Starting phenix.real_space_refine on Fri Jul 3 12:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgi_52135/07_2026/9hgi_52135.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 88 5.16 5 C 8504 2.51 5 N 2439 2.21 5 O 2578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6333 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 46, 'TRANS': 764} Chain breaks: 1 Chain: "B" Number of atoms: 6340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6340 Classifications: {'peptide': 812} Link IDs: {'PTRANS': 46, 'TRANS': 765} Chain breaks: 1 Chain: "C" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 498 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 3.56, per 1000 atoms: 0.26 Number of scatterers: 13657 At special positions: 0 Unit cell: (116.45, 117.3, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 48 15.00 O 2578 8.00 N 2439 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3022 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 10 sheets defined 53.9% alpha, 9.2% beta 24 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 41 through 50 Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 115 through 123 removed outlier: 4.289A pdb=" N LEU A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 155 through 164 removed outlier: 5.616A pdb=" N HIS A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 161 " --> pdb=" O HIS A 158 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.530A pdb=" N GLN A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.817A pdb=" N SER A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.605A pdb=" N ALA A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 296 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.565A pdb=" N ILE A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 4.099A pdb=" N GLY A 340 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.500A pdb=" N ARG A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'A' and resid 458 through 474 removed outlier: 5.021A pdb=" N TYR A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 506 through 531 removed outlier: 3.669A pdb=" N GLN A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.514A pdb=" N ALA A 545 " --> pdb=" O PRO A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 637 through 654 Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 702 through 716 Processing helix chain 'A' and resid 723 through 741 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 761 through 772 removed outlier: 3.571A pdb=" N HIS A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 41 through 50 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 111 through 115 removed outlier: 4.065A pdb=" N PHE B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'B' and resid 306 through 321 removed outlier: 3.805A pdb=" N ILE B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 removed outlier: 4.109A pdb=" N GLY B 340 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.836A pdb=" N VAL B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 458 through 474 removed outlier: 5.011A pdb=" N TYR B 466 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.655A pdb=" N GLN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP B 527 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.587A pdb=" N GLN B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 637 through 654 removed outlier: 3.618A pdb=" N MET B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 removed outlier: 3.540A pdb=" N LEU B 673 " --> pdb=" O PRO B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 698 through 701 removed outlier: 3.584A pdb=" N LEU B 701 " --> pdb=" O GLY B 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 698 through 701' Processing helix chain 'B' and resid 702 through 715 Processing helix chain 'B' and resid 723 through 740 Processing helix chain 'B' and resid 756 through 760 Processing helix chain 'B' and resid 761 through 770 Processing helix chain 'B' and resid 771 through 774 Processing helix chain 'B' and resid 781 through 797 removed outlier: 3.571A pdb=" N LEU B 785 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 794 " --> pdb=" O MET B 790 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 797 " --> pdb=" O LYS B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 834 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.680A pdb=" N THR A 54 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 76 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL A 235 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 