Starting phenix.real_space_refine on Wed Feb 4 15:22:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.map" model { file = "/net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ked_62290/02_2026/9ked_62290.cif" } resolution = 2.95 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= 0.001 sd= 0.025 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 90 5.16 5 C 7026 2.51 5 N 1962 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11277 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3731 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3731 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3731 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 25, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.85, per 1000 atoms: 0.25 Number of scatterers: 11277 At special positions: 0 Unit cell: (89.01, 89.01, 142.14, 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 90 16.00 O 2199 8.00 N 1962 7.00 C 7026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 479 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 319 " distance=2.02 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 479 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 272 " distance=2.04 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 319 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 479 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 272 " distance=2.04 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 319 " distance=2.02 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 490 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 31 " " NAG A 602 " - " ASN A 331 " " NAG B 601 " - " ASN B 31 " " NAG B 602 " - " ASN B 331 " " NAG C 601 " - " ASN C 31 " " NAG C 602 " - " ASN C 331 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 448.9 milliseconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 32 sheets defined 25.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.547A pdb=" N THR A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 399 removed outlier: 3.872A pdb=" N THR A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 416 through 467 removed outlier: 3.727A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 462 " --> pdb=" O HIS A 458 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.511A pdb=" N ASN B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.622A pdb=" N LYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 416 through 467 removed outlier: 3.791A pdb=" N ASP B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 462 " --> pdb=" O HIS B 458 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.593A pdb=" N LEU C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 379 through 399 removed outlier: 3.844A pdb=" N THR C 383 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'C' and resid 416 through 467 removed outlier: 3.817A pdb=" N ASP C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C 462 " --> pdb=" O HIS C 458 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 500 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.450A pdb=" N ASP A 43 " --> pdb=" O SER A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.242A pdb=" N ALA A 82 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 119 removed outlier: 6.955A pdb=" N GLU A 275 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 117 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 273 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 119 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP A 271 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL A 187 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE A 264 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 159 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 160 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 136 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 114 through 119 removed outlier: 6.955A pdb=" N GLU A 275 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 117 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 273 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 119 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N TRP A 271 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 144 removed outlier: 4.558A pdb=" N CYS A 143 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB1, first strand: chain 'A' and resid 299 through 301 Processing sheet with id=AB2, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.642A pdb=" N TYR A 308 " --> pdb=" O LYS A 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AB4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.493A pdb=" N ASP B 43 " --> pdb=" O SER B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.255A pdb=" N ALA B 82 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 114 through 119 removed outlier: 6.964A pdb=" N GLU B 275 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 117 