Starting phenix.real_space_refine on Thu Feb 5 16:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8s_63720/02_2026/9m8s_63720.cif" } resolution = 3.1 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= 0.003 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12008 2.51 5 N 3036 2.21 5 O 3128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s 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: 18304 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4576 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 20, 'TRANS': 557} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Restraints were copied for chains: A, C, D Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18304 At special positions: 0 Unit cell: (107.12, 107.12, 146.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3128 8.00 N 3036 7.00 C 12008 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: 1.78 Conformation dependent library (CDL) restraints added in 916.8 milliseconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 74.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.892A pdb=" N TRP B 515 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 535 removed outlier: 4.267A pdb=" N ASP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.513A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 590 Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 Processing helix chain 'B' and resid 714 through 740 removed outlier: 4.271A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 790 Processing helix chain 'B' and resid 803 through 819 Processing helix chain 'B' and resid 820 through 823 Processing helix chain 'B' and resid 827 through 850 removed outlier: 3.594A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 892 removed outlier: 4.805A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 928 removed outlier: 4.714A pdb=" N GLU B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Proline residue: B 925 - end of helix Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 970 removed outlier: 4.057A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 990 Processing helix chain 'B' and resid 992 through 999 removed outlier: 3.854A pdb=" N ARG B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.892A pdb=" N TRP A 515 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 535 removed outlier: 4.267A pdb=" N ASP A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.512A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 714 through 740 removed outlier: 4.271A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 790 Processing helix chain 'A' and resid 803 through 819 Processing helix chain 'A' and resid 820 through 823 Processing helix chain 'A' and resid 827 through 850 removed outlier: 3.595A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 892 removed outlier: 4.804A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 928 removed outlier: 4.714A pdb=" N GLU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.057A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 990 Processing helix chain 'A' and resid 992 through 999 removed outlier: 3.854A pdb=" N ARG A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.892A pdb=" N TRP C 515 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 535 removed outlier: 4.267A pdb=" N ASP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.513A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 590 Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 604 through 611 Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 714 through 740 removed outlier: 4.270A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 790 Processing helix chain 'C' and resid 803 through 819 Processing helix chain 'C' and resid 820 through 823 Processing helix chain 'C' and resid 827 through 850 removed outlier: 3.594A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 892 removed outlier: 4.804A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 928 removed outlier: 4.714A pdb=" N GLU C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Proline residue: C 925 - end of helix Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 970 removed outlier: 4.056A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 990 Processing helix chain 'C' and resid 992 through 999 removed outlier: 3.854A pdb=" N ARG