Starting phenix.real_space_refine on Thu Sep 18 05:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyt_39678/09_2025/8yyt_39678.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 117 5.16 5 C 8962 2.51 5 N 2443 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14147 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6337 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 41, 'TRANS': 743} Chain breaks: 20 Chain: "B" Number of atoms: 6358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6358 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 41, 'TRANS': 746} Chain breaks: 17 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "E" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Chain: "F" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.23 Number of scatterers: 14147 At special positions: 0 Unit cell: (125.4, 125.4, 165, 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 117 16.00 O 2625 8.00 N 2443 7.00 C 8962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 887 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 215 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 36 " - pdb=" SG CYS D 41 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 41 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 36 " - pdb=" SG CYS F 41 " 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 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 588.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3298 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 29 sheets defined 16.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.537A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.617A pdb=" N ILE A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 removed outlier: 3.561A pdb=" N GLU A 670 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 741 removed outlier: 3.513A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.537A pdb=" N CYS B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 294 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 378 through 386 Processing helix chain 'B' and resid 462 through 473 removed outlier: 3.606A pdb=" N ILE B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 removed outlier: 3.562A pdb=" N GLU B 670 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 741 removed outlier: 3.706A pdb=" N PHE B 728 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'C' and resid 9 through 15 removed outlier: 3.665A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.046A pdb=" N GLU C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.624A pdb=" N GLU D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 42 through 47 removed outlier: 4.043A pdb=" N GLU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'E' and resid 8 through 20 removed outlier: 4.541A pdb=" N TYR E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.631A pdb=" N TYR F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 5.941A pdb=" N LEU A 60 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE A 91 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 62 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 88 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE A 123 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 90 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 307 removed outlier: 3.725A pdb=" N ILE A 312 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 561 removed outlier: 3.534A pdb=" N TYR A 534 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 529 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 626 through 626 Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 626 Processing sheet with id=AB3, first strand: chain 'A' and resid 786 through 789 removed outlier: 3.639A pdb=" N TYR A 806 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 830 " --> pdb=" O TYR A 806 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 846 through 849 removed outlier: 3.549A pdb=" N THR A 846 " --> pdb=" O MET A 858 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 855 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 883 through 889 removed outlier: 3.806A pdb=" N LEU A 871 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE A 913 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP A 924 " --> pdb=" O ILE A 913 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA A 915 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 883 through 889 removed outlier: 3.806A pdb=" N LEU A 871 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.027A pdb=" N LEU B 60 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE B 91 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B 62 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 88 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 123 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 90 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'B' and resid 198 through 201 Processing sheet with id=AC1, first strand: chain 'B' and resid 305 through 307 removed outlier: 3.727A pdb=" N ILE B 312 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AC3, first strand: chain 'B' and resid 345 through 348 Processing sheet with