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU B 273 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B 119 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP B 271 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 187 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE B 264 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 159 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 114 through 119 removed outlier: 6.964A pdb=" N GLU B 275 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 117 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU B 273 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS B 119 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TRP B 271 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 144 removed outlier: 3.799A pdb=" N SER B 151 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AC4, first strand: chain 'B' and resid 307 through 308 removed outlier: 3.580A pdb=" N TYR B 308 " --> pdb=" O LYS B 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 374 through 376 Processing sheet with id=AC6, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AC7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.398A pdb=" N ASP C 43 " --> pdb=" O SER C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AD1, first strand: chain 'C' and resid 114 through 119 removed outlier: 6.993A pdb=" N GLU C 275 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 117 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 273 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS C 119 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP C 271 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 187 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE C 264 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C 159 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 160 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 114 through 119 removed outlier: 6.993A pdb=" N GLU C 275 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 117 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU C 273 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS C 119 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TRP C 271 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AD4, first strand: chain 'C' and resid 299 through 301 Processing sheet with id=AD5, first strand: chain 'C' and resid 307 through 308 removed outlier: 3.503A pdb=" N TYR C 308 " --> pdb=" O LYS C 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 432 hydrogen bonds defined for protein. 1128 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: 1.76 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3761 1.35 - 1.47: 2515 1.47 - 1.59: 5073 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 11487 Sorted by residual: bond pdb=" CB LYS C 463 " pdb=" CG LYS C 463 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB MET A 475 " pdb=" CG MET A 475 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.74e+00 bond pdb=" CB LYS A 463 " pdb=" CG LYS A 463 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" CG LYS A 463 " pdb=" CD LYS A 463 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" CG GLU C 455 " pdb=" CD GLU C 455 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.98e+00 ... (remaining 11482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15200 2.03 - 4.06: 308 4.06 - 6.10: 40 6.10 - 8.13: 11 8.13 - 10.16: 5 Bond angle restraints: 15564 Sorted by residual: angle pdb=" CB LYS C 463 " pdb=" CG LYS C 463 " pdb=" CD LYS C 463 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB GLU B 455 " pdb=" CG GLU B 455 " pdb=" CD GLU B 455 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.70e+00 3.46e-01 1.48e+01 angle pdb=" C ASP A 474 " pdb=" N MET A 475 " pdb=" CA MET A 475 " ideal model delta sigma weight residual 120.60 126.66 -6.06 1.60e+00 3.91e-01 1.43e+01 angle pdb=" CB GLU A 455 " pdb=" CG GLU A 455 " pdb=" CD GLU A 455 " ideal model delta sigma weight residual 112.60 119.03 -6.43 1.70e+00 3.46e-01 1.43e+01 angle pdb=" CB LYS A 463 " pdb=" CG LYS A 463 " pdb=" CD LYS A 463 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 ... (remaining 15559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 5959 17.25 - 34.50: 795 34.50 - 51.75: 252 51.75 - 69.00: 71 69.00 - 86.25: 15 Dihedral angle restraints: 7092 sinusoidal: 2916 harmonic: 4176 Sorted by residual: dihedral pdb=" CB CYS A 293 " pdb=" SG CYS A 293 " pdb=" SG CYS A 319 " pdb=" CB CYS A 319 " ideal model delta sinusoidal sigma weight residual 93.00 28.27 64.73 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS B 293 " pdb=" SG CYS B 293 " pdb=" SG CYS B 319 " pdb=" CB CYS B 319 " ideal model delta sinusoidal sigma weight residual 93.00 36.47 56.53 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS C 293 " pdb=" SG CYS C 293 " pdb=" SG CYS C 319 " pdb=" CB CYS C 319 " ideal model delta sinusoidal sigma weight residual 93.00 