78 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY A 237 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 80 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 107 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASP A 174 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 109 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.426A pdb=" N LEU A 325 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG A 248 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 398 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 250 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET A 400 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 615 through 620 Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 Processing sheet with id=AA5, first strand: chain 'A' and resid 743 through 746 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.812A pdb=" N THR B 54 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 236 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU B 56 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 76 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL B 235 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 78 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY B 237 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 80 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 107 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP B 174 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 109 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.242A pdb=" N ARG B 248 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 398 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU B 250 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET B 400 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 620 Processing sheet with id=AA9, first strand: chain 'B' and resid 656 through 657 Processing sheet with id=AB1, first strand: chain 'B' and resid 743 through 746 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2195 1.31 - 1.44: 3952 1.44 - 1.57: 7692 1.57 - 1.69: 96 1.69 - 1.82: 134 Bond restraints: 14069 Sorted by residual: bond pdb=" C GLY A 615 " pdb=" O GLY A 615 " ideal model delta sigma weight residual 1.236 1.199 0.036 5.30e-03 3.56e+04 4.73e+01 bond pdb=" NE ARG A 813 " pdb=" CZ ARG A 813 " ideal model delta sigma weight residual 1.326 1.253 0.073 1.10e-02 8.26e+03 4.43e+01 bond pdb=" NE ARG A 594 " pdb=" CZ ARG A 594 " ideal model delta sigma weight residual 1.326 1.258 0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" NE ARG B 594 " pdb=" CZ ARG B 594 " ideal model delta sigma weight residual 1.326 1.258 0.068 1.10e-02 8.26e+03 3.78e+01 bond pdb=" C GLY B 615 " pdb=" O GLY B 615 " ideal model delta sigma weight residual 1.237 1.201 0.036 7.00e-03 2.04e+04 2.65e+01 ... (remaining 14064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 18948 4.42 - 8.84: 350 8.84 - 13.26: 22 13.26 - 17.67: 2 17.67 - 22.09: 2 Bond angle restraints: 19324 Sorted by residual: angle pdb=" N PRO B 840 " pdb=" CA PRO B 840 " pdb=" C PRO B 840 " ideal model delta sigma weight residual 112.47 90.38 22.09 2.06e+00 2.36e-01 1.15e+02 angle pdb=" N PRO A 840 " pdb=" CA PRO A 840 " pdb=" C PRO A 840 " ideal model delta sigma weight residual 112.47 91.59 20.88 2.06e+00 2.36e-01 1.03e+02 angle pdb=" O4' DA C 40 " pdb=" C1' DA C 40 " pdb=" N9 DA C 40 " ideal model delta sigma weight residual 108.00 113.82 -5.82 7.00e-01 2.04e+00 6.91e+01 angle pdb=" O4' DA D 40 " pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 108.00 113.62 -5.62 7.00e-01 2.04e+00 6.46e+01 angle pdb=" C PRO B 840 " pdb=" CA PRO B 840 " pdb=" CB PRO B 840 " ideal model delta sigma weight residual 111.56 124.61 -13.05 1.65e+00 3.67e-01 6.25e+01 ... (remaining 19319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7973 35.99 - 71.98: 302 71.98 - 107.97: 20 107.97 - 143.97: 0 143.97 - 179.96: 1 Dihedral angle restraints: 8296 sinusoidal: 3609 harmonic: 4687 Sorted by residual: dihedral pdb=" CA SER B 114 " pdb=" C SER B 114 " pdb=" N PHE B 115 " pdb=" CA PHE B 115 " ideal model delta harmonic sigma weight residual 180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" N TRP B 839 " pdb=" C TRP B 839 " pdb=" CA TRP B 839 " pdb=" CB TRP B 839 " ideal model delta harmonic sigma weight residual 122.80 137.52 -14.72 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA ALA B 538 " pdb=" C ALA B 538 " pdb=" N SER B 539 " pdb=" CA SER B 539 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 