C 996 " --> pdb=" O LEU C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1072 Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 458 through 467 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.892A pdb=" N TRP D 515 " --> pdb=" O HIS D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 535 removed outlier: 4.267A pdb=" N ASP D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.513A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 559 " --> pdb=" O ALA D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 590 Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 604 through 611 Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 Processing helix chain 'D' and resid 714 through 740 removed outlier: 4.270A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 790 Processing helix chain 'D' and resid 803 through 819 Processing helix chain 'D' and resid 820 through 823 Processing helix chain 'D' and resid 827 through 850 removed outlier: 3.595A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 892 removed outlier: 4.805A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 928 removed outlier: 4.714A pdb=" N GLU D 924 " --> pdb=" O GLU D 920 " (cutoff:3.500A) Proline residue: D 925 - end of helix Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 970 removed outlier: 4.057A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 990 Processing helix chain 'D' and resid 992 through 999 removed outlier: 3.854A pdb=" N ARG D 996 " --> pdb=" O LEU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'B' and resid 657 through 659 Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AA3, first strand: chain 'C' and resid 657 through 659 Processing sheet with id=AA4, first strand: chain 'D' and resid 657 through 659 1177 hydrogen bonds defined for protein. 3483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2848 1.29 - 1.42: 4760 1.42 - 1.55: 10875 1.55 - 1.68: 13 1.68 - 1.81: 212 Bond restraints: 18708 Sorted by residual: bond pdb=" C ILE B 957 " pdb=" O ILE B 957 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.21e+01 bond pdb=" C ILE D 957 " pdb=" O ILE D 957 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.21e+01 bond pdb=" C ILE C 957 " pdb=" O ILE C 957 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.17e-02 7.31e+03 4.12e+01 bond pdb=" C ILE A 957 " pdb=" O ILE A 957 " ideal model delta sigma weight residual 1.237 1.163 0.075 1.17e-02 7.31e+03 4.06e+01 bond pdb=" C VAL C 961 " pdb=" O VAL C 961 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.19e-02 7.06e+03 1.42e+01 ... (remaining 18703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 25010 2.29 - 4.57: 286 4.57 - 6.86: 48 6.86 - 9.14: 12 9.14 - 11.43: 8 Bond angle restraints: 25364 Sorted by residual: angle pdb=" C ASP D 915 " pdb=" CA ASP D 915 " pdb=" CB ASP D 915 " ideal model delta sigma weight residual 111.50 100.07 11.43 1.29e+00 6.01e-01 7.85e+01 angle pdb=" C ASP C 915 " pdb=" CA ASP C 915 " pdb=" CB ASP C 915 " ideal model delta sigma weight residual 111.50 100.08 11.42 1.29e+00 6.01e-01 7.84e+01 angle pdb=" C ASP B 915 " pdb=" CA ASP B 915 " pdb=" CB ASP B 915 " ideal model delta sigma weight residual 111.50 100.08 11.42 1.29e+00 6.01e-01 7.84e+01 angle pdb=" C ASP A 915 " pdb=" CA ASP A 915 " pdb=" CB ASP A 915 " ideal model delta sigma weight residual 111.50 100.10 11.40 1.29e+00 6.01e-01 7.81e+01 angle pdb=" CA ILE A 957 " pdb=" C ILE A 957 " pdb=" O ILE A 957 " ideal model delta sigma weight residual 120.95 114.14 6.81 1.04e+00 9.25e-01 4.29e+01 ... (remaining 25359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 9406 17.04 - 34.08: 1249 34.08 - 51.12: 421 51.12 - 68.15: 72 68.15 - 85.19: 20 Dihedral angle restraints: 11168 sinusoidal: 4364 harmonic: 6804 Sorted by residual: dihedral pdb=" CA LEU D 992 " pdb=" C LEU D 992 " pdb=" N TRP D 993 " pdb=" CA TRP D 993 " ideal model delta harmonic sigma weight residual 180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 992 " pdb=" C LEU B 992 " pdb=" N TRP B 993 " pdb=" CA TRP B 993 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU A 992 " pdb=" C LEU A 992 " pdb=" N TRP A 993 " pdb=" CA TRP A 993 " ideal model delta harmonic sigma weight residual -180.00 -159.51 -20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 11165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2715 