37.19 55.81 1 1.00e+01 1.00e-02 4.21e+01 ... (remaining 7089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1215 0.037 - 0.074: 386 0.074 - 0.111: 146 0.111 - 0.148: 35 0.148 - 0.186: 6 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE B 117 " pdb=" N ILE B 117 " pdb=" C ILE B 117 " pdb=" CB ILE B 117 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 1785 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 509 " -0.026 2.00e-02 2.50e+03 2.76e-02 1.33e+01 pdb=" CG PHE B 509 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE B 509 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 509 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 509 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 509 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 509 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 455 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" CD GLU B 455 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU B 455 " 0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU B 455 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 455 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" CD GLU A 455 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU A 455 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 455 " 0.015 2.00e-02 2.50e+03 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 832 2.73 - 3.27: 10648 3.27 - 3.81: 17419 3.81 - 4.36: 19766 4.36 - 4.90: 35702 Nonbonded interactions: 84367 Sorted by model distance: nonbonded pdb=" OD1 ASN C 138 " pdb=" OG1 THR C 160 " model vdw 2.183 3.040 nonbonded pdb=" OE1 GLU B 493 " pdb=" OH TYR B 504 " model vdw 2.204 3.040 nonbonded pdb=" O ALA A 404 " pdb=" NH2 ARG C 324 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN B 95 " pdb=" ND2 ASN B 142 " model vdw 2.216 3.120 nonbonded pdb=" O CYS B 143 " pdb=" OG SER B 151 " model vdw 2.230 3.040 ... (remaining 84362 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.330 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11514 Z= 0.172 Angle : 0.706 10.161 15624 Z= 0.368 Chirality : 0.043 0.186 1788 Planarity : 0.005 0.052 2016 Dihedral : 17.842 86.248 4353 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.53 % Allowed : 37.46 % Favored : 58.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.65 (0.21), residues: 1461 helix: 1.82 (0.30), residues: 312 sheet: 0.50 (0.32), residues: 273 loop : -1.70 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 492 TYR 0.012 0.001 TYR B 210 PHE 0.062 0.002 PHE B 509 TRP 0.011 0.001 TRP A 271 HIS 0.009 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00367 (11487) covalent geometry : angle 0.70012 (15564) SS BOND : bond 0.00510 ( 21) SS BOND : angle 1.61690 ( 42) hydrogen bonds : bond 0.14236 ( 417) hydrogen bonds : angle 5.72812 ( 1128) link_NAG-ASN : bond 0.00418 ( 6) link_NAG-ASN : angle 1.53547 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 72 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.7975 (pmm) cc_final: 0.7711 (ptp) outliers start: 56 outliers final: 50 residues processed: 127 average time/residue: 0.4950 time to fit residues: 69.0932 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 69 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.046381 restraints weight = 37112.645| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.00 r_work: 0.2580 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11514 Z= 0.148 Angle : 0.580 7.040 15624 Z= 0.300 Chirality : 0.043 0.215 1788 Planarity : 0.004 0.040 2016 Dihedral : 7.096 57.913 1742 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.74 % Allowed : 30.74 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.52 (0.22), residues: 1461 helix: 2.32 (0.30), residues: 318 sheet: 0.21 (0.30), residues: 258 loop : -1.64 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.008 0.001 TYR C 210 PHE 0.014 0.001 PHE B 153 TRP 0.009 0.001 TRP B 271 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00328 (11487) covalent geometry : angle 0.57449 (15564) SS BOND : bond 0.00364 ( 21) SS BOND : angle 1.34312 ( 42) hydrogen bonds : bond 0.06201 ( 417) hydrogen bonds : angle 4.71178 ( 1128) link_NAG-ASN : bond 0.00506 ( 6) link_NAG-ASN : angle 1.62276 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 77 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 4 CYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6587 (m) REVERT: A 78 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: A 136 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9092 (pp) REVERT: A 506 MET cc_start: 0.7957 (mpt) cc_final: 0.7584 (mpp) REVERT: B 4 CYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6878 (m) REVERT: B 473 GLN cc_start: 0.6679 (mp10) cc_final: 0.6430 (mp10) REVERT: C 4 CYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6732 (m) REVERT: C 32 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8796 (mtp) REVERT: C 251 