id=AC4, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC5, first strand: chain 'B' and resid 504 through 507 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 561 removed outlier: 3.545A pdb=" N TYR B 534 " --> pdb=" O THR B 557 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 626 through 631 removed outlier: 5.132A pdb=" N ASP B 627 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 643 " --> pdb=" O ASP B 627 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 795 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 786 through 789 removed outlier: 3.638A pdb=" N TYR B 806 " --> pdb=" O ALA B 830 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 830 " --> pdb=" O TYR B 806 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 846 through 849 removed outlier: 3.557A pdb=" N THR B 846 " --> pdb=" O MET B 858 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 855 " --> pdb=" O LEU B 901 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.810A pdb=" N LEU B 871 " --> pdb=" O THR B 916 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 913 " --> pdb=" O TRP B 924 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP B 924 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA B 915 " --> pdb=" O GLY B 922 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.810A pdb=" N LEU B 871 " --> pdb=" O THR B 916 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4633 1.35 - 1.47: 3447 1.47 - 1.59: 6235 1.59 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14453 Sorted by residual: bond pdb=" C ARG B 436 " pdb=" N GLN B 437 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.07e+00 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 1.440 0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" CB ASP B 431 " pdb=" CG ASP B 431 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CB PRO A 270 " pdb=" CG PRO A 270 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.03e+00 bond pdb=" C GLU B 864 " pdb=" N PRO B 865 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.26e-01 ... (remaining 14448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 19165 2.12 - 4.24: 317 4.24 - 6.35: 44 6.35 - 8.47: 5 8.47 - 10.59: 6 Bond angle restraints: 19537 Sorted by residual: angle pdb=" C VAL E 12 " pdb=" N GLU E 13 " pdb=" CA GLU E 13 " ideal model delta sigma weight residual 122.54 116.24 6.30 1.65e+00 3.67e-01 1.46e+01 angle pdb=" CB MET A 83 " pdb=" CG MET A 83 " pdb=" SD MET A 83 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CB MET B 83 " pdb=" CG MET B 83 " pdb=" SD MET B 83 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA LYS B 67 " pdb=" CB LYS B 67 " pdb=" CG LYS B 67 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.54e+00 angle pdb=" CA LYS A 67 " pdb=" CB LYS A 67 " pdb=" CG LYS A 67 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.40e+00 ... (remaining 19532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 7502 18.03 - 36.07: 939 36.07 - 54.10: 224 54.10 - 72.13: 36 72.13 - 90.17: 26 Dihedral angle restraints: 8727 sinusoidal: 3639 harmonic: 5088 Sorted by residual: dihedral pdb=" CB CYS F 36 " pdb=" SG CYS F 36 " pdb=" SG CYS F 41 " pdb=" CB CYS F 41 " ideal model delta sinusoidal sigma weight residual -86.00 -176.17 90.17 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS E 36 " pdb=" SG CYS E 36 " pdb=" SG CYS E 41 " pdb=" CB CYS E 41 " ideal model delta sinusoidal sigma weight residual 93.00 -176.94 -90.06 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS C 36 " pdb=" SG CYS C 36 " pdb=" SG CYS C 41 " pdb=" CB CYS C 41 " ideal model delta sinusoidal sigma weight residual 93.00 22.98 70.02 1 1.00e+01 1.00e-02 6.32e+01 ... (remaining 8724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1568 0.044 - 0.087: 391 0.087 - 0.130: 161 0.130 - 0.174: 9 0.174 - 0.217: 1 Chirality restraints: 2130 Sorted by residual: chirality pdb=" CB VAL E 12 " pdb=" CA VAL E 12 " pdb=" CG1 VAL E 12 " pdb=" CG2 VAL E 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU B 528 " pdb=" CB LEU B 528 " pdb=" CD1 LEU B 528 " pdb=" CD2 LEU B 528 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CG LEU A 528 " pdb=" CB LEU A 528 " pdb=" CD1 LEU A 528 " pdb=" CD2 LEU A 528 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2127 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 270 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 269 " 0.046 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO B 270 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 268 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO B 269 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 269 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 269 " -0.035 5.00e-02 4.00e+02 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1032 2.74 - 3.28: 14427 3.28 - 3.82: 23630 3.82 - 4.36: 27358 4.36 - 4.90: 45460 Nonbonded interactions: 111907 Sorted by model distance: nonbonded pdb=" O HIS A 802 " pdb=" OG1 THR A 832 " model vdw 2.195 3.040 nonbonded pdb=" O HIS B 802 " pdb=" OG1 THR B 832 " model vdw 2.214 3.040 nonbonded pdb=" NZ LYS A 294 " pdb=" OD1 ASN A 295 " model vdw 2.264 3.120 nonbonded pdb=" NZ LYS B 294 " pdb=" OD1 ASN B 295 " model vdw 2.265 