0.068 - 0.137: 257 0.137 - 0.205: 12 0.205 - 0.273: 0 0.273 - 0.341: 4 Chirality restraints: 2988 Sorted by residual: chirality pdb=" CB VAL D 961 " pdb=" CA VAL D 961 " pdb=" CG1 VAL D 961 " pdb=" CG2 VAL D 961 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL C 961 " pdb=" CA VAL C 961 " pdb=" CG1 VAL C 961 " pdb=" CG2 VAL C 961 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL B 961 " pdb=" CA VAL B 961 " pdb=" CG1 VAL B 961 " pdb=" CG2 VAL B 961 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2985 not shown) Planarity restraints: 3120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 579 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLN A 579 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN A 579 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 580 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 579 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLN C 579 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN C 579 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN C 580 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 579 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C GLN B 579 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN B 579 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 580 " 0.014 2.00e-02 2.50e+03 ... (remaining 3117 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5843 2.84 - 3.36: 18040 3.36 - 3.87: 30062 3.87 - 4.39: 33222 4.39 - 4.90: 58906 Nonbonded interactions: 146073 Sorted by model distance: nonbonded pdb=" NZ LYS D 591 " pdb=" OH TYR D1049 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS B 591 " pdb=" OH TYR B1049 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS A 591 " pdb=" OH TYR A1049 " model vdw 2.328 3.120 nonbonded pdb=" NZ LYS C 591 " pdb=" OH TYR C1049 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN C 577 " pdb=" N LYS C 578 " model vdw 2.329 3.120 ... (remaining 146068 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.350 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18708 Z= 0.196 Angle : 0.646 11.430 25364 Z= 0.377 Chirality : 0.041 0.341 2988 Planarity : 0.004 0.039 3120 Dihedral : 17.791 85.192 6744 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.42 % Rotamer: Outliers : 1.58 % Allowed : 24.59 % Favored : 73.82 % Cbeta Deviations : 0.18 % 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 (0.18), residues: 2272 helix: 1.73 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 975 TYR 0.010 0.001 TYR C 456 PHE 0.006 0.001 PHE A 583 TRP 0.011 0.001 TRP B 832 HIS 0.002 0.001 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00332 (18708) covalent geometry : angle 0.64571 (25364) hydrogen bonds : bond 0.11909 ( 1177) hydrogen bonds : angle 4.56804 ( 3483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 0.722 Fit side-chains REVERT: B 486 LEU cc_start: 0.8650 (tp) cc_final: 0.8420 (tp) REVERT: B 721 MET cc_start: 0.7435 (tpt) cc_final: 0.6895 (mmt) REVERT: B 842 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: B 911 MET cc_start: 0.9058 (ptp) cc_final: 0.8628 (ptm) REVERT: B 912 MET cc_start: 0.8857 (ttp) cc_final: 0.8632 (ptm) REVERT: B 915 ASP cc_start: 0.8696 (t0) cc_final: 0.8169 (t70) REVERT: A 486 LEU cc_start: 0.8647 (tp) cc_final: 0.8410 (tp) REVERT: A 664 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7346 (tp-100) REVERT: A 721 MET cc_start: 0.7453 (tpt) cc_final: 0.6904 (mmt) REVERT: A 842 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 911 MET cc_start: 0.9060 (ptp) cc_final: 0.8644 (ptm) REVERT: A 912 MET cc_start: 0.8868 (ttp) cc_final: 0.8636 (ptm) REVERT: A 915 ASP cc_start: 0.8689 (t0) cc_final: 0.8159 (t70) REVERT: C 486 LEU cc_start: 0.8826 (tp) cc_final: 0.8599 (tp) REVERT: C 721 MET cc_start: 0.7431 (tpt) cc_final: 0.6890 (mmt) REVERT: C 842 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: C 911 MET cc_start: 0.9059 (ptp) cc_final: 0.8648 (ptm) REVERT: C 912 MET cc_start: 0.8881 (ttp) cc_final: 0.8643 (ptm) REVERT: C 915 ASP cc_start: 0.8686 (t0) cc_final: 0.8153 (t70) REVERT: D 486 LEU cc_start: 0.8710 (tp) cc_final: 0.8473 (tp) REVERT: D 721 MET cc_start: 0.7453 (tpt) cc_final: 0.6904 (mmt) REVERT: D 842 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: D 911 MET cc_start: 0.9055 (ptp) cc_final: 