8293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1817 0.131 - 0.262: 341 0.262 - 0.394: 33 0.394 - 0.525: 2 0.525 - 0.656: 3 Chirality restraints: 2196 Sorted by residual: chirality pdb=" P DA D 19 " pdb=" OP1 DA D 19 " pdb=" OP2 DA D 19 " pdb=" O5' DA D 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" P DT C 39 " pdb=" OP1 DT C 39 " pdb=" OP2 DT C 39 " pdb=" O5' DT C 39 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA TRP B 839 " pdb=" N TRP B 839 " pdb=" C TRP B 839 " pdb=" CB TRP B 839 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 2193 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 839 " -0.137 2.00e-02 2.50e+03 6.92e-02 1.20e+02 pdb=" CG TRP B 839 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 839 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 839 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP B 839 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 839 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 839 " 0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 839 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 839 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP B 839 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 839 " 0.121 2.00e-02 2.50e+03 5.98e-02 8.95e+01 pdb=" CG TRP A 839 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 839 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 839 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 839 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 839 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 839 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 839 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 839 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP A 839 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 38 " -0.104 2.00e-02 2.50e+03 5.43e-02 5.90e+01 pdb=" CG TYR B 38 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 38 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR B 38 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR B 38 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 38 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 38 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 38 " -0.051 2.00e-02 2.50e+03 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 12 2.44 - 3.06: 8356 3.06 - 3.67: 20249 3.67 - 4.29: 31551 4.29 - 4.90: 50999 Nonbonded interactions: 111167 Sorted by model distance: nonbonded pdb=" NE ARG B 495 " pdb=" NH2 ARG B 497 " model vdw 1.830 3.200 nonbonded pdb=" CZ ARG B 495 " pdb=" NH2 ARG B 497 " model vdw 2.177 3.350 nonbonded pdb=" O TRP B 839 " pdb=" N MET B 841 " model vdw 2.263 3.120 nonbonded pdb=" OD2 ASP A 824 " pdb=" NH2 ARG B 607 " model vdw 2.318 3.120 nonbonded pdb=" O TRP A 839 " pdb=" N MET A 841 " model vdw 2.339 3.120 ... (remaining 111162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 16 through 433 or resid 451 through 843)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.630 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 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 : 0.012 0.104 14069 Z= 0.742 Angle : 1.666 22.093 19324 Z= 1.093 Chirality : 0.102 0.656 2196 Planarity : 0.018 0.186 2325 Dihedral : 16.696 179.957 5274 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.65 % Rotamer: Outliers : 0.22 % Allowed : 3.20 % Favored : 96.59 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1615 helix: -1.01 (0.16), residues: 780 sheet: 0.73 (0.33), residues: 208 loop : -0.17 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.004 ARG A 149 TYR 0.104 0.015 TYR B 38 PHE 0.059 0.011 PHE A 411 TRP 0.137 0.020 TRP B 839 HIS 0.026 0.005 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.74 (14069) covalent geometry : angle 1.66562 / 1.09 (19324) hydrogen bonds : bond 0.17505 / 11.60 ( 686) hydrogen bonds : angle 7.03135 / 5.04 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.9221 (p0) cc_final: 0.8814 (t0) REVERT: A 63 VAL cc_start: 0.9408 (m) cc_final: 0.9163 (p) REVERT: A 64 THR cc_start: 0.9432 (m) cc_final: 0.9205 (p) REVERT: A 164 LEU cc_start: 0.8882 (mt) cc_final: 0.8652 (mm) REVERT: A 177 MET cc_start: 0.9476 (mmm) cc_final: 0.9228 (mmt) REVERT: A 355 LEU cc_start: 0.9100 (mt) cc_final: 0.8891 (pt) REVERT: A 535 ASP cc_start: 0.8518 (m-30) cc_final: 0.8246 (p0) REVERT: A 685 GLN cc_start: 0.9319 (tp40) cc_final: 0.9035 (tt0) REVERT: B 65 PHE cc_start: 0.9258 (m-10) cc_final: 0.8993 (m-10) REVERT: B 112 ARG cc_start: 0.8683 (mtt180) cc_final: 0.8483 (mtt90) REVERT: B 131 PHE cc_start: 0.8276 (p90) cc_final: 0.8026 (p90) REVERT: B 578 MET cc_start: 0.9157 (ttp) cc_final: 0.8937 (tpt) REVERT: B 790 MET cc_start: 0.4587 (mmm) cc_final: 0.3747 (ptm) outliers start: 3 outliers final: 3 residues processed: 174 average time/residue: 0.8498 time to fit residues: 158.7657 Evaluate side-chains 105 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain B residue 377 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0070 chunk 149 optimal weight: 0.6980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 727 HIS A 749 GLN B 100 HIS B 143 ASN B 167 ASN B 486 HIS B 727 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075031 restraints weight = 24681.540| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.21 r_work: 0.2754 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14069 Z= 0.168 Angle : 0.733 10.986 19324 Z= 0.391 Chirality : 0.048 0.248 2196 Planarity : 0.005 0.064 2325 Dihedral : 18.537 179.976 2325 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.45 % Allowed : 8.93 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1615 helix: 0.86 (0.18), residues: 780 sheet: 0.84 (0.33), residues: 215 loop : 0.35 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 653 TYR 0.017 0.002 TYR A 382 PHE 0.024 0.002 PHE B 732 TRP 0.031 0.002 TRP B 839 HIS 0.007 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (14069) covalent geometry : angle 0.73336 / 0.39 (19324) hydrogen bonds : bond 0.05451 / 3.79 ( 686) hydrogen bonds : angle 4.68737 / 3.35 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8725 (m90) REVERT: A 64 THR cc_start: 0.9296 (m) cc_final: 0.9056 (p) REVERT: A 355 LEU cc_start: 0.8891 (mt) cc_final: 0.8519 (pt) REVERT: A 389 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8271 (mtm110) REVERT: B 131 PHE cc_start: 0.7586 (p90) cc_final: 0.7291 (p90) REVERT: B 790 MET cc_start: 0.5027 (mmm) cc_final: 0.3696 (ptm) REVERT: B 842 MET cc_start: 0.7804 (mpt) cc_final: 0.7253 (tmt) outliers start: 20 outliers final: 6 residues processed: 123 average time/residue: 0.6391 time to fit residues: 85.8581 Evaluate side-chains 97 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 841 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS A 233 HIS B 50 HIS B 100 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071827 restraints weight = 24804.028| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.27 r_work: 0.2777 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14069 Z= 0.153 Angle : 0.638 8.668 19324 Z= 0.338 Chirality : 0.046 0.228 2196 Planarity : 0.005 0.040 2325 Dihedral : 18.402 175.623 2321 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.03 % Allowed : 9.51 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1615 helix: 1.33 (0.18), residues: 789 sheet: 0.88 (0.34), residues: 217 loop : 0.48 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 193 TYR 0.022 0.002 TYR A 239 PHE 0.022 0.001 PHE A 732 TRP 0.016 0.002 TRP B 839 HIS 0.005 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14069) covalent geometry : angle 0.63806 / 0.34 (19324) hydrogen bonds : bond 0.04467 / 3.07 ( 686) hydrogen bonds : angle 4.36019 / 3.12 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8718 (m90) REVERT: A 230 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9088 (ptpp) REVERT: A 355 LEU cc_start: 0.8837 (mt) cc_final: 0.8447 (pt) REVERT: A 389 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8201 (mtm110) REVERT: B 131 PHE cc_start: 0.7626 (p90) cc_final: 0.7356 (p90) REVERT: B 155 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: B 395 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 527 ASP cc_start: 0.8957 (m-30) cc_final: 0.8653 (m-30) REVERT: B 682 ARG cc_start: 0.8718 (mtp180) cc_final: 0.8478 (mpp-170) REVERT: B 790 MET cc_start: 0.5092 (mmm) cc_final: 0.4626 (mtm) REVERT: B 842 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7210 (tmt) outliers start: 28 outliers final: 7 residues processed: 112 average time/residue: 0.6215 time to fit residues: 76.2633 Evaluate side-chains 97 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 115 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 163 ASN B 233 HIS B 261 GLN B 749 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.120386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.072386 restraints weight = 24713.454| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.27 r_work: 0.2780 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14069 Z= 0.135 Angle : 0.608 9.241 19324 Z= 