3.120 nonbonded pdb=" O ASP B 734 " pdb=" ND2 ASN B 738 " model vdw 2.265 3.120 ... (remaining 111902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 454 or resid 456 through 934)) selection = (chain 'B' and (resid 28 through 124 or resid 126 through 430 or resid 433 throu \ gh 437 or resid 439 through 626 or resid 628 through 934)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.003 0.052 14493 Z= 0.125 Angle : 0.684 10.591 19617 Z= 0.354 Chirality : 0.043 0.217 2130 Planarity : 0.005 0.089 2512 Dihedral : 16.574 85.474 5309 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.06 % Allowed : 25.64 % Favored : 74.29 % 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 aren not related in a simple way. whole: -1.63 (0.21), residues: 1663 helix: -1.75 (0.33), residues: 213 sheet: -0.67 (0.28), residues: 315 loop : -1.09 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 145 TYR 0.029 0.001 TYR B 401 PHE 0.014 0.001 PHE A 732 TRP 0.025 0.002 TRP A 642 HIS 0.004 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00273 (14453) covalent geometry : angle 0.68389 (19537) SS BOND : bond 0.00162 ( 40) SS BOND : angle 0.71973 ( 80) hydrogen bonds : bond 0.26585 ( 313) hydrogen bonds : angle 10.62398 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 MET cc_start: 0.8765 (pmm) cc_final: 0.8519 (pmm) REVERT: B 833 MET cc_start: 0.8870 (pmm) cc_final: 0.8630 (pmm) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1302 time to fit residues: 12.2417 Evaluate side-chains 60 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 325 ASN C 51 ASN D 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.143571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.112882 restraints weight = 86130.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.115551 restraints weight = 52914.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115579 restraints weight = 33931.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.116138 restraints weight = 28795.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.116139 restraints weight = 27429.712| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14493 Z= 0.149 Angle : 0.613 6.057 19617 Z= 0.321 Chirality : 0.044 0.162 2130 Planarity : 0.005 0.067 2512 Dihedral : 4.805 39.099 1894 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.89 % Allowed : 22.25 % Favored : 74.86 % 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 aren not related in a simple way. whole: -1.42 (0.21), residues: 1663 helix: -1.35 (0.33), residues: 226 sheet: -0.66 (0.27), residues: 336 loop : -0.94 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.015 0.001 TYR B 457 PHE 0.021 0.001 PHE B 658 TRP 0.011 0.001 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00330 (14453) covalent geometry : angle 0.61292 (19537) SS BOND : bond 0.00218 ( 40) SS BOND : angle 0.61798 ( 80) hydrogen bonds : bond 0.04204 ( 313) hydrogen bonds : angle 7.23579 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 62 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.8735 (pmm) cc_final: 0.8493 (pmm) REVERT: B 321 MET cc_start: 0.8185 (ppp) cc_final: 0.7915 (ppp) REVERT: B 531 MET cc_start: 0.8765 (pmm) cc_final: 0.8534 (pmm) REVERT: B 580 MET cc_start: 0.9562 (pmm) cc_final: 0.9182 (pmm) outliers start: 46 outliers final: 20 residues processed: 107 average time/residue: 0.1166 time to fit residues: 19.2492 Evaluate side-chains 77 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 88 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 123 optimal weight: 0.0980 chunk 44 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 654 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 HIS ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.121793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.096601 restraints weight = 85535.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.098081 restraints weight = 52597.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099027 restraints weight = 38989.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099669 restraints weight = 32272.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.099807 restraints weight = 28694.211| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14493 Z= 0.219 Angle : 0.656 8.235 19617 Z= 0.339 Chirality : 0.045 0.176 2130 Planarity : 0.005 0.064 2512 Dihedral : 5.064 40.622 1894 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.46 % Allowed : 22.82 % Favored : 73.73 % 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 aren not related in a simple way. whole: -1.45 (0.21), residues: 1663 helix: -0.94 (0.36), residues: 222 sheet: -0.73 (0.27), residues: 350 loop : -1.05 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 729 TYR 0.019 0.002 TYR B 171 PHE 0.021 0.002 PHE B 732 TRP 0.013 0.001 TRP B 578 HIS 0.004 0.001 HIS B 654 Details of bonding type rmsd covalent geometry : bond 0.00494 (14453) covalent geometry : angle 0.65582 (19537) SS BOND : bond 0.00396 ( 40) SS BOND : angle 0.77414 ( 80) hydrogen bonds : bond 0.04359 ( 313) hydrogen bonds : angle 6.53487 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 58 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 