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: C 467 MET cc_start: 0.9256 (pmm) cc_final: 0.8735 (pmm) REVERT: C 506 MET cc_start: 0.8351 (mpt) cc_final: 0.7979 (mpt) outliers start: 71 outliers final: 26 residues processed: 142 average time/residue: 0.5582 time to fit residues: 86.2397 Evaluate side-chains 106 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 0.0770 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.047470 restraints weight = 37418.401| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.02 r_work: 0.2610 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11514 Z= 0.115 Angle : 0.546 7.253 15624 Z= 0.281 Chirality : 0.041 0.198 1788 Planarity : 0.004 0.040 2016 Dihedral : 5.736 55.012 1705 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.34 % Allowed : 30.34 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.34 (0.22), residues: 1461 helix: 2.57 (0.29), residues: 315 sheet: 0.42 (0.30), residues: 267 loop : -1.61 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.007 0.001 TYR A 210 PHE 0.039 0.001 PHE B 509 TRP 0.008 0.001 TRP A 271 HIS 0.003 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00251 (11487) covalent geometry : angle 0.54135 (15564) SS BOND : bond 0.00290 ( 21) SS BOND : angle 1.11009 ( 42) hydrogen bonds : bond 0.05700 ( 417) hydrogen bonds : angle 4.51727 ( 1128) link_NAG-ASN : bond 0.00422 ( 6) link_NAG-ASN : angle 1.46273 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 80 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 CYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6727 (m) REVERT: A 78 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8640 (mm-30) REVERT: A 167 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8578 (pp) REVERT: A 467 MET cc_start: 0.9161 (pmm) cc_final: 0.8804 (pmm) REVERT: A 506 MET cc_start: 0.7949 (mpt) cc_final: 0.7576 (mpp) REVERT: B 4 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6871 (m) REVERT: B 78 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8664 (mm-30) REVERT: B 127 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9224 (tt) REVERT: B 251 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: B 506 MET cc_start: 0.8958 (mpp) cc_final: 0.8100 (pmm) REVERT: C 4 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6949 (m) REVERT: C 251 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: C 463 LYS cc_start: 0.9537 (tppt) cc_final: 0.9330 (tmtt) REVERT: C 467 MET cc_start: 0.9253 (pmm) cc_final: 0.9042 (pmm) REVERT: C 506 MET cc_start: 0.8268 (mpt) cc_final: 0.7640 (mpt) outliers start: 66 outliers final: 26 residues processed: 141 average time/residue: 0.4805 time to fit residues: 74.1539 Evaluate side-chains 107 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 73 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.046384 restraints weight = 37750.477| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.93 r_work: 0.2585 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11514 Z= 0.145 Angle : 0.552 8.440 15624 Z= 0.282 Chirality : 0.042 0.193 1788 Planarity : 0.004 0.040 2016 Dihedral : 5.398 53.799 1699 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.99 % Allowed : 30.34 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.22), residues: 1461 helix: 2.60 (0.29), residues: 318 sheet: 0.44 (0.30), residues: 267 loop : -1.60 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.007 0.001 TYR B 202 PHE 0.013 0.001 PHE B 153 TRP 0.008 0.001 TRP B 271 HIS 0.002 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00336 (11487) covalent geometry : angle 0.54594 (15564) SS BOND : bond 0.00308 ( 21) SS BOND : angle 1.29699 ( 42) hydrogen bonds : bond 0.05899 ( 417) hydrogen bonds : angle 4.52240 ( 1128) link_NAG-ASN : bond 0.00309 ( 6) link_NAG-ASN : angle 1.54019 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 76 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8642 (mm-30) REVERT: A 136 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9047 (pp) REVERT: A 167 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8613 (pp) REVERT: A 251 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: A 463 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8772 (tmtt) REVERT: A 467 MET cc_start: 0.9132 (pmm) cc_final: 0.8778 (pmm) REVERT: A 506 MET cc_start: 0.7923 (mpt) cc_final: 0.7638 (mpt) REVERT: B 4 CYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6939 (m) REVERT: B 251 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 506 MET cc_start: 0.8945 (mpp) cc_final: 0.8120 (pmm) REVERT: C 32 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8862 (mtp) REVERT: C 251 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: C 463 LYS cc_start: 0.9550 (tppt) cc_final: 0.9334 (tppt) REVERT: C 467 MET cc_start: 0.9267 (pmm) cc_final: 0.8760 (pmm) REVERT: C 506 MET cc_start: 0.8231 (mpt) cc_final: 0.7831 (mpt) outliers start: 74 outliers final: 35 residues processed: 145 