Starting phenix.real_space_refine on Thu Feb 5 00:26:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgi_52135/02_2026/9hgi_52135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgi_52135/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hgi_52135/02_2026/9hgi_52135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgi_52135/02_2026/9hgi_52135.map" model { file = "/net/cci-nas-00/data/ceres_data/9hgi_52135/02_2026/9hgi_52135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgi_52135/02_2026/9hgi_52135.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.70, per 1000 atoms: 0.20 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: 1.10 Conformation dependent library (CDL) restraints added in 393.2 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: 1.75 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: 2.29 Time building geometry restraints manager: 1.46 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: 18944 4.42 - 8.84: 354 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=" 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 angle pdb=" OG1 THR A 306 " pdb=" CB THR A 306 " pdb=" CG2 THR A 306 " ideal model delta sigma weight residual 109.30 94.47 14.83 2.00e+00 2.50e-01 5.50e+01 angle pdb=" C PRO A 840 " pdb=" CA PRO A 840 " pdb=" CB PRO A 840 " ideal model delta sigma weight residual 111.56 122.86 -11.30 1.65e+00 3.67e-01 4.69e+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 - 0.129: 1808 0.129 - 0.258: 350 0.258 - 0.387: 33 0.387 - 0.517: 2 0.517 - 0.646: 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 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+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 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.04e+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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.050 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 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= 0.720 Angle : 1.666 22.093 19324 Z= 1.063 Chirality : 0.101 0.646 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 covalent geometry : bond 0.01167 (14069) covalent geometry : angle 1.66636 (19324) hydrogen bonds : bond 0.17505 ( 686) hydrogen bonds : angle 7.03135 ( 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 : 0.458 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: 0.8010 time to fit residues: 148.8164 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 : 0.315 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 59 GLN A 486 HIS ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.122277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076202 restraints weight = 24794.773| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.18 r_work: 0.2779 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14069 Z= 0.153 Angle : 0.666 11.010 19324 Z= 0.356 Chirality : 0.044 0.211 2196 Planarity : 0.005 0.041 2325 Dihedral : 18.266 175.197 2325 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.67 % Allowed : 8.35 % Favored : 89.98 % 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: 1.12 (0.21), residues: 1615 helix: 1.12 (0.18), residues: 773 sheet: 0.88 (0.34), residues: 217 loop : 0.40 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 93 TYR 0.017 0.002 TYR B 184 PHE 0.024 0.001 PHE B 732 TRP 0.031 0.002 TRP B 839 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00333 (14069) covalent geometry : angle 0.66633 (19324) hydrogen bonds : bond 0.04768 ( 686) hydrogen bonds : angle 4.54637 ( 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 134 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8698 (m90) REVERT: A 64 THR cc_start: 0.9299 (m) cc_final: 0.9064 (p) REVERT: A 355 LEU cc_start: 0.8893 (mt) cc_final: 0.8505 (pt) REVERT: A 389 ARG cc_start: 0.8557 (mtm110) cc_final: 0.8274 (mtm110) REVERT: B 131 PHE cc_start: 0.7644 (p90) cc_final: 0.7372 (p90) REVERT: B 527 ASP cc_start: 0.9004 (m-30) cc_final: 0.8735 (m-30) REVERT: B 642 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8679 (mt-10) REVERT: B 682 ARG cc_start: 0.8715 (mtp180) cc_final: 0.8492 (mpp-170) REVERT: B 684 MET cc_start: 0.9186 (mtp) cc_final: 0.8972 (mtp) REVERT: B 790 MET cc_start: 0.4970 (mmm) cc_final: 0.4491 (mtm) REVERT: B 842 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7255 (tmt) outliers start: 23 outliers final: 6 residues processed: 125 average time/residue: 0.5701 time to fit residues: 78.1529 Evaluate side-chains 101 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 690 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 842 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 141 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 