368 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8778 (pp) REVERT: A 382 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: A 470 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: A 659 TRP cc_start: 0.5957 (OUTLIER) cc_final: 0.5315 (p90) REVERT: B 327 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 368 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8751 (pp) REVERT: B 382 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: B 470 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: B 659 TRP cc_start: 0.5938 (OUTLIER) cc_final: 0.5251 (p90) REVERT: B 833 MET cc_start: 0.9015 (pmm) cc_final: 0.8796 (pmm) REVERT: E 4 GLN cc_start: 0.2581 (OUTLIER) cc_final: 0.2123 (tt0) REVERT: F 4 GLN cc_start: 0.2509 (OUTLIER) cc_final: 0.2148 (tt0) outliers start: 55 outliers final: 36 residues processed: 112 average time/residue: 0.1260 time to fit residues: 21.2025 Evaluate side-chains 104 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 56 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 4 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 151 optimal weight: 40.0000 chunk 83 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.121781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096903 restraints weight = 87677.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.098396 restraints weight = 52420.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.099281 restraints weight = 38298.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.099921 restraints weight = 31612.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.100430 restraints weight = 28239.050| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14493 Z= 0.111 Angle : 0.580 7.764 19617 Z= 0.297 Chirality : 0.042 0.141 2130 Planarity : 0.005 0.096 2512 Dihedral : 4.843 41.660 1894 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.83 % Allowed : 22.50 % Favored : 73.66 % 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 aren not related in a simple way. whole: -1.33 (0.21), residues: 1663 helix: -0.89 (0.35), residues: 222 sheet: -0.74 (0.27), residues: 357 loop : -0.93 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.011 0.001 TYR A 118 PHE 0.015 0.001 PHE B 658 TRP 0.010 0.001 TRP A 439 HIS 0.003 0.000 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00255 (14453) covalent geometry : angle 0.58006 (19537) SS BOND : bond 0.00201 ( 40) SS BOND : angle 0.59683 ( 80) hydrogen bonds : bond 0.03513 ( 313) hydrogen bonds : angle 6.25748 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 57 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8545 (mt) REVERT: A 382 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: A 531 MET cc_start: 0.8805 (pmm) cc_final: 0.8503 (pmm) REVERT: A 580 MET cc_start: 0.9540 (pmm) cc_final: 0.9013 (pmm) REVERT: A 659 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.5533 (p90) REVERT: B 261 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: B 327 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (mt) REVERT: B 368 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8716 (pp) REVERT: B 382 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: B 531 MET cc_start: 0.8821 (pmm) cc_final: 0.8581 (pmm) REVERT: B 659 TRP cc_start: 0.6035 (OUTLIER) cc_final: 0.5529 (p90) REVERT: B 733 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8330 (mm-30) REVERT: E 4 GLN cc_start: 0.2637 (OUTLIER) cc_final: 0.2381 (tt0) outliers start: 61 outliers final: 32 residues processed: 116 average time/residue: 0.1248 time to fit residues: 21.9449 Evaluate side-chains 97 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 214 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.123645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.098499 restraints weight = 87095.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.099970 restraints weight = 52871.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.100988 restraints weight = 39135.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101631 restraints weight = 32066.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101910 restraints weight = 28323.481| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14493 Z= 0.227 Angle : 0.659 7.574 19617 Z= 0.338 Chirality : 0.045 0.270 2130 Planarity : 0.005 0.062 2512 Dihedral : 5.091 42.532 1894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.34 % Allowed : 24.01 % Favored : 71.65 % 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 aren not related in a simple way. whole: -1.40 (0.21), residues: 1663 helix: -0.89 (0.36), residues: 222 sheet: -0.51 (0.27), residues: 339 loop : -1.09 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 297 TYR 0.017 0.002 TYR B 457 PHE 0.014 0.002 PHE B 115 TRP 0.012 0.001 TRP A 578 HIS 0.006 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00513 (14453) covalent geometry : angle 0.65868 (19537) SS BOND : bond 0.00368 ( 40) SS BOND : angle 0.74738 ( 80) hydrogen bonds : bond 0.03795 ( 313) hydrogen bonds : angle 6.13820 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 58 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7412 (mmm) cc_final: 0.7209 (mmm) REVERT: A 327 