average time/residue: 0.5320 time to fit residues: 84.0044 Evaluate side-chains 115 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 134 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.045593 restraints weight = 37854.983| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.96 r_work: 0.2561 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11514 Z= 0.180 Angle : 0.585 8.013 15624 Z= 0.301 Chirality : 0.043 0.193 1788 Planarity : 0.004 0.039 2016 Dihedral : 5.404 53.532 1696 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.15 % Allowed : 30.50 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.38 (0.22), residues: 1461 helix: 2.58 (0.29), residues: 318 sheet: 0.33 (0.30), residues: 267 loop : -1.64 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 336 TYR 0.009 0.001 TYR B 202 PHE 0.009 0.001 PHE A 480 TRP 0.008 0.001 TRP B 271 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00422 (11487) covalent geometry : angle 0.57847 (15564) SS BOND : bond 0.00324 ( 21) SS BOND : angle 1.47668 ( 42) hydrogen bonds : bond 0.06241 ( 417) hydrogen bonds : angle 4.60674 ( 1128) link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.58670 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 72 time to evaluate : 0.376 Fit side-chains REVERT: A 78 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: A 167 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8652 (pp) REVERT: A 251 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: A 492 ARG cc_start: 0.9469 (mtm110) cc_final: 0.9203 (mtm110) REVERT: A 506 MET cc_start: 0.7939 (mpt) cc_final: 0.7609 (mpt) REVERT: B 78 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8670 (mm-30) REVERT: B 127 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9247 (tt) REVERT: B 251 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 463 LYS cc_start: 0.9609 (ttmm) cc_final: 0.9304 (tppt) REVERT: B 467 MET cc_start: 0.9524 (ptp) cc_final: 0.9111 (ptp) REVERT: B 506 MET cc_start: 0.8894 (mpp) cc_final: 0.8074 (pmm) REVERT: C 251 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: C 506 MET cc_start: 0.8281 (mpt) cc_final: 0.7839 (mpt) outliers start: 76 outliers final: 37 residues processed: 143 average time/residue: 0.5293 time to fit residues: 81.8308 Evaluate side-chains 111 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.045728 restraints weight = 37828.092| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 4.02 r_work: 0.2565 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11514 Z= 0.151 Angle : 0.584 9.059 15624 Z= 0.299 Chirality : 0.042 0.189 1788 Planarity : 0.004 0.039 2016 Dihedral : 5.260 52.275 1695 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.83 % Allowed : 30.91 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.36 (0.22), residues: 1461 helix: 2.60 (0.29), residues: 318 sheet: 0.32 (0.30), residues: 267 loop : -1.62 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 336 TYR 0.008 0.001 TYR B 202 PHE 0.008 0.001 PHE A 480 TRP 0.007 0.001 TRP B 271 HIS 0.003 0.001 HIS C 458 Details of bonding type rmsd covalent geometry : bond 0.00353 (11487) covalent geometry : angle 0.57838 (15564) SS BOND : bond 0.00342 ( 21) SS BOND : angle 1.34803 ( 42) hydrogen bonds : bond 0.06067 ( 417) hydrogen bonds : angle 4.53169 ( 1128) link_NAG-ASN : bond 0.00311 ( 6) link_NAG-ASN : angle 1.52319 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 69 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8626 (mm-30) REVERT: A 136 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9040 (pp) REVERT: A 167 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8643 (pp) REVERT: A 251 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: A 463 LYS cc_start: 0.9640 (tppt) cc_final: 0.9416 (tmtt) REVERT: A 506 MET cc_start: 0.7945 (mpt) cc_final: 0.7582 (mpt) REVERT: B 78 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: B 127 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9234 (tt) REVERT: B 251 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: B 506 MET cc_start: 0.8892 (mpp) cc_final: 0.8060 (pmm) REVERT: C 251 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: C 506 MET cc_start: 0.8289 (mpt) cc_final: 0.7865 (mpt) outliers start: 72 outliers final: 43 residues processed: 137 average time/residue: 0.5204 time to fit residues: 77.5480 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 68 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.044959 restraints weight = 38123.354| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 4.02 r_work: 0.2544 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11514 Z= 0.193 Angle : 0.607 8.949 15624 Z= 0.312 Chirality : 0.043 0.191 1788 Planarity : 0.004 0.039 2016 Dihedral : 5.390 51.824 1695 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.23 % Allowed : 30.74 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.45 (0.22), residues: 1461 helix: 2.53 (0.29), residues: 318 sheet: -0.01 (0.30), residues: 273 loop : -1.59 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.009 0.001 TYR C 202 PHE 0.008 0.001 PHE B 153 TRP 0.008 0.001 TRP B 271 HIS 0.003 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00454 (11487) covalent geometry : angle 0.60039 (15564) SS BOND : bond 0.00390 ( 21) SS BOND : angle 1.50253 ( 42) hydrogen bonds : bond 0.06357 ( 417) hydrogen bonds : angle 4.63098 ( 1128) link_NAG-ASN : bond 0.00258 ( 6) link_NAG-ASN : angle 1.60838 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 69 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: A 167 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 251 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: A 506 MET cc_start: 0.7951 (mpt) cc_final: 0.7553 (mpt) REVERT: B 78 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8792 (mm-30) REVERT: B 127 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9243 (tt) REVERT: B 251 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 463 LYS cc_start: 0.9602 (ttmm) cc_final: 0.9334 (tppt) REVERT: B 506 MET cc_start: 0.8883 (mpp) cc_final: 0.8052 (pmm) REVERT: C 32 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8883 (mtp) REVERT: C 251 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: C 467 MET cc_start: 0.9574 (ptp) cc_final: 0.9209 (pmm) REVERT: C 506 MET cc_start: 0.8268 (mpt) cc_final: 0.7743 (mpt) outliers start: 77 outliers final: 49 residues processed: 141 average time/residue: 0.4767 time to fit residues: 73.3978 Evaluate side-chains 125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 68 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN B 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.045260 restraints weight = 37828.137| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 4.01 r_work: 0.2551 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11514 Z= 0.172 Angle : 0.610 11.408 15624 Z= 0.311 Chirality : 0.043 0.190 1788 Planarity : 0.004 0.039 2016 Dihedral : 5.346 51.169 1695 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.58 % Allowed : 31.80 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.43 (0.22), residues: 1461 helix: 2.52 (0.29), residues: 318 sheet: -0.03 (0.29), residues: 288 loop : -1.58 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.009 0.001 TYR B 202 PHE 0.009 0.001 PHE B 153 TRP 0.007 0.001 TRP B 271 HIS 0.005 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00404 (11487) covalent geometry : angle 0.60459 (15564) SS BOND : bond 0.00363 ( 21) SS BOND : angle 1.44508 ( 42) hydrogen bonds : bond 0.06255 ( 417) hydrogen bonds : angle 4.62264 ( 1128) link_NAG-ASN : bond 0.00292 ( 6) link_NAG-ASN : angle 1.57714 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 69 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8633 (mm-30) REVERT: A 167 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8681 (pp) REVERT: A 251 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: A 506 MET cc_start: 0.7930 (mpt) cc_final: 0.7518 (mpt) REVERT: B 78 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8698 (mm-30) REVERT: B 127 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9240 (tt) REVERT: B 251 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 506 MET cc_start: 0.8902 (mpp) cc_final: 0.8041 (pmm) REVERT: B 510 LYS cc_start: 0.7945 (mppt) cc_final: 0.7653 (mppt) REVERT: C 32 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8863 (mtp) REVERT: C 251 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: C 463 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8839 (tmtt) REVERT: C 467 MET cc_start: 0.9593 (ptp) cc_final: 0.9201 (pmm) REVERT: C 506 MET cc_start: 0.8253 (mpt) cc_final: 0.7731 (mpt) outliers start: 69 outliers final: 53 residues processed: 137 average time/residue: 0.4780 time to fit residues: 71.2042 Evaluate side-chains 130 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 69 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN C 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.045091 restraints weight = 37978.755| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.98 r_work: 0.2548 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11514 Z= 0.184 Angle : 0.631 10.056 15624 Z= 0.323 Chirality : 0.043 0.190 1788 Planarity : 0.004 0.039 2016 Dihedral : 5.377 50.547 1695 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.58 % Allowed : 31.80 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.45 (0.22), residues: 1461 helix: 2.49 (0.29), residues: 318 sheet: -0.03 (0.29), residues: 288 loop : -1.59 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.009 0.001 TYR B 202 PHE 0.009 0.001 PHE A 509 TRP 0.007 0.001 TRP B 271 HIS 0.002 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00434 (11487) covalent geometry : angle 0.62503 (15564) SS BOND : bond 0.00384 ( 21) SS BOND : angle 1.48139 ( 42) hydrogen bonds : bond 0.06340 ( 