0.319 Chirality : 0.044 0.237 2196 Planarity : 0.004 0.043 2325 Dihedral : 18.245 173.621 2321 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.67 % Allowed : 10.24 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.21), residues: 1615 helix: 1.59 (0.18), residues: 777 sheet: 0.91 (0.35), residues: 218 loop : 0.49 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 112 TYR 0.015 0.002 TYR A 382 PHE 0.020 0.001 PHE A 732 TRP 0.013 0.001 TRP B 839 HIS 0.019 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14069) covalent geometry : angle 0.60812 / 0.32 (19324) hydrogen bonds : bond 0.04046 / 2.79 ( 686) hydrogen bonds : angle 4.22543 / 3.04 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8780 (m90) REVERT: A 230 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9074 (ptpp) REVERT: A 389 ARG cc_start: 0.8534 (mtm110) cc_final: 0.8170 (mtm110) REVERT: B 131 PHE cc_start: 0.7620 (p90) cc_final: 0.7361 (p90) REVERT: B 155 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: B 195 ASP cc_start: 0.9283 (m-30) cc_final: 0.9018 (t0) REVERT: B 395 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7121 (pt0) REVERT: B 682 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8458 (mpp-170) REVERT: B 790 MET cc_start: 0.5170 (mmm) cc_final: 0.4736 (mtm) REVERT: B 804 ARG cc_start: 0.8417 (mtt-85) cc_final: 0.8147 (ttm-80) REVERT: B 842 MET cc_start: 0.7666 (mpt) cc_final: 0.7182 (tmt) outliers start: 23 outliers final: 7 residues processed: 107 average time/residue: 0.6446 time to fit residues: 75.7394 Evaluate side-chains 94 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071146 restraints weight = 24822.370| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.27 r_work: 0.2753 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14069 Z= 0.180 Angle : 0.612 9.296 19324 Z= 0.319 Chirality : 0.045 0.230 2196 Planarity : 0.005 0.062 2325 Dihedral : 18.161 172.565 2321 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.53 % Allowed : 10.82 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1615 helix: 1.66 (0.18), residues: 784 sheet: 0.91 (0.35), residues: 218 loop : 0.39 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 112 TYR 0.016 0.002 TYR B 382 PHE 0.020 0.001 PHE A 732 TRP 0.011 0.001 TRP A 839 HIS 0.011 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (14069) covalent geometry : angle 0.61237 / 0.32 (19324) hydrogen bonds : bond 0.04183 / 2.86 ( 686) hydrogen bonds : angle 4.17692 / 3.00 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9076 (ptpp) REVERT: A 389 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8114 (mtm110) REVERT: A 820 ASN cc_start: 0.8849 (p0) cc_final: 0.8615 (p0) REVERT: B 131 PHE cc_start: 0.7610 (p90) cc_final: 0.7398 (p90) REVERT: B 155 GLU cc_start: 0.9101 (tt0) cc_final: 0.8348 (tp30) REVERT: B 195 ASP cc_start: 0.9255 (m-30) cc_final: 0.8993 (t0) REVERT: B 395 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7127 (pt0) REVERT: B 682 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8470 (mpp-170) REVERT: B 790 MET cc_start: 0.5199 (mmm) cc_final: 0.4745 (mtm) REVERT: B 842 MET cc_start: 0.7675 (mpt) cc_final: 0.7190 (tmt) outliers start: 21 outliers final: 9 residues processed: 103 average time/residue: 0.6305 time to fit residues: 71.3818 Evaluate side-chains 95 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 20.0000 chunk 31 optimal weight: 0.0470 chunk 106 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.0470 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS B 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075381 restraints weight = 25140.891| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.23 r_work: 0.2752 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14069 Z= 0.110 Angle : 0.580 10.389 19324 Z= 0.300 Chirality : 0.042 0.265 2196 Planarity : 0.005 0.077 2325 Dihedral : 18.018 173.525 2321 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.67 % Allowed : 11.04 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1615 helix: 1.80 (0.18), residues: 787 sheet: 1.07 (0.35), residues: 216 loop : 0.36 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 112 TYR 0.021 0.001 TYR A 239 PHE 0.019 0.001 PHE A 732 TRP 0.012 0.001 TRP B 839 HIS 0.014 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (14069) covalent geometry : angle 0.57993 / 0.30 (19324) hydrogen bonds : bond 0.03630 / 2.50 ( 686) hydrogen bonds : angle 4.10486 / 2.96 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9085 (ptpp) REVERT: A 389 