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 368 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 382 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8648 (tm-30) REVERT: A 659 TRP cc_start: 0.6035 (OUTLIER) cc_final: 0.5321 (p90) REVERT: B 65 MET cc_start: 0.7535 (mmm) cc_final: 0.7307 (mmm) REVERT: B 261 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: B 327 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8599 (mt) REVERT: B 368 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8678 (pp) REVERT: B 659 TRP cc_start: 0.5961 (OUTLIER) cc_final: 0.5195 (p90) REVERT: D 45 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8954 (pm20) outliers start: 69 outliers final: 45 residues processed: 121 average time/residue: 0.1281 time to fit residues: 22.4755 Evaluate side-chains 109 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 55 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 786 PHE Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 44 TYR Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 56 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.119472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.094475 restraints weight = 88128.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.095916 restraints weight = 53251.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.096890 restraints weight = 39169.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.097483 restraints weight = 32343.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097684 restraints weight = 28626.012| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14493 Z= 0.211 Angle : 0.640 12.966 19617 Z= 0.330 Chirality : 0.045 0.221 2130 Planarity : 0.004 0.064 2512 Dihedral : 5.196 44.804 1894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.71 % Allowed : 23.82 % Favored : 71.46 % 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 aren not related in a simple way. whole: -1.39 (0.21), residues: 1663 helix: -0.93 (0.36), residues: 222 sheet: -0.46 (0.27), residues: 336 loop : -1.09 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.018 0.001 TYR A 534 PHE 0.024 0.002 PHE A 454 TRP 0.018 0.002 TRP A 556 HIS 0.006 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00476 (14453) covalent geometry : angle 0.63936 (19537) SS BOND : bond 0.00362 ( 40) SS BOND : angle 0.79662 ( 80) hydrogen bonds : bond 0.03727 ( 313) hydrogen bonds : angle 6.13789 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 59 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7516 (mmm) cc_final: 0.7300 (mmm) REVERT: A 382 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: A 531 MET cc_start: 0.8750 (pmm) cc_final: 0.8444 (pmm) REVERT: A 659 TRP cc_start: 0.6227 (OUTLIER) cc_final: 0.5417 (p90) REVERT: B 65 MET cc_start: 0.7411 (mmm) cc_final: 0.7209 (mmm) REVERT: B 368 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8555 (pp) REVERT: B 382 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: B 531 MET cc_start: 0.8884 (pmm) cc_final: 0.8630 (pmm) REVERT: B 659 TRP cc_start: 0.6092 (OUTLIER) cc_final: 0.5285 (p90) REVERT: B 733 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8461 (mm-30) REVERT: B 833 MET cc_start: 0.8927 (pmm) cc_final: 0.8637 (pmm) outliers start: 75 outliers final: 51 residues processed: 127 average time/residue: 0.1291 time to fit residues: 24.5410 Evaluate side-chains 113 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 56 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 655 TYR Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 786 PHE Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 44 TYR Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 82 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 0.0370 chunk 140 optimal weight: 0.6980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.105068 restraints weight = 66016.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.104699 restraints weight = 56825.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104405 restraints weight = 55018.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.104586 restraints weight = 48727.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.104783 restraints weight = 44059.388| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14493 Z= 0.103 Angle : 0.592 11.308 19617 Z= 0.301 Chirality : 0.043 0.245 2130 Planarity : 0.004 0.063 2512 Dihedral : 4.903 45.256 1894 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.33 % Allowed : 25.27 % Favored : 71.40 % 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 aren not related in a simple way. whole: -1.15 (0.21), residues: 1663 helix: -0.61 (0.37), residues: 210 sheet: -0.31 (0.28), residues: 324 loop : -0.95 (0.20), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.012 0.001 TYR B 872 PHE 0.020 0.001 PHE A 283 TRP 0.015 0.001 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00238 (14453) covalent geometry : angle 0.59154 (19537) SS BOND : bond 0.00157 ( 40) SS BOND : angle 0.63511 ( 80) hydrogen bonds : bond 0.03319 ( 313) hydrogen bonds : angle 5.97777 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7199 (mmm) cc_final: 0.6989 (mmm) REVERT: A 382 