417) hydrogen bonds : angle 4.64913 ( 1128) link_NAG-ASN : bond 0.00276 ( 6) link_NAG-ASN : angle 1.60018 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 70 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: A 167 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8732 (pp) REVERT: A 251 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: A 506 MET cc_start: 0.7935 (mpt) cc_final: 0.7501 (mpt) REVERT: B 78 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8808 (mm-30) REVERT: B 127 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9250 (tt) REVERT: B 251 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: B 437 GLN cc_start: 0.9145 (tt0) cc_final: 0.8878 (tt0) REVERT: B 463 LYS cc_start: 0.9618 (ttmm) cc_final: 0.9374 (tppt) REVERT: B 506 MET cc_start: 0.8889 (mpp) cc_final: 0.8022 (pmm) REVERT: C 32 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8900 (mtp) REVERT: C 251 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: C 463 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9059 (tmtt) REVERT: C 506 MET cc_start: 0.8274 (mpt) cc_final: 0.7718 (mpt) outliers start: 69 outliers final: 51 residues processed: 138 average time/residue: 0.4722 time to fit residues: 71.2046 Evaluate side-chains 125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 66 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 490 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047305 restraints weight = 37426.146| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.99 r_work: 0.2611 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11514 Z= 0.117 Angle : 0.600 11.979 15624 Z= 0.301 Chirality : 0.042 0.185 1788 Planarity : 0.004 0.040 2016 Dihedral : 4.937 47.122 1695 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.96 % Allowed : 33.33 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.33 (0.22), residues: 1461 helix: 2.59 (0.29), residues: 315 sheet: 0.31 (0.29), residues: 267 loop : -1.56 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.008 0.001 TYR B 202 PHE 0.009 0.001 PHE A 480 TRP 0.008 0.001 TRP A 271 HIS 0.003 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00262 (11487) covalent geometry : angle 0.59674 (15564) SS BOND : bond 0.00258 ( 21) SS BOND : angle 0.99031 ( 42) hydrogen bonds : bond 0.05385 ( 417) hydrogen bonds : angle 4.49151 ( 1128) link_NAG-ASN : bond 0.00424 ( 6) link_NAG-ASN : angle 1.40512 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 75 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: A 251 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: A 506 MET cc_start: 0.7976 (mpt) cc_final: 0.7555 (mpt) REVERT: B 78 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8710 (mm-30) REVERT: B 127 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9201 (tt) REVERT: B 251 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 437 GLN cc_start: 0.9097 (tt0) cc_final: 0.8782 (tt0) REVERT: B 463 LYS cc_start: 0.9568 (ttmm) cc_final: 0.9119 (tppt) REVERT: B 467 MET cc_start: 0.9462 (ptp) cc_final: 0.8299 (pmm) REVERT: B 506 MET cc_start: 0.8876 (mpp) cc_final: 0.8020 (pmm) REVERT: C 251 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: C 408 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7353 (m) REVERT: C 463 LYS cc_start: 0.9262 (tmtt) cc_final: 0.8895 (tmtt) REVERT: C 506 MET cc_start: 0.8183 (mpt) cc_final: 0.7646 (mpt) outliers start: 49 outliers final: 31 residues processed: 120 average time/residue: 0.5452 time to fit residues: 70.9265 Evaluate side-chains 110 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 CYS Chi-restraints excluded: chain B residue 490 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 CYS Chi-restraints excluded: chain C residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.044656 restraints weight = 38078.932| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.96 r_work: 0.2538 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11514 Z= 0.226 Angle : 0.692 12.326 15624 Z= 0.351 Chirality : 0.044 0.192 1788 Planarity : 0.004 0.038 2016 Dihedral : 5.377 48.256 1693 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.48 % Allowed : 34.47 % Favored : 62.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.40 (0.22), residues: 1461 helix: 2.49 (0.29), residues: 318 sheet: 0.33 (0.30), residues: 267 loop : -1.63 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.009 0.001 TYR C 202 PHE 0.010 0.001 PHE B 153 TRP 0.008 0.001 TRP B 271 HIS 0.003 0.001 HIS A 458 Details of bonding type rmsd covalent geometry : bond 0.00535 (11487) covalent geometry : angle 0.68532 (15564) SS BOND : bond 0.00452 ( 21) SS BOND : angle 1.67026 ( 42) hydrogen bonds : bond 0.06497 ( 417) hydrogen bonds : angle 4.71492 ( 1128) link_NAG-ASN : bond 0.00209 ( 6) link_NAG-ASN : angle 1.66394 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.58 seconds wall clock time: 51 minutes 38.89 seconds (3098.89 seconds total)