50 HIS B 100 HIS B 163 ASN B 233 HIS B 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.120447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.072423 restraints weight = 24914.634| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.28 r_work: 0.2772 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2588 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= 0.145 Angle : 0.594 8.257 19324 Z= 0.315 Chirality : 0.042 0.177 2196 Planarity : 0.004 0.043 2325 Dihedral : 18.020 176.716 2321 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.53 % Allowed : 9.88 % Favored : 88.60 % 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: 1.58 (0.21), residues: 1615 helix: 1.57 (0.18), residues: 777 sheet: 0.93 (0.34), residues: 218 loop : 0.58 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 529 TYR 0.015 0.002 TYR B 382 PHE 0.021 0.001 PHE A 732 TRP 0.013 0.001 TRP B 839 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00321 (14069) covalent geometry : angle 0.59444 (19324) hydrogen bonds : bond 0.04098 ( 686) hydrogen bonds : angle 4.25725 ( 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 123 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9109 (ptpp) REVERT: A 389 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8243 (mtm110) REVERT: B 155 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: B 395 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 684 MET cc_start: 0.9207 (mtp) cc_final: 0.8900 (mtp) REVERT: B 790 MET cc_start: 0.5121 (mmm) cc_final: 0.4642 (mtm) REVERT: B 842 MET cc_start: 0.7651 (mpt) cc_final: 0.7241 (tmt) outliers start: 21 outliers final: 6 residues processed: 116 average time/residue: 0.6160 time to fit residues: 77.5404 Evaluate side-chains 94 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.119398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071446 restraints weight = 24867.829| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.26 r_work: 0.2750 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14069 Z= 0.172 Angle : 0.591 9.000 19324 Z= 0.311 Chirality : 0.042 0.172 2196 Planarity : 0.005 0.047 2325 Dihedral : 17.875 174.236 2321 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.82 % Allowed : 10.68 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.21), residues: 1615 helix: 1.69 (0.18), residues: 784 sheet: 0.93 (0.35), residues: 218 loop : 0.49 (0.28), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 682 TYR 0.017 0.002 TYR A 382 PHE 0.020 0.001 PHE A 732 TRP 0.011 0.001 TRP A 839 HIS 0.019 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00398 (14069) covalent geometry : angle 0.59084 (19324) hydrogen bonds : bond 0.04075 ( 686) hydrogen bonds : angle 4.19196 ( 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 118 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8804 (m90) REVERT: A 230 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9109 (ptpp) REVERT: A 389 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8199 (mtm110) REVERT: B 155 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: B 395 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7264 (pt0) REVERT: B 642 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 683 TYR cc_start: 0.8270 (m-80) cc_final: 0.8040 (m-80) REVERT: B 684 MET cc_start: 0.9206 (mtp) cc_final: 0.8870 (mtp) REVERT: B 790 MET cc_start: 0.5220 (mmm) cc_final: 0.4750 (mtm) REVERT: B 842 MET cc_start: 0.7637 (mpt) cc_final: 0.7255 (tmt) outliers start: 25 outliers final: 9 residues processed: 108 average time/residue: 0.6290 time to fit residues: 74.0590 Evaluate side-chains 102 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 658 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.0060 chunk 126 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS B 501 HIS B 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.072840 restraints weight = 24935.068| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.26 r_work: 0.2766 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3103 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= 0.123 Angle : 0.560 10.405 19324 Z= 0.290 Chirality : 0.040 0.197 2196 Planarity : 0.004 0.039 2325 Dihedral : 17.645 171.445 2321 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.11 % Allowed : 10.75 % Favored : 87.15 % 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: 1.78 (0.22), residues: 1615 helix: 1.87 (0.18), residues: 788 sheet: 1.10 (0.35), residues: 216 loop : 0.41 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 682 TYR 0.019 0.001 TYR A 239 PHE 0.021 0.001 PHE B 688 TRP 0.010 0.001 TRP B 839 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00274 (14069) covalent