Starting phenix.real_space_refine on Thu Jun 12 20:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyt_39678/06_2025/8yyt_39678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyt_39678/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yyt_39678/06_2025/8yyt_39678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyt_39678/06_2025/8yyt_39678.map" model { file = "/net/cci-nas-00/data/ceres_data/8yyt_39678/06_2025/8yyt_39678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyt_39678/06_2025/8yyt_39678.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.27, per 1000 atoms: 0.58 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: 3.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.57 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: 4.53 Time building geometry restraints manager: 4.21 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.390 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (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 TRP 0.025 0.002 TRP A 642 HIS 0.004 0.001 HIS A 456 PHE 0.014 0.001 PHE A 732 TYR 0.029 0.001 TYR B 401 ARG 0.010 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.26585 ( 313) hydrogen bonds : angle 10.62398 ( 897) SS BOND : bond 0.00162 ( 40) SS BOND : angle 0.71973 ( 80) covalent geometry : bond 0.00273 (14453) covalent geometry : angle 0.68389 (19537) *********************** 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 : 1.723 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: 0.2802 time to fit residues: 26.9385 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 : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 156 optimal weight: 0.0980 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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** A 434 ASN A 654 HIS B 214 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 HIS C 51 ASN D 51 ASN F 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.125669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100329 restraints weight = 82728.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.101743 restraints weight = 51211.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.102678 restraints weight = 38505.406| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14493 Z= 0.238 Angle : 0.691 7.554 19617 Z= 0.359 Chirality : 0.046 0.167 2130 Planarity : 0.005 0.065 2512 Dihedral : 5.126 39.859 1894 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.09 % Allowed : 22.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1663 helix: -1.35 (0.35), residues: 214 sheet: -0.35 (0.29), residues: 292 loop : -1.14 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 578 HIS 0.004 0.001 HIS B 654 PHE 0.021 0.002 PHE B 658 TYR 0.021 0.002 TYR B 171 ARG 0.004 0.001 ARG B 784 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 313) hydrogen bonds : angle 7.20863 ( 897) SS BOND : bond 0.00389 ( 40) SS BOND : angle 0.79388 ( 80) covalent geometry : bond 0.00535 (14453) covalent geometry : angle 0.69043 (19537) *********************** 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 123 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 58 time to evaluate : 1.848 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 83 MET cc_start: 0.8109 (tpp) cc_final: 0.7870 (tpp) REVERT: A 321 MET cc_start: 0.8434 (ppp) cc_final: 0.8181 (ppp) REVERT: A 368 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8858 (pp) REVERT: A 470 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: A 531 MET cc_start: 0.8733 (pmm) cc_final: 0.8522 (pmm) REVERT: B 83 MET cc_start: 0.7997 (tpp) cc_final: 0.7791 (tpp) REVERT: B 321 MET cc_start: 0.8355 (ppp) cc_final: 0.8127 (ppp) REVERT: B 368 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8854 (pp) REVERT: B 531 MET cc_start: 0.8760 (pmm) cc_final: 0.8556 (pmm) REVERT: B 736 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9441 (tp) REVERT: F 4 GLN cc_start: 0.2100 (OUTLIER) cc_final: 0.1635 (tt0) outliers start: 65 outliers final: 35 residues processed: 122 average time/residue: 0.2560 time to fit residues: 47.8450 Evaluate side-chains 95 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 252 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 494 SER 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 80 LYS 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 252 CYS 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 593 VAL 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 736 LEU Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 4 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.0000 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.122308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097569 restraints weight = 86130.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.099058 restraints weight = 51878.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.100045 restraints weight = 38141.303| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1445 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= 0.115 Angle : 0.589 9.277 19617 Z= 0.305 Chirality : 0.043 0.150 2130 Planarity : 0.004 0.067 2512 Dihedral : 4.874 40.904 1894 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.51 % Allowed : 23.38 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1663 helix: -1.15 (0.35), residues: 214 sheet: -0.75 (0.27), residues: 344 loop : -0.96 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 439 HIS 0.004 0.000 HIS D 5 PHE 0.016 0.001 PHE B 658 TYR 0.013 0.001 TYR B 457 ARG 0.005 0.000 ARG B 581 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 313) hydrogen bonds : angle 6.67249 ( 897) SS BOND : bond 0.00220 ( 40) SS BOND : angle 0.58544 ( 80) covalent geometry : bond 0.00263 (14453) covalent geometry : angle 0.58868 (19537) *********************** 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 100 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 1.748 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 382 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: A 470 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: B 382 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: B 470 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: B 643 LYS cc_start: 0.9655 (mmtm) cc_final: 0.9362 (ptmm) REVERT: B 736 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9439 (tp) REVERT: F 11 LEU cc_start: 0.7791 (mp) cc_final: 0.7296 (mp) outliers start: 40 outliers final: 23 residues processed: 99 average time/residue: 0.2709 time to fit residues: 41.0201 Evaluate side-chains 84 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 513 LEU 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 155 LEU Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 252 CYS Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 736 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.120602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.095344 restraints weight = 87556.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.096798 restraints weight = 52910.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.097754 restraints weight = 39076.564| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14493 Z= 0.181 Angle : 0.617 7.526 19617 Z= 0.318 Chirality : 0.044 0.150 2130 Planarity : 0.004 0.064 2512 Dihedral : 4.980 41.836 1894 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.21 % Allowed : 22.44 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1663 helix: -0.67 (0.37), residues: 212 sheet: -0.71 (0.27), residues: 354 loop : -1.01 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 578 HIS 0.004 0.001 HIS D 5 PHE 0.014 0.002 PHE B 658 TYR 0.014 0.001 TYR B 171 ARG 0.005 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 313) hydrogen bonds : angle 6.27328 ( 897) SS BOND : bond 0.00305 ( 40) SS BOND : angle 0.72960 ( 80) covalent geometry : bond 0.00408 (14453) covalent geometry : angle 0.61641 (19537) *********************** 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 126 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 59 time to evaluate : 1.616 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 368 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 382 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8612 (tm-30) REVERT: A 470 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 531 MET cc_start: 0.8876 (pmm) cc_final: 0.8600 (pmm) REVERT: A 659 TRP cc_start: 0.6051 (OUTLIER) cc_final: 0.5415 (p90) REVERT: B 368 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8671 (pp) REVERT: B 382 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: B 470 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: B 531 MET cc_start: 0.8886 (pmm) cc_final: 0.8604 (pmm) REVERT: B 659 TRP cc_start: 0.6043 (OUTLIER) cc_final: 0.5373 (p90) REVERT: B 736 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9457 (tp) outliers start: 67 outliers final: 33 residues processed: 121 average time/residue: 0.2661 time to fit residues: 48.2665 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 : 1.602 ------------------------------------------------------------------------------- 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 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 358 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 382 GLU 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 640 LEU Chi-restraints excluded: chain A residue 659 TRP 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 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 358 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 470 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 736 LEU 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 D residue 44 TYR 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 9 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 171 optimal weight: 30.0000 chunk 81 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.120113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.095121 restraints weight = 88302.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096101 restraints weight = 55694.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.096974 restraints weight = 44476.924| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14493 Z= 0.175 Angle : 0.619 9.473 19617 Z= 0.317 Chirality : 0.044 0.275 2130 Planarity : 0.005 0.075 2512 Dihedral : 5.008 43.139 1894 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.21 % Allowed : 24.20 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1663 helix: -0.67 (0.37), residues: 212 sheet: -0.63 (0.27), residues: 351 loop : -1.00 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 439 HIS 0.005 0.001 HIS A 456 PHE 0.014 0.002 PHE B 732 TYR 0.017 0.001 TYR B 872 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 313) hydrogen bonds : angle 6.13692 ( 897) SS BOND : bond 0.00284 ( 40) SS BOND : angle 0.63188 ( 80) covalent geometry : bond 0.00401 (14453) covalent geometry : angle 0.61866 (19537) *********************** 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: 67 poor density : 60 time to evaluate : 1.538 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 368 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8696 (pp) REVERT: A 382 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8683 (tm-30) REVERT: A 470 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: A 580 MET cc_start: 0.9568 (pmm) cc_final: 0.9167 (pmm) REVERT: A 659 TRP cc_start: 0.6160 (OUTLIER) cc_final: 0.5608 (p90) REVERT: B 368 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8698 (pp) REVERT: B 382 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: B 470 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: B 659 TRP cc_start: 0.6054 (OUTLIER) cc_final: 0.5399 (p90) REVERT: B 733 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: B 736 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9455 (tp) outliers start: 67 outliers final: 39 residues processed: 123 average time/residue: 0.2890 time to fit residues: 