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8099 (mtm110) REVERT: A 820 ASN cc_start: 0.8824 (p0) cc_final: 0.8585 (p0) REVERT: B 155 GLU cc_start: 0.9121 (tt0) cc_final: 0.8178 (tp30) REVERT: B 195 ASP cc_start: 0.9191 (m-30) cc_final: 0.8969 (t0) REVERT: B 400 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8965 (mmm) REVERT: B 487 MET cc_start: 0.9103 (tpt) cc_final: 0.8878 (tpp) REVERT: B 682 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8452 (mpp-170) REVERT: B 790 MET cc_start: 0.5201 (mmm) cc_final: 0.4769 (mtm) REVERT: B 842 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7161 (tmt) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 0.6114 time to fit residues: 72.5571 Evaluate side-chains 96 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 749 GLN Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 0.0050 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072963 restraints weight = 24734.788| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.27 r_work: 0.2789 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14069 Z= 0.123 Angle : 0.586 12.146 19324 Z= 0.300 Chirality : 0.042 0.235 2196 Planarity : 0.007 0.232 2325 Dihedral : 17.961 174.756 2321 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.67 % Allowed : 11.26 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1615 helix: 1.88 (0.18), residues: 788 sheet: 1.08 (0.35), residues: 216 loop : 0.35 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 112 TYR 0.014 0.001 TYR A 786 PHE 0.022 0.001 PHE B 688 TRP 0.008 0.001 TRP B 839 HIS 0.013 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14069) covalent geometry : angle 0.58567 / 0.30 (19324) hydrogen bonds : bond 0.03636 / 2.49 ( 686) hydrogen bonds : angle 4.05337 / 2.92 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9097 (ptpp) REVERT: A 389 ARG cc_start: 0.8470 (mtm110) cc_final: 0.8121 (mtm110) REVERT: A 820 ASN cc_start: 0.8814 (p0) cc_final: 0.8578 (p0) REVERT: B 195 ASP cc_start: 0.9161 (m-30) cc_final: 0.8956 (t0) REVERT: B 395 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7185 (pt0) REVERT: B 400 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (mmm) REVERT: B 487 MET cc_start: 0.9179 (tpt) cc_final: 0.8953 (tpp) REVERT: B 708 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7021 (ttp80) REVERT: B 790 MET cc_start: 0.5315 (mmm) cc_final: 0.4868 (mtm) REVERT: B 842 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7164 (tmt) outliers start: 23 outliers final: 10 residues processed: 103 average time/residue: 0.6530 time to fit residues: 73.4472 Evaluate side-chains 96 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 749 GLN Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074003 restraints weight = 25000.270| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.18 r_work: 0.2762 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14069 Z= 0.174 Angle : 0.621 13.693 19324 Z= 0.316 Chirality : 0.043 0.227 2196 Planarity : 0.006 0.190 2325 Dihedral : 17.920 176.167 2321 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.53 % Allowed : 11.69 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1615 helix: 1.89 (0.18), residues: 782 sheet: 0.93 (0.35), residues: 218 loop : 0.30 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.023 0.002 TYR A 239 PHE 0.033 0.002 PHE B 131 TRP 0.009 0.001 TRP B 499 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (14069) covalent geometry : angle 0.62124 / 0.32 (19324) hydrogen bonds : bond 0.03997 / 2.72 ( 686) hydrogen bonds : angle 4.07293 / 2.91 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9118 (ptpp) REVERT: A 389 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8127 (mtm110) REVERT: A 820 ASN cc_start: 0.8834 (p0) cc_final: 0.8603 (p0) REVERT: B 131 PHE cc_start: 0.7544 (p90) cc_final: 0.7320 (p90) REVERT: B 395 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7243 (pt0) REVERT: B 400 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9039 (mmm) REVERT: B 790 MET cc_start: 0.5342 (mmm) cc_final: 0.4885 (mtm) REVERT: B 842 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7222 (tmt) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 0.6209 time to fit residues: 65.6241 Evaluate side-chains 99 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 0.0040 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 162 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 HIS ** B 163 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074365 restraints weight = 