0.8640 (ptm) REVERT: D 912 MET cc_start: 0.8882 (ttp) cc_final: 0.8653 (ptm) REVERT: D 915 ASP cc_start: 0.8646 (t0) cc_final: 0.8126 (t70) outliers start: 31 outliers final: 19 residues processed: 342 average time/residue: 0.1353 time to fit residues: 71.9183 Evaluate side-chains 326 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1072 MET Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 1058 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 ASN B 692 ASN B 829 HIS B 907 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 692 ASN A 829 HIS A 907 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 ASN C 692 ASN C 829 HIS C 907 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN D 692 ASN D 829 HIS D 907 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140539 restraints weight = 20710.988| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.54 r_work: 0.3265 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18708 Z= 0.118 Angle : 0.508 6.041 25364 Z= 0.261 Chirality : 0.038 0.144 2988 Planarity : 0.004 0.038 3120 Dihedral : 4.816 49.678 2493 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.51 % Rotamer: Outliers : 1.48 % Allowed : 25.36 % Favored : 73.16 % 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 (0.18), residues: 2272 helix: 1.94 (0.13), residues: 1656 sheet: -1.47 (0.97), residues: 40 loop : -1.29 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1050 TYR 0.008 0.001 TYR B 456 PHE 0.008 0.001 PHE B 660 TRP 0.010 0.001 TRP B 832 HIS 0.002 0.000 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00262 (18708) covalent geometry : angle 0.50792 (25364) hydrogen bonds : bond 0.04338 ( 1177) hydrogen bonds : angle 3.88129 ( 3483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.742 Fit side-chains REVERT: B 486 LEU cc_start: 0.8858 (tp) cc_final: 0.8636 (tp) REVERT: B 721 MET cc_start: 0.7603 (tpt) cc_final: 0.7001 (mmt) REVERT: B 785 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6566 (t80) REVERT: B 842 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 912 MET cc_start: 0.8887 (ttp) cc_final: 0.8595 (ptm) REVERT: B 981 GLU cc_start: 0.7934 (tp30) cc_final: 0.7688 (tp30) REVERT: A 486 LEU cc_start: 0.8845 (tp) cc_final: 0.8619 (tp) REVERT: A 721 MET cc_start: 0.7604 (tpt) cc_final: 0.7020 (mmt) REVERT: A 785 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 842 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: A 912 MET cc_start: 0.8897 (ttp) cc_final: 0.8601 (ptm) REVERT: A 981 GLU cc_start: 0.7895 (tp30) cc_final: 0.7630 (tp30) REVERT: C 486 LEU cc_start: 0.8879 (tp) cc_final: 0.8663 (tp) REVERT: C 721 MET cc_start: 0.7568 (tpt) cc_final: 0.7029 (mmt) REVERT: C 785 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6479 (t80) REVERT: C 842 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: C 912 MET cc_start: 0.8904 (ttp) cc_final: 0.8602 (ptm) REVERT: C 981 GLU cc_start: 0.7893 (tp30) cc_final: 0.7643 (tp30) REVERT: D 486 LEU cc_start: 0.8863 (tp) cc_final: 0.8636 (tp) REVERT: D 721 MET cc_start: 0.7599 (tpt) cc_final: 0.7029 (mmt) REVERT: D 785 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6543 (t80) REVERT: D 842 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: D 912 MET cc_start: 0.8917 (ttp) cc_final: 0.8606 (ptm) REVERT: D 981 GLU cc_start: 0.7909 (tp30) cc_final: 0.7640 (tp30) outliers start: 29 outliers final: 1 residues processed: 346 average time/residue: 0.1271 time to fit residues: 67.4071 Evaluate side-chains 311 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 302 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 224 optimal weight: 0.0030 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.191162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147445 restraints weight = 20771.094| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.35 r_work: 0.3390 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18708 Z= 0.116 Angle : 0.498 6.709 25364 Z= 0.257 Chirality : 0.038 0.147 2988 Planarity : 0.004 0.036 3120 Dihedral : 4.223 49.274 2456 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.23 % Favored : 95.55 % Rotamer: Outliers : 2.20 % Allowed : 26.07 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.18), residues: 2272 helix: 1.95 (0.13), residues: 1672 sheet: -1.36 (0.99), residues: 40 loop : -1.38 