geometry : angle 0.55969 (19324) hydrogen bonds : bond 0.03554 ( 686) hydrogen bonds : angle 4.05359 ( 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 129 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9098 (ptpp) REVERT: A 389 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8125 (mtm110) REVERT: B 131 PHE cc_start: 0.7431 (p90) cc_final: 0.6877 (p90) REVERT: B 155 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: B 195 ASP cc_start: 0.8896 (t0) cc_final: 0.8582 (t0) REVERT: B 395 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7178 (pt0) REVERT: B 487 MET cc_start: 0.9151 (tpt) cc_final: 0.8930 (tpp) REVERT: B 642 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8662 (mt-10) REVERT: B 682 ARG cc_start: 0.7888 (mpp-170) cc_final: 0.7680 (mpp-170) REVERT: B 684 MET cc_start: 0.9212 (mtp) cc_final: 0.8923 (mtp) REVERT: B 790 MET cc_start: 0.5325 (mmm) cc_final: 0.4875 (mtm) REVERT: B 842 MET cc_start: 0.7595 (mpt) cc_final: 0.7160 (tmt) outliers start: 29 outliers final: 12 residues processed: 116 average time/residue: 0.6364 time to fit residues: 80.1876 Evaluate side-chains 103 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 193 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 734 ILE 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: 0.8980 chunk 106 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS B 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074738 restraints weight = 25147.806| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.19 r_work: 0.2788 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14069 Z= 0.143 Angle : 0.572 11.379 19324 Z= 0.293 Chirality : 0.040 0.179 2196 Planarity : 0.004 0.055 2325 Dihedral : 17.559 171.233 2321 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.67 % Allowed : 11.62 % 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: 1.83 (0.22), residues: 1615 helix: 1.94 (0.19), residues: 788 sheet: 1.12 (0.35), residues: 216 loop : 0.39 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 159 TYR 0.015 0.001 TYR A 786 PHE 0.019 0.001 PHE B 732 TRP 0.008 0.001 TRP A 839 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00330 (14069) covalent geometry : angle 0.57178 (19324) hydrogen bonds : bond 0.03646 ( 686) hydrogen bonds : angle 4.01807 ( 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 112 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 HIS cc_start: 0.9006 (OUTLIER) cc_final: 0.8805 (m90) REVERT: A 230 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9117 (ptpp) REVERT: A 389 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8100 (mtm110) REVERT: B 131 PHE cc_start: 0.7403 (p90) cc_final: 0.6816 (p90) REVERT: B 147 PHE cc_start: 0.7292 (m-80) cc_final: 0.7027 (m-80) REVERT: B 155 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: B 195 ASP cc_start: 0.8866 (t0) cc_final: 0.8542 (t0) REVERT: B 395 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7222 (pt0) REVERT: B 487 MET cc_start: 0.9189 (tpt) cc_final: 0.8970 (tpp) REVERT: B 642 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8665 (mt-10) REVERT: B 684 MET cc_start: 0.9251 (mtp) cc_final: 0.8962 (mtp) REVERT: B 790 MET cc_start: 0.5460 (mmm) cc_final: 0.4983 (mtm) REVERT: B 842 MET cc_start: 0.7520 (mpt) cc_final: 0.7180 (tmt) outliers start: 23 outliers final: 11 residues processed: 104 average time/residue: 0.6669 time to fit residues: 75.6877 Evaluate side-chains 104 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 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 = 0.3820 r_free = 0.3820 target = 0.121163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074226 restraints weight = 24924.117| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.23 r_work: 0.2765 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14069 Z= 0.131 Angle : 0.571 12.002 19324 Z= 0.290 Chirality : 0.040 0.172 2196 Planarity : 0.004 0.049 2325 Dihedral : 17.466 170.647 2321 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.67 % Allowed : 11.69 % Favored : 86.64 % 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: 1.89 (0.22), residues: 1615 helix: 2.06 (0.19), residues: 782 sheet: 1.06 (0.35), residues: 223 loop : 0.38 (0.28), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 159 TYR 0.022 0.002 TYR A 239 PHE 0.026 0.001 PHE B 688 TRP 0.008 0.001 TRP A 839 HIS 0.013 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00296 (14069) covalent geometry : angle 0.57062 (19324) hydrogen bonds : bond 0.03478 ( 686) hydrogen bonds : angle 3.96450 ( 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 114 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9108 (ptpp) REVERT: A 389 