50.8630 Evaluate side-chains 104 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 55 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 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 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 470 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 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 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 358 ARG 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 513 LEU Chi-restraints excluded: chain B residue 524 PHE 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 736 LEU 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 D residue 6 LEU Chi-restraints excluded: chain D residue 44 TYR 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 6 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 77 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 170 optimal weight: 0.0170 chunk 24 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.119294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094133 restraints weight = 88486.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.095590 restraints weight = 53261.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.096573 restraints weight = 39091.840| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14493 Z= 0.230 Angle : 0.674 13.023 19617 Z= 0.344 Chirality : 0.045 0.286 2130 Planarity : 0.005 0.065 2512 Dihedral : 5.264 44.870 1894 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.03 % Allowed : 24.07 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1663 helix: -0.88 (0.36), residues: 222 sheet: -0.61 (0.27), residues: 345 loop : -1.12 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 578 HIS 0.005 0.001 HIS B 456 PHE 0.015 0.002 PHE B 533 TYR 0.017 0.002 TYR A 425 ARG 0.008 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 313) hydrogen bonds : angle 6.14776 ( 897) SS BOND : bond 0.00375 ( 40) SS BOND : angle 0.80173 ( 80) covalent geometry : bond 0.00516 (14453) covalent geometry : angle 0.67376 (19537) *********************** 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 137 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 57 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (pp) REVERT: A 382 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: A 390 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: A 428 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 470 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: A 531 MET cc_start: 0.8870 (pmm) cc_final: 0.8593 (pmm) REVERT: A 659 TRP cc_start: 0.6223 (OUTLIER) cc_final: 0.5360 (p90) REVERT: A 833 MET cc_start: 0.9013 (pmm) cc_final: 0.8813 (pmm) REVERT: B 368 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8583 (pp) REVERT: B 382 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8630 (tm-30) REVERT: B 390 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 470 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: B 531 MET cc_start: 0.8889 (pmm) cc_final: 0.8628 (pmm) REVERT: B 659 TRP cc_start: 0.6115 (OUTLIER) cc_final: 0.5271 (p90) REVERT: B 733 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8496 (mm-30) outliers start: 80 outliers final: 51 residues processed: 130 average time/residue: 0.2568 time to fit residues: 50.8592 Evaluate side-chains 114 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 51 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 293 CYS 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 390 GLU Chi-restraints excluded: chain A residue 428 TYR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 470 GLU 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 514 LEU Chi-restraints excluded: chain A residue 524 PHE 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 290 HIS 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 390 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 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 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 6 LEU 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 24 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.123758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098430 restraints weight = 84689.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099568 restraints weight = 55488.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100310 restraints weight = 44387.331| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14493 Z= 0.198 Angle : 0.645 10.618 19617 Z= 0.331 Chirality : 0.045 0.304 2130 Planarity : 0.004 0.064 2512 Dihedral : 5.246 46.365 1894 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.15 % Allowed : 23.95 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1663 helix: -0.67 (0.38), residues: 210 sheet: -0.48 (0.27), residues: 336 loop : -1.06 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 439 HIS 0.004 0.001 HIS D 5 PHE 0.033 0.002 PHE B 728 TYR 0.018 0.001 TYR A 171 ARG 0.012 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 313) hydrogen bonds : angle 6.07519 ( 897) SS BOND : bond 0.00331 ( 40) SS BOND : angle 0.74265 ( 80) covalent geometry : bond 0.00450 (14453) covalent geometry : angle 0.64502 (19537) *********************** 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 134 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 52 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (pptt) REVERT: A 368 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8736 (pp) REVERT: A 382 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8730 (tm-30) REVERT: A 428 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 531 MET cc_start: 0.8827 (pmm) cc_final: 0.8584 (pmm) REVERT: A 659 TRP cc_start: 0.6206 (OUTLIER) cc_final: 0.5303 (p90) REVERT: B 368 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 382 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: B 390 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 470 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: B 531 MET cc_start: 0.8816 (pmm) cc_final: 0.8584 (pmm) REVERT: B 659 TRP cc_start: 0.6073 (OUTLIER) cc_final: 0.5253 (p90) REVERT: B 733 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: B 833 MET cc_start: 0.9009 (pmm) cc_final: 0.8790 (pmm) outliers start: 82 outliers final: 50 residues processed: 129 average time/residue: 0.2332 time to fit residues: 47.2798 Evaluate side-chains 111 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 50 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 67 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 81 LEU 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 368 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 428 TYR 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 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 248 ASP 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 368 ILE 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 470 GLU 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 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 D residue 12 VAL Chi-restraints excluded: chain D residue 44 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 167 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN 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 = 0.119503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094724 restraints weight = 86657.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.096313 restraints weight = 55732.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.096794 restraints weight = 41740.014| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14493 Z= 0.155 Angle : 0.637 9.278 19617 Z= 0.321 Chirality : 0.044 0.260 2130 Planarity : 0.005 0.149 2512 Dihedral : 5.200 47.116 1894 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.46 % Allowed : 24.83 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1663 helix: -0.60 (0.38), residues: 210 sheet: -0.47 (0.27), residues: 339 loop : -1.03 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 439 HIS 0.005 0.001 HIS D 5 PHE 0.015 0.002 PHE A 732 TYR 0.016 0.001 TYR A 171 ARG 0.006 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 313) hydrogen bonds : angle 5.96402 ( 897) SS BOND : bond 0.00264 ( 40) SS BOND : angle 0.68618 ( 80) covalent geometry : bond 0.00357 (14453) covalent geometry : angle 0.63662 (19537) *********************** 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 124 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 53 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 382 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: A 390 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: A 428 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 531 MET cc_start: 0.8901 (pmm) cc_final: 0.8624 (pmm) REVERT: A 659 TRP cc_start: 0.6231 (OUTLIER) cc_final: 0.5398 (p90) REVERT: A 833 MET cc_start: 0.8992 (pmm) cc_final: 0.8781 (pmm) REVERT: B 368 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8578 (pp) REVERT: B 382 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: B 470 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: B 531 MET cc_start: 0.8863 (pmm) cc_final: 0.8607 (pmm) REVERT: B 659 TRP cc_start: 0.5941 (OUTLIER) cc_final: 0.5156 (p90) outliers start: 71 outliers final: 53 residues processed: 121 average time/residue: 0.2320 time to fit residues: 43.9839 Evaluate side-chains 112 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 50 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 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 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 358 ARG Chi-restraints excluded: chain A residue 368 ILE 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 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 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 729 ARG 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 A residue 925 THR 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 248 ASP 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 368 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 406 LEU 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 524 PHE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 659 TRP 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 B residue 925 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 139 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 155 optimal weight: 40.0000 chunk 40 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.122464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097342 restraints weight = 85294.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.099319 restraints weight = 55439.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.099489 restraints weight = 37955.185| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14493 Z= 0.263 Angle : 0.720 8.640 19617 Z= 0.367 Chirality : 0.046 0.207 2130 Planarity : 0.006 0.156 2512 Dihedral : 5.564 48.507 1894 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.46 % Allowed : 25.14 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1663 helix: -0.69 (0.38), residues: 212 sheet: -0.57 (0.27), residues: 337 loop : -1.19 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 439 HIS 0.006 0.001 HIS B 456 PHE 0.031 0.002 PHE B 455 TYR 0.021 0.002 TYR A 171 ARG 0.005 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 313) hydrogen bonds : angle 6.08587 ( 897) SS BOND : bond 0.00458 ( 40) SS BOND : angle 0.94683 ( 80) covalent geometry : bond 0.00589 (14453) covalent geometry : angle 0.71889 (19537) *********************** 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 122 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 51 time to evaluate : 1.580 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 368 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 382 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: A 390 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: A 428 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 531 MET cc_start: 0.8879 (pmm) cc_final: 