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.011 0.001 TYR A 456 PHE 0.008 0.001 PHE A 877 TRP 0.009 0.001 TRP B 832 HIS 0.002 0.000 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00261 (18708) covalent geometry : angle 0.49823 (25364) hydrogen bonds : bond 0.04211 ( 1177) hydrogen bonds : angle 3.76421 ( 3483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 0.791 Fit side-chains REVERT: B 486 LEU cc_start: 0.8850 (tp) cc_final: 0.8589 (tp) REVERT: B 721 MET cc_start: 0.7690 (tpt) cc_final: 0.7189 (mmt) REVERT: B 723 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8008 (mp) REVERT: B 785 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6630 (t80) REVERT: B 912 MET cc_start: 0.8866 (ttp) cc_final: 0.8531 (ptm) REVERT: B 981 GLU cc_start: 0.7993 (tp30) cc_final: 0.7739 (tp30) REVERT: A 486 LEU cc_start: 0.8847 (tp) cc_final: 0.8580 (tp) REVERT: A 721 MET cc_start: 0.7680 (tpt) cc_final: 0.7193 (mmt) REVERT: A 723 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 785 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6601 (t80) REVERT: A 912 MET cc_start: 0.8865 (ttp) cc_final: 0.8528 (ptm) REVERT: A 981 GLU cc_start: 0.7962 (tp30) cc_final: 0.7716 (tp30) REVERT: C 486 LEU cc_start: 0.8936 (tp) cc_final: 0.8683 (tp) REVERT: C 721 MET cc_start: 0.7661 (tpt) cc_final: 0.7180 (mmt) REVERT: C 723 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7986 (mp) REVERT: C 785 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6620 (t80) REVERT: C 912 MET cc_start: 0.8862 (ttp) cc_final: 0.8540 (ptm) REVERT: C 981 GLU cc_start: 0.7949 (tp30) cc_final: 0.7714 (tp30) REVERT: D 486 LEU cc_start: 0.8849 (tp) cc_final: 0.8585 (tp) REVERT: D 721 MET cc_start: 0.7682 (tpt) cc_final: 0.7197 (mmt) REVERT: D 723 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7999 (mp) REVERT: D 785 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6613 (t80) REVERT: D 912 MET cc_start: 0.8868 (ttp) cc_final: 0.8500 (ptm) REVERT: D 981 GLU cc_start: 0.7967 (tp30) cc_final: 0.7717 (tp30) outliers start: 43 outliers final: 13 residues processed: 363 average time/residue: 0.1362 time to fit residues: 76.4587 Evaluate side-chains 335 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 190 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 0.0670 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.189841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133519 restraints weight = 20842.500| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.93 r_work: 0.3029 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18708 Z= 0.179 Angle : 0.560 7.319 25364 Z= 0.289 Chirality : 0.041 0.206 2988 Planarity : 0.004 0.037 3120 Dihedral : 3.774 19.611 2448 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 26.94 % Favored : 70.91 % 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: 1.37 (0.18), residues: 2272 helix: 1.74 (0.13), residues: 1668 sheet: -1.38 (0.91), residues: 48 loop : -1.44 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 975 TYR 0.011 0.001 TYR C 889 PHE 0.011 0.002 PHE C 877 TRP 0.009 0.001 TRP A 711 HIS 0.004 0.001 HIS C 983 Details of bonding type rmsd covalent geometry : bond 0.00441 (18708) covalent geometry : angle 0.55992 (25364) hydrogen bonds : bond 0.05063 ( 1177) hydrogen bonds : angle 4.04752 ( 3483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 319 time to evaluate : 0.760 Fit side-chains REVERT: B 486 LEU cc_start: 0.8851 (tp) cc_final: 0.8628 (tp) REVERT: B 499 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: B 504 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7867 (ttpt) REVERT: B 721 MET cc_start: 0.7650 (tpt) cc_final: 0.6958 (mmt) REVERT: B 723 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 785 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6573 (t80) REVERT: B 953 MET cc_start: 0.9030 (mmm) cc_final: 0.8807 (mmt) REVERT: B 981 GLU cc_start: 0.7946 (tp30) cc_final: 0.7641 (tp30) REVERT: A 486 LEU cc_start: 0.8847 (tp) cc_final: 0.8622 (tp) REVERT: A 499 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 504 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7881 (ttpt) REVERT: A 721 MET cc_start: 0.7668 (tpt) cc_final: 0.6967 (mmt) REVERT: A 723 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7787 (mp) REVERT: A 785 