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8105 (mtm110) REVERT: A 770 ASP cc_start: 0.9190 (m-30) cc_final: 0.8853 (p0) REVERT: B 131 PHE cc_start: 0.7395 (p90) cc_final: 0.6816 (p90) REVERT: B 155 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8074 (tp30) REVERT: B 195 ASP cc_start: 0.8832 (t0) cc_final: 0.8511 (t0) REVERT: B 395 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7155 (pt0) REVERT: B 487 MET cc_start: 0.9139 (tpt) cc_final: 0.8928 (tpp) REVERT: B 642 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8652 (mt-10) REVERT: B 684 MET cc_start: 0.9268 (mtp) cc_final: 0.8912 (mtp) REVERT: B 790 MET cc_start: 0.5469 (mmm) cc_final: 0.4997 (mtm) REVERT: B 842 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7154 (tmt) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.6649 time to fit residues: 76.0275 Evaluate side-chains 103 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 824 ASP 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: 0.7980 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 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 = 0.3824 r_free = 0.3824 target = 0.121587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075242 restraints weight = 24861.320| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.19 r_work: 0.2793 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3372 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= 0.130 Angle : 0.568 12.475 19324 Z= 0.289 Chirality : 0.040 0.164 2196 Planarity : 0.006 0.189 2325 Dihedral : 17.367 170.290 2319 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.31 % Allowed : 11.84 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.22), residues: 1615 helix: 2.04 (0.19), residues: 789 sheet: 1.07 (0.34), residues: 223 loop : 0.39 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 112 TYR 0.014 0.001 TYR A 786 PHE 0.018 0.001 PHE B 732 TRP 0.008 0.001 TRP B 499 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00294 (14069) covalent geometry : angle 0.56811 (19324) hydrogen bonds : bond 0.03415 ( 686) hydrogen bonds : angle 3.93478 ( 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 110 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9104 (ptpp) REVERT: A 389 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8102 (mtm110) REVERT: A 770 ASP cc_start: 0.9170 (m-30) cc_final: 0.8834 (p0) REVERT: B 25 GLU cc_start: 0.8894 (tp30) cc_final: 0.8694 (tp30) REVERT: B 131 PHE cc_start: 0.7427 (p90) cc_final: 0.6832 (p90) REVERT: B 142 MET cc_start: 0.7307 (ptt) cc_final: 0.6525 (pmm) REVERT: B 155 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: B 188 MET cc_start: 0.7520 (tpp) cc_final: 0.7250 (tpp) REVERT: B 195 ASP cc_start: 0.8834 (t0) cc_final: 0.8591 (t0) REVERT: B 395 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7175 (pt0) REVERT: B 487 MET cc_start: 0.9157 (tpt) cc_final: 0.8943 (tpp) REVERT: B 642 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 684 MET cc_start: 0.9277 (mtp) cc_final: 0.8931 (mtp) REVERT: B 790 MET cc_start: 0.5544 (mmm) cc_final: 0.5068 (mtm) REVERT: B 842 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7159 (tmt) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 0.6934 time to fit residues: 77.7045 Evaluate side-chains 107 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 193 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 688 PHE Chi-restraints excluded: chain B residue 713 LEU 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 162 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.075257 restraints weight = 24997.785| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.19 r_work: 0.2771 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14069 Z= 0.132 Angle : 0.575 12.817 19324 Z= 0.290 Chirality : 0.040 0.166 2196 Planarity : 0.005 0.163 2325 Dihedral : 17.277 170.062 2319 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.38 % Allowed : 12.06 % Favored : 86.56 % 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: 1.88 (0.22), residues: 1615 helix: 2.02 (0.19), residues: 790 sheet: 1.09 (0.34), residues: 223 loop : 0.36 (0.28), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 112 TYR 0.022 0.002 TYR A 239 PHE 0.018 0.001 PHE B 732 TRP 0.007 0.001 TRP B 499 HIS 0.006 0.001 HIS B 692 Details of bonding type rmsd covalent geometry : bond 0.00302 (14069) covalent geometry : angle 0.57497 (19324) hydrogen bonds : bond 0.03396 ( 686) hydrogen bonds : angle 3.94121 ( 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 112 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9101 (ptpp) REVERT: A 389 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8097 (mtm110) REVERT: A 685 GLN cc_start: 0.8880 (tp40) cc_final: 0.8668 (tt0) REVERT: B 25 GLU cc_start: 0.8912 (tp30) cc_final: 0.8702 (tp30) REVERT: B 131 PHE cc_start: 0.7458 (p90) cc_final: 0.6864 (p90) REVERT: B 142 MET cc_start: 0.7359 (ptt) cc_final: 0.6350 (pmm) REVERT: B 147 PHE cc_start: 0.7223 (m-80) cc_final: 0.6924 (m-80) REVERT: B 155 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: B 188 MET cc_start: 0.7458 (tpp) cc_final: 0.7120 (tpp) REVERT: B 195 ASP cc_start: 0.8839 (t0) cc_final: 0.8599 (t0) REVERT: B 395 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7140 (pt0) REVERT: B 487 MET cc_start: 0.9138 (tpt) cc_final: 0.8925 (tpp) REVERT: B 642 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8645 (mt-10) REVERT: B 684 MET cc_start: 0.9292 (mtp) cc_final: 0.8984 (mtp) REVERT: B 790 MET cc_start: 0.5545 (mmm) cc_final: 0.5061 (mtm) REVERT: B 842 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7198 (tmm) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.6510 time to fit residues: 74.1953 Evaluate side-chains 102 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 100 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU 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: 0.0980 chunk 85 optimal weight: 0.2980 chunk 37 optimal weight: 0.0270 chunk 148 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 159 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 776 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 = 0.3844 r_free = 0.3844 target = 0.122424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074878 restraints weight = 24610.229| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.25 r_work: 0.2820 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14069 Z= 0.106 Angle : 0.561 14.068 19324 Z= 0.281 Chirality : 0.039 0.162 2196 Planarity : 0.005 0.097 2325 Dihedral : 17.077 168.941 2319 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.31 % Allowed : 12.06 % Favored : 86.64 % 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: 1.95 (0.22), residues: 1615 helix: 2.11 (0.19), residues: 788 sheet: 1.16 (0.35), residues: 223 loop : 0.34 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 112 TYR 0.013 0.001 TYR A 786 PHE 0.018 0.001 PHE B 732 TRP 0.007 0.001 TRP B 499 HIS 0.019 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00228 (14069) covalent geometry : angle 0.56108 (19324) hydrogen bonds : bond 0.03004 ( 686) hydrogen bonds : angle 3.86775 ( 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 110 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9098 (ptpp) REVERT: A 389 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8071 (mtm110) REVERT: A 685 GLN cc_start: 0.8898 (tp40) cc_final: 0.8692 (tt0) REVERT: B 25 GLU cc_start: 0.8900 (tp30) cc_final: 0.8698 (tp30) REVERT: B 131 PHE cc_start: 0.7478 (p90) cc_final: 0.6896 (p90) REVERT: B 155 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: B 389 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8571 (mmm-85) REVERT: B 642 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8620 (mt-10) REVERT: B 684 MET cc_start: 0.9298 (mtp) cc_final: 0.9016 (mtp) REVERT: B 790 MET cc_start: 0.5599 (mmm) cc_final: 0.5101 (mtm) REVERT: B 842 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7216 (tmm) outliers start: 18 outliers final: 7 residues processed: 105 average time/residue: 0.5962 time to fit residues: 68.4763 Evaluate side-chains 100 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 686 LEU 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 160 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 85 optimal weight: 0.0570 chunk 54 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076746 restraints weight = 25219.377| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.23 r_work: 0.2824 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14069 Z= 0.111 Angle : 0.576 14.570 19324 Z= 0.285 Chirality : 0.039 0.164 2196 Planarity : 0.004 0.063 2325 Dihedral : 16.999 169.125 2319 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.80 % Allowed : 12.49 % 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: 2.01 (0.22), residues: 1615 helix: 2.16 (0.19), residues: 788 sheet: 1.23 (0.35), residues: 223 loop : 0.35 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 682 TYR 0.022 0.001 TYR A 239 PHE 0.031 0.001 PHE B 688 TRP 0.008 0.001 TRP B 499 HIS 0.017 0.001 HIS A 776 Details of bonding type rmsd covalent geometry : bond 0.00247 (14069) covalent geometry : angle 0.57633 (19324) hydrogen bonds : bond 0.03083 ( 686) hydrogen bonds : angle 3.83902 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.31 seconds wall clock time: 76 minutes 28.26 seconds (4588.26 seconds total)