 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 222 GLU 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 291 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain D residue 18 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 D residue 106 TRP Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 VAL 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 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 494 GLN 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 33 LEU 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 145 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 29 optimal weight: 0.4980 chunk 187 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 108 GLN G 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.197957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160480 restraints weight = 22126.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.158749 restraints weight = 18139.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161007 restraints weight = 16138.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.161765 restraints weight = 11033.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.162120 restraints weight = 10363.872| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 15975 Z= 0.121 Angle : 0.639 13.988 21681 Z= 0.326 Chirality : 0.043 0.141 2502 Planarity : 0.003 0.031 2727 Dihedral : 4.681 44.050 2154 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.40 % Allowed : 25.60 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.19), residues: 1989 helix: 1.66 (0.25), residues: 453 sheet: -1.53 (0.21), residues: 651 loop : -1.70 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 235 TYR 0.017 0.001 TYR E 105 PHE 0.024 0.001 PHE E 64 TRP 0.015 0.001 TRP D 106 HIS 0.001 0.000 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00305 (15942) covalent geometry : angle 0.62602 (21615) SS BOND : bond 0.00383 ( 33) SS BOND : angle 2.43998 ( 66) hydrogen bonds : bond 0.03030 ( 615) hydrogen bonds : angle 5.01915 ( 1665) *********************** 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 371 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: A 92 ASP cc_start: 0.7891 (t0) cc_final: 0.7472 (t0) REVERT: A 222 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: A 232 GLU cc_start: 0.6910 (mp0) cc_final: 0.6674 (mp0) REVERT: H 38 LYS cc_start: 0.7702 (tptt) cc_final: 0.7346 (tptp) REVERT: H 48 MET cc_start: 0.7342 (mmm) cc_final: 0.7039 (mtt) REVERT: B 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7428 (t0) REVERT: B 222 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: B 275 SER cc_start: 0.8269 (t) cc_final: 0.7930 (p) REVERT: F 87 TYR cc_start: 0.8118 (m-80) cc_final: 0.7826 (m-80) REVERT: C 222 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: C 289 MET cc_start: 0.8117 (tpp) cc_final: 0.7401 (tpt) REVERT: E 48 MET cc_start: 0.7395 (mmp) cc_final: 0.6771 (mmp) REVERT: E 65 LYS cc_start: 0.6759 (mtpp) cc_final: 0.6303 (tttm) outliers start: 79 outliers final: 54 residues processed: 348 average time/residue: 0.1392 time to fit residues: 70.4688 Evaluate side-chains 336 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 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 296 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 18 VAL 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 F residue 33 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 CYS Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 33 LEU 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 23 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 105 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 6 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN E 108 GLN G 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.195117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158966 restraints weight = 21806.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157948 restraints weight = 15560.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.159349 restraints weight = 18672.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160456 restraints weight = 11778.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162126 restraints weight = 10309.143| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 15975 Z= 0.126 Angle : 0.655 14.115 21681 Z= 0.330 Chirality : 0.043 0.140 2502 Planarity : 0.004 0.042 2727 Dihedral : 4.559 38.678 2154 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.67 % Allowed : 27.10 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.19), residues: 1989 helix: 1.72 (0.25), residues: 447 sheet: -1.48 (0.21), residues: 642 loop : -1.65 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 429 TYR 0.036 0.001 TYR B 441 PHE 0.024 0.001 PHE E 64 TRP 0.014 0.001 TRP D 106 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00331 (15942) covalent geometry : angle 0.64410 (21615) SS BOND : bond 0.00363 ( 33) SS BOND : angle 2.22174 ( 66) hydrogen bonds : bond 0.02974 ( 615) hydrogen bonds : angle 4.97388 ( 1665) *********************** 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 351 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 0.640 Fit side-chains REVERT: A 81 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: A 92 ASP cc_start: 0.7900 (t0) cc_final: 0.7475 (t0) REVERT: A 222 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: A 232 GLU cc_start: 0.6815 (mp0) cc_final: 0.6600 (mm-30) REVERT: H 48 MET cc_start: 0.7314 (mmm) cc_final: 0.7011 (mtt) REVERT: H 87 LYS cc_start: 0.7289 (mptt) cc_final: 0.7020 (mptt) REVERT: B 92 ASP cc_start: 0.7622 (t0) cc_final: 0.7333 (t0) REVERT: B 222 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: B 232 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: B 260 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 275 SER cc_start: 0.8241 (t) cc_final: 0.7929 (p) REVERT: B 503 LEU cc_start: 0.9027 (tt) cc_final: 0.8502 (mm) REVERT: D 34 MET cc_start: 0.8061 (mmm) cc_final: 0.7658 (mmt) REVERT: F 46 PHE cc_start: 0.7254 (p90) cc_final: 0.6922 (p90) REVERT: F 87 TYR cc_start: 0.8079 (m-80) cc_final: 0.7830 (m-80) REVERT: C 92 ASP cc_start: 0.7684 (t0) cc_final: 0.7437 (t0) REVERT: C 222 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 260 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7662 (tt) REVERT: E 48 MET cc_start: 0.7119 (mmp) cc_final: 0.6472 (mmp) REVERT: E 65 LYS cc_start: 0.6698 (mtpp) cc_final: 0.6274 (tttm) outliers start: 66 outliers final: 51 residues processed: 327 average time/residue: 0.1432 time to fit residues: 67.4698 Evaluate side-chains 331 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS 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 260 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 CYS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 33 LEU 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 113 optimal weight: 4.9990 chunk 190 optimal weight: 0.0000 chunk 194 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN E 108 GLN G 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.196143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158582 restraints weight = 21931.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156833 restraints weight = 16821.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158335 restraints weight = 20605.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159834 restraints weight = 13031.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160296 restraints weight = 11184.804| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15975 Z= 0.162 Angle : 0.710 20.812 21681 Z= 0.356 Chirality : 0.045 0.297 2502 Planarity : 0.004 0.035 2727 Dihedral : 4.763 39.110 2154 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.73 % Allowed : 27.55 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 1989 helix: 1.59 (0.25), residues: 447 sheet: -1.53 (0.20), residues: 693 loop : -1.64 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 429 TYR 0.038 0.002 TYR B 441 PHE 0.022 0.002 PHE E 64 TRP 0.013 0.002 TRP D 106 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00409 (15942) covalent geometry : angle 0.69675 (21615) SS BOND : bond 0.00418 ( 33) SS BOND : angle 2.52870 ( 66) hydrogen bonds : bond 0.03213 ( 615) hydrogen bonds : angle 5.12418 ( 1665) ********************** 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 344 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: A 92 ASP cc_start: 0.7858 (t0) cc_final: 0.7408 (t0) REVERT: A 222 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: A 232 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: H 48 MET cc_start: 0.7448 (mmm) cc_final: 0.7091 (mtt) REVERT: B 92 ASP cc_start: 0.7719 (t0) cc_final: 0.7464 (t0) REVERT: B 222 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: B 232 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: B 260 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7654 (tt) REVERT: B 275 SER cc_start: 0.8255 (t) cc_final: 0.7954 (p) REVERT: D 48 MET cc_start: 0.7374 (mmp) cc_final: 0.6890 (mmp) REVERT: D 87 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7339 (mmtt) REVERT: C 92 ASP cc_start: 0.7668 (t0) cc_final: 0.7418 (t0) REVERT: C 222 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: C 260 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7679 (tt) REVERT: E 48 MET cc_start: 0.7169 (mmp) cc_final: 0.6522 (mmp) REVERT: E 65 LYS cc_start: 0.6777 (mtpp) cc_final: 0.6396 (tttm) outliers start: 67 outliers final: 53 residues processed: 323 average time/residue: 0.1385 time to fit residues: 64.3865 Evaluate side-chains 334 residues out of total 1797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 70 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 159 HIS 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 260 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 TRP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 106 TRP Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain G residue 33 LEU 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 26 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.0670 chunk 20 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 496 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN E 108 GLN G 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.199213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.161700 restraints weight = 21983.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.161626 restraints weight = 15645.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162525 restraints weight = 18939.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163658 restraints weight = 11980.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164342 restraints weight = 10414.864| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 15975 Z= 0.129 Angle : 0.681 14.201 21681 Z= 0.343 Chirality : 0.044 0.217 2502 Planarity : 0.004 0.051 2727 Dihedral : 4.608 34.596 2154 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.67 % Allowed : 27.60 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.19), residues: 1989 helix: 1.82 (0.25), residues: 429 sheet: -1.54 (0.20), residues: 705 loop : -1.68 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 507 TYR 0.030 0.001 TYR B 441 PHE 0.022 0.001 PHE E 64 TRP 0.014 0.001 TRP H 106 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00342 (15942) covalent geometry : angle 0.67110 (21615) SS BOND : bond 0.00407 ( 33) SS BOND : angle 2.18290 ( 66) hydrogen bonds : bond 0.02982 ( 615) hydrogen bonds : angle 5.03748 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.73 seconds wall clock time: 50 minutes 40.46 seconds (3040.46 seconds total)