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: A 531 MET cc_start: 0.8814 (pmm) cc_final: 0.8528 (pmm) REVERT: A 659 TRP cc_start: 0.5821 (OUTLIER) cc_final: 0.5112 (p90) REVERT: A 833 MET cc_start: 0.8991 (pmm) cc_final: 0.8786 (pmm) REVERT: B 65 MET cc_start: 0.7205 (mmm) cc_final: 0.6990 (mmm) REVERT: B 346 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (tttp) REVERT: B 382 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: B 531 MET cc_start: 0.8843 (pmm) cc_final: 0.8555 (pmm) REVERT: B 659 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.5337 (p90) REVERT: B 833 MET cc_start: 0.8988 (pmm) cc_final: 0.8763 (pmm) outliers start: 53 outliers final: 36 residues processed: 106 average time/residue: 0.1287 time to fit residues: 20.2812 Evaluate side-chains 95 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 104 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS C 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.119722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.095029 restraints weight = 88234.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095993 restraints weight = 56145.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.096734 restraints weight = 44886.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.097476 restraints weight = 33380.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.097613 restraints weight = 29908.289| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14493 Z= 0.150 Angle : 0.594 8.412 19617 Z= 0.304 Chirality : 0.043 0.202 2130 Planarity : 0.004 0.062 2512 Dihedral : 4.945 44.963 1894 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.39 % Allowed : 25.08 % Favored : 71.53 % 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 aren not related in a simple way. whole: -1.11 (0.21), residues: 1663 helix: -0.59 (0.37), residues: 211 sheet: -0.32 (0.28), residues: 335 loop : -0.90 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 297 TYR 0.012 0.001 TYR B 872 PHE 0.013 0.002 PHE B 658 TRP 0.010 0.001 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00347 (14453) covalent geometry : angle 0.59370 (19537) SS BOND : bond 0.00228 ( 40) SS BOND : angle 0.60558 ( 80) hydrogen bonds : bond 0.03354 ( 313) hydrogen bonds : angle 5.88518 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 55 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: A 390 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: A 531 MET cc_start: 0.8888 (pmm) cc_final: 0.8602 (pmm) REVERT: A 659 TRP cc_start: 0.6134 (OUTLIER) cc_final: 0.5503 (p90) REVERT: B 382 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8677 (tm-30) REVERT: B 390 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 531 MET cc_start: 0.8890 (pmm) cc_final: 0.8584 (pmm) REVERT: B 659 TRP cc_start: 0.6066 (OUTLIER) cc_final: 0.5388 (p90) REVERT: B 733 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: B 858 MET cc_start: -0.6189 (tpt) cc_final: -0.6496 (tpt) outliers start: 54 outliers final: 38 residues processed: 107 average time/residue: 0.1141 time to fit residues: 18.7837 Evaluate side-chains 100 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 55 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 861 GLU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.124215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099223 restraints weight = 84347.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100724 restraints weight = 50370.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.101736 restraints weight = 36318.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.102317 restraints weight = 29658.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.102760 restraints weight = 26228.872| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14493 Z= 0.153 Angle : 0.633 12.297 19617 Z= 0.316 Chirality : 0.044 0.158 2130 Planarity : 0.004 0.060 2512 Dihedral : 4.999 45.445 1894 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.33 % Allowed : 24.89 % Favored : 71.78 % 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 aren not related in a simple way. whole: -1.10 (0.21), residues: 1663 helix: -0.57 (0.37), residues: 211 sheet: -0.27 (0.28), residues: 335 loop : -0.92 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 297 TYR 0.015 0.001 TYR C 16 PHE 0.019 0.002 PHE B 283 TRP 0.013 0.001 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00352 (14453) covalent geometry : angle 0.63336 (19537) SS BOND : bond 0.00244 ( 40) SS BOND : angle 0.64412 ( 80) hydrogen bonds : bond 0.03314 ( 313) hydrogen bonds : angle 5.90194 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 57 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.6903 (tttm) REVERT: A 382 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: A 390 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: A 531 MET cc_start: 0.8826 (pmm) cc_final: 0.8536 (pmm) REVERT: A 659 TRP cc_start: 0.5963 (OUTLIER) cc_final: 0.4972 (p90) REVERT: B 346 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7040 (tttm) REVERT: B 382 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8695 (tm-30) REVERT: B 390 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: B 531 MET