0.8615 (pmm) REVERT: A 729 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5864 (mmt180) REVERT: B 368 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 382 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: B 390 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: B 470 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: B 531 MET cc_start: 0.8816 (pmm) cc_final: 0.8550 (pmm) REVERT: B 580 MET cc_start: 0.9230 (pmm) cc_final: 0.8985 (pmm) REVERT: B 833 MET cc_start: 0.9110 (pmm) cc_final: 0.8896 (pmm) outliers start: 71 outliers final: 58 residues processed: 119 average time/residue: 0.2386 time to fit residues: 44.3569 Evaluate side-chains 116 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 49 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 252 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 ILE 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 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 640 LEU Chi-restraints excluded: chain A residue 659 TRP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 736 LEU 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 A residue 925 THR 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 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 368 ILE Chi-restraints excluded: chain B residue 371 ILE 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 456 HIS 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 524 PHE Chi-restraints excluded: chain B residue 655 TYR Chi-restraints excluded: chain B residue 659 TRP Chi-restraints excluded: chain B residue 736 LEU 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 B residue 925 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 156 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 50.0000 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 ASN E 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.119428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.094902 restraints weight = 85226.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.096673 restraints weight = 55642.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.097146 restraints weight = 39670.959| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14493 Z= 0.136 Angle : 0.637 9.745 19617 Z= 0.320 Chirality : 0.044 0.206 2130 Planarity : 0.005 0.127 2512 Dihedral : 5.282 49.927 1894 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.71 % Allowed : 26.08 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1663 helix: -0.53 (0.37), residues: 214 sheet: -0.25 (0.28), residues: 315 loop : -1.09 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 439 HIS 0.005 0.001 HIS D 5 PHE 0.014 0.002 PHE A 732 TYR 0.019 0.001 TYR A 171 ARG 0.005 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 313) hydrogen bonds : angle 5.92850 ( 897) SS BOND : bond 0.00248 ( 40) SS BOND : angle 0.74706 ( 80) covalent geometry : bond 0.00316 (14453) covalent geometry : angle 0.63636 (19537) ********************** 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 110 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 51 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 382 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: A 390 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: A 580 MET cc_start: 0.9404 (pmm) cc_final: 0.9204 (pmm) REVERT: A 596 LEU cc_start: 0.9364 (tt) cc_final: 0.9150 (pt) REVERT: A 729 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.5669 (mmt180) REVERT: B 368 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 382 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: B 390 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: B 531 MET cc_start: 0.8770 (pmm) cc_final: 0.8504 (pmm) REVERT: B 580 MET cc_start: 0.9176 (pmm) cc_final: 0.8925 (pmm) outliers start: 59 outliers final: 46 residues processed: 108 average time/residue: 0.2447 time to fit residues: 40.8326 Evaluate side-chains 103 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 50 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 358 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 390 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 640 LEU Chi-restraints excluded: chain A residue 729 ARG 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 A residue 925 THR 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 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 368 ILE Chi-restraints excluded: chain B residue 371 ILE 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 524 PHE 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 B residue 925 THR Chi-restraints excluded: chain E residue 4 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 95 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 0.2980 chunk 127 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.119746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.095134 restraints weight = 85890.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.097123 restraints weight = 56493.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.097255 restraints weight = 38786.486| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14493 Z= 0.123 Angle : 0.647 11.314 19617 Z= 0.324 Chirality : 0.044 0.276 2130 Planarity : 0.005 0.122 2512 Dihedral : 5.209 49.758 1894 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.58 % Allowed : 26.21 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1663 helix: -0.49 (0.37), residues: 212 sheet: -0.26 (0.28), residues: 326 loop : -1.04 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 439 HIS 0.006 0.001 HIS E 5 PHE 0.042 0.002 PHE B 728 TYR 0.015 0.001 TYR A 171 ARG 0.009 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 313) hydrogen bonds : angle 5.87153 ( 897) SS BOND : bond 0.00221 ( 40) SS BOND : angle 0.70597 ( 80) covalent geometry : bond 0.00287 (14453) covalent geometry : angle 0.64628 (19537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5500.03 seconds wall clock time: 95 minutes 55.08 seconds (5755.08 seconds total)