24923.044| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.21 r_work: 0.2785 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14069 Z= 0.126 Angle : 0.594 13.440 19324 Z= 0.303 Chirality : 0.042 0.226 2196 Planarity : 0.006 0.173 2325 Dihedral : 17.842 178.821 2321 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.23 % Allowed : 12.06 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.22), residues: 1615 helix: 1.93 (0.18), residues: 788 sheet: 0.94 (0.34), residues: 223 loop : 0.33 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 112 TYR 0.013 0.001 TYR A 786 PHE 0.028 0.001 PHE B 131 TRP 0.010 0.001 TRP A 839 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14069) covalent geometry : angle 0.59443 / 0.30 (19324) hydrogen bonds : bond 0.03579 / 2.45 ( 686) hydrogen bonds : angle 4.03561 / 2.90 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9103 (ptpp) REVERT: A 389 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8134 (mtm110) REVERT: A 770 ASP cc_start: 0.9187 (m-30) cc_final: 0.8853 (p0) REVERT: B 155 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: B 195 ASP cc_start: 0.8658 (t0) cc_final: 0.8250 (t0) REVERT: B 487 MET cc_start: 0.9183 (tpt) cc_final: 0.8963 (tpp) REVERT: B 708 ARG cc_start: 0.7368 (ttp80) cc_final: 0.7056 (ttp80) REVERT: B 790 MET cc_start: 0.5346 (mmm) cc_final: 0.4883 (mtm) REVERT: B 842 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7173 (tmt) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 0.6120 time to fit residues: 65.1138 Evaluate side-chains 97 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0060 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.121563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075262 restraints weight = 24793.093| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.20 r_work: 0.2804 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14069 Z= 0.116 Angle : 0.596 14.368 19324 Z= 0.300 Chirality : 0.041 0.217 2196 Planarity : 0.005 0.116 2325 Dihedral : 17.656 175.336 2321 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.80 % Allowed : 12.78 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1615 helix: 2.06 (0.19), residues: 782 sheet: 1.01 (0.34), residues: 223 loop : 0.32 (0.28), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 112 TYR 0.025 0.002 TYR A 239 PHE 0.019 0.001 PHE A 732 TRP 0.009 0.001 TRP B 499 HIS 0.002 0.000 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14069) covalent geometry : angle 0.59567 / 0.30 (19324) hydrogen bonds : bond 0.03364 / 2.30 ( 686) hydrogen bonds : angle 3.91838 / 2.84 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9096 (ptpp) REVERT: A 389 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8082 (mtm110) REVERT: A 770 ASP cc_start: 0.9166 (m-30) cc_final: 0.8819 (p0) REVERT: A 820 ASN cc_start: 0.8847 (m-40) cc_final: 0.8618 (p0) REVERT: B 131 PHE cc_start: 0.7494 (p90) cc_final: 0.6945 (p90) REVERT: B 142 MET cc_start: 0.7249 (ptt) cc_final: 0.6596 (pmm) REVERT: B 147 PHE cc_start: 0.7225 (m-80) cc_final: 0.6960 (m-80) REVERT: B 155 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: B 195 ASP cc_start: 0.8557 (t0) cc_final: 0.8229 (t0) REVERT: B 241 MET cc_start: 0.8313 (mmm) cc_final: 0.8068 (mmt) REVERT: B 395 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7156 (pt0) REVERT: B 790 MET cc_start: 0.5421 (mmm) cc_final: 0.4948 (mtm) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.6167 time to fit residues: 67.9026 Evaluate side-chains 95 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074382 restraints weight = 25202.733| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.23 r_work: 0.2780 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14069 Z= 0.143 Angle : 0.601 14.166 19324 Z= 0.301 Chirality : 0.042 0.215 2196 Planarity : 0.005 0.109 2325 Dihedral : 17.578 174.351 2319 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 12.71 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.22), residues: 1615 helix: 1.97 (0.19), residues: 795 sheet: 1.01 (0.35), residues: 223 loop : 0.33 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 113 TYR 0.016 0.001 TYR A 786 PHE 0.029 0.001 PHE B 688 TRP 0.011 0.001 TRP B 499 HIS 0.003 0.000 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14069) covalent geometry : angle 0.60130 / 0.30 (19324) hydrogen bonds : bond 0.03535 / 2.41 ( 686) hydrogen bonds : angle 3.93140 / 2.84 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4523.26 seconds wall clock time: 78 minutes 0.93 seconds (4680.93 seconds total)