cc_start: 0.8942 (pmm) cc_final: 0.8658 (pmm) REVERT: B 580 MET cc_start: 0.9191 (pmm) cc_final: 0.8948 (pmm) REVERT: B 659 TRP cc_start: 0.5818 (OUTLIER) cc_final: 0.4984 (p90) REVERT: B 733 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: B 858 MET cc_start: -0.5909 (tpt) cc_final: -0.6268 (tpt) outliers start: 53 outliers final: 42 residues processed: 107 average time/residue: 0.1255 time to fit residues: 20.4007 Evaluate side-chains 106 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 55 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 786 PHE Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 861 GLU Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.119304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.094640 restraints weight = 86709.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.096365 restraints weight = 54056.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.096782 restraints weight = 40134.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.097028 restraints weight = 30498.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097320 restraints weight = 28397.201| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14493 Z= 0.181 Angle : 0.647 9.656 19617 Z= 0.325 Chirality : 0.044 0.157 2130 Planarity : 0.004 0.061 2512 Dihedral : 5.121 46.418 1894 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.39 % Allowed : 25.20 % Favored : 71.40 % 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 aren not related in a simple way. whole: -1.16 (0.21), residues: 1663 helix: -0.58 (0.38), residues: 211 sheet: -0.35 (0.28), residues: 339 loop : -0.96 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.015 0.001 TYR A 425 PHE 0.017 0.002 PHE B 455 TRP 0.021 0.002 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00414 (14453) covalent geometry : angle 0.64672 (19537) SS BOND : bond 0.00289 ( 40) SS BOND : angle 0.70988 ( 80) hydrogen bonds : bond 0.03376 ( 313) hydrogen bonds : angle 5.89246 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 58 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7531 (tmm) cc_final: 0.7326 (tmm) REVERT: A 346 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (tttm) REVERT: A 382 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: A 390 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 428 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7551 (t80) REVERT: A 531 MET cc_start: 0.8866 (pmm) cc_final: 0.8576 (pmm) REVERT: A 659 TRP cc_start: 0.6172 (OUTLIER) cc_final: 0.5283 (p90) REVERT: B 346 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7661 (tttp) REVERT: B 382 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: B 390 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: B 531 MET cc_start: 0.8965 (pmm) cc_final: 0.8677 (pmm) REVERT: B 580 MET cc_start: 0.9212 (pmm) cc_final: 0.8949 (pmm) REVERT: B 659 TRP cc_start: 0.5993 (OUTLIER) cc_final: 0.5204 (p90) REVERT: B 733 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8390 (mm-30) REVERT: B 858 MET cc_start: -0.6321 (tpt) cc_final: -0.6619 (tpt) outliers start: 54 outliers final: 40 residues processed: 110 average time/residue: 0.1160 time to fit residues: 19.4538 Evaluate side-chains 105 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 55 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 428 TYR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 630 SER Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain E residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 90 optimal weight: 0.0030 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 0.0010 chunk 17 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 76 optimal weight: 40.0000 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.120069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.095684 restraints weight = 87536.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.097492 restraints weight = 54807.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.097931 restraints weight = 38946.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.098269 restraints weight = 29942.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.098485 restraints weight = 27504.964| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14493 Z= 0.119 Angle : 0.628 10.487 19617 Z= 0.310 Chirality : 0.043 0.175 2130 Planarity : 0.004 0.062 2512 Dihedral : 4.978 47.051 1894 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.83 % Allowed : 25.77 % Favored : 71.40 % 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 aren not related in a simple way. whole: -1.03 (0.21), residues: 1663 helix: -0.50 (0.37), residues: 211 sheet: -0.11 (0.28), residues: 328 loop : -0.92 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.013 0.001 TYR B 872 PHE 0.016 0.001 PHE B 283 TRP 0.015 0.001 TRP A 439 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00280 (14453) covalent geometry : angle 0.62824 (19537) SS BOND : bond 0.00195 ( 40) SS BOND : angle 0.65009 ( 80) hydrogen bonds : bond 0.03119 ( 313) hydrogen bonds : angle 5.83579 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.09 seconds wall clock time: 57 minutes 49.44 seconds (3469.44 seconds total)