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6558 (t80) REVERT: A 953 MET cc_start: 0.9038 (mmm) cc_final: 0.8817 (mmt) REVERT: C 486 LEU cc_start: 0.8831 (tp) cc_final: 0.8611 (tp) REVERT: C 499 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: C 721 MET cc_start: 0.7666 (tpt) cc_final: 0.6976 (mmt) REVERT: C 723 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7758 (mp) REVERT: C 785 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6555 (t80) REVERT: C 953 MET cc_start: 0.9039 (mmm) cc_final: 0.8816 (mmt) REVERT: D 486 LEU cc_start: 0.8840 (tp) cc_final: 0.8617 (tp) REVERT: D 499 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: D 721 MET cc_start: 0.7692 (tpt) cc_final: 0.6997 (mmt) REVERT: D 723 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7774 (mp) REVERT: D 785 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6547 (t80) REVERT: D 953 MET cc_start: 0.9028 (mmm) cc_final: 0.8806 (mmt) outliers start: 42 outliers final: 10 residues processed: 348 average time/residue: 0.1443 time to fit residues: 76.4923 Evaluate side-chains 315 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain C residue 499 GLN Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 213 optimal weight: 0.0570 chunk 145 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 219 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1061 GLN A1061 GLN C 512 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139814 restraints weight = 20711.539| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.98 r_work: 0.3136 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18708 Z= 0.109 Angle : 0.512 6.912 25364 Z= 0.265 Chirality : 0.038 0.166 2988 Planarity : 0.004 0.037 3120 Dihedral : 3.630 20.474 2448 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % Rotamer: Outliers : 2.40 % Allowed : 26.74 % Favored : 70.86 % 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: 1.74 (0.18), residues: 2272 helix: 2.00 (0.13), residues: 1656 sheet: -1.47 (0.90), residues: 48 loop : -1.18 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.011 0.001 TYR A 456 PHE 0.007 0.001 PHE B 853 TRP 0.010 0.001 TRP D 832 HIS 0.002 0.000 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00238 (18708) covalent geometry : angle 0.51206 (25364) hydrogen bonds : bond 0.03947 ( 1177) hydrogen bonds : angle 3.79267 ( 3483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.899 Fit side-chains REVERT: B 486 LEU cc_start: 0.8821 (tp) cc_final: 0.8591 (tp) REVERT: B 504 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7750 (ttpt) REVERT: B 611 ILE cc_start: 0.8266 (mp) cc_final: 0.8065 (mp) REVERT: B 721 MET cc_start: 0.7572 (tpt) cc_final: 0.6873 (mmt) REVERT: B 723 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7715 (mp) REVERT: B 785 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6678 (t80) REVERT: B 842 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: B 981 GLU cc_start: 0.7994 (tp30) cc_final: 0.7695 (tp30) REVERT: B 1061 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: A 486 LEU cc_start: 0.8819 (tp) cc_final: 0.8589 (tp) REVERT: A 504 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7732 (ttpt) REVERT: A 611 ILE cc_start: 0.8267 (mp) cc_final: 0.8065 (mp) REVERT: A 721 MET cc_start: 0.7571 (tpt) cc_final: 0.6874 (mmt) REVERT: A 723 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 785 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6647 (t80) REVERT: A 842 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: A 981 GLU cc_start: 0.7976 (tp30) cc_final: 0.7719 (tp30) REVERT: C 486 LEU cc_start: 0.8813 (tp) cc_final: 0.8585 (tp) REVERT: C 721 MET cc_start: 0.7578 (tpt) cc_final: 0.6890 (mmt) REVERT: C 723 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7652 (mp) REVERT: C 785 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.6660 (t80) REVERT: C 842 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: C 981 GLU cc_start: 0.7972 (tp30) cc_final: 0.7732 (tp30) REVERT: D 486 LEU cc_start: 0.8817 (tp) cc_final: 0.8581 (tp) REVERT: D 721 MET cc_start: 0.7576 (tpt) cc_final: 0.6888 (mmt) REVERT: D 723 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7721 (mp) REVERT: D 785 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6640 (t80) REVERT: D 842 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: D 981 GLU cc_start: 0.7984 (tp30) cc_final: 0.7725 (tp30) outliers start: 47 outliers final: 12 residues processed: 358 average time/residue: 0.1409 time to fit residues: 77.7924 Evaluate side-chains 337 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 312 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 215 optimal weight: 0.0870 chunk 129 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 173 optimal weight: 0.0470 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1061 GLN C 512 HIS C1061 GLN D1061 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.193365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136750 restraints weight = 20632.978| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.89 r_work: 0.3098 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18708 Z= 0.118 Angle : 0.519 7.949 25364 Z= 0.267 Chirality : 0.038 0.148 2988 Planarity : 0.004 0.037 3120 Dihedral : 3.613 20.341 2448 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.01 % Favored : 95.77 % Rotamer: Outliers : 2.20 % Allowed : 26.33 % Favored : 71.47 % 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 (0.18), residues: 2272 helix: 2.02 (0.13), residues: 1656 sheet: -1.56 (0.89), residues: 48 loop : -1.21 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 975 TYR 0.011 0.001 TYR A 456 PHE 0.007 0.001 PHE A 877 TRP 0.010 0.001 TRP C 832 HIS 0.002 0.000 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00272 (18708) covalent geometry : angle 0.51879 (25364) hydrogen bonds : bond 0.04101 ( 1177) hydrogen bonds : angle 3.84527 ( 3483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 0.714 Fit side-chains REVERT: B 486 LEU cc_start: 0.8746 (tp) cc_final: 0.8500 (tp) REVERT: B 499 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7999 (tp40) REVERT: B 504 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7738 (ttpt) REVERT: B 691 GLN cc_start: 0.8236 (mt0) cc_final: 0.7860 (mt0) REVERT: B 721 MET cc_start: 0.7697 (tpt) cc_final: 0.7023 (mmt) REVERT: B 723 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7811 (mp) REVERT: B 785 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6647 (t80) REVERT: B 842 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: B 981 GLU cc_start: 0.8015 (tp30) cc_final: 0.7719 (tp30) REVERT: A 486 LEU cc_start: 0.8749 (tp) cc_final: 0.8513 (tp) REVERT: A 499 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7987 (tp40) REVERT: A 504 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7727 (ttpt) REVERT: A 691 GLN cc_start: 0.8187 (mt0) cc_final: 0.7804 (mt0) REVERT: A 721 MET cc_start: 0.7696 (tpt) cc_final: 0.7029 (mmt) REVERT: A 723 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 785 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6627 (t80) REVERT: A 842 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: A 981 GLU cc_start: 0.8002 (tp30) cc_final: 0.7749 (tp30) REVERT: A 1061 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: C 486 LEU cc_start: 0.8743 (tp) cc_final: 0.8498 (tp) REVERT: C 499 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8001 (tp40) REVERT: C 691 GLN cc_start: 0.8243 (mt0) cc_final: 0.7866 (mt0) REVERT: C 721 MET cc_start: 0.7706 (tpt) cc_final: 0.7016 (mmt) REVERT: C 723 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7739 (mp) REVERT: C 785 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6660 (t80) REVERT: C 842 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: C 981 GLU cc_start: 0.7976 (tp30) cc_final: 0.7720 (tp30) REVERT: D 486 LEU cc_start: 0.8736 (tp) cc_final: 0.8501 (tp) REVERT: D 499 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8011 (tp40) REVERT: D 721 MET cc_start: 0.7720 (tpt) cc_final: 0.7048 (mmt) REVERT: D 723 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7766 (mp) REVERT: D 785 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6624 (t80) REVERT: D 842 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: D 981 GLU cc_start: 0.8001 (tp30) cc_final: 0.7747 (tp30) outliers start: 43 outliers final: 16 residues processed: 347 average time/residue: 0.1397 time to fit residues: 74.6363 Evaluate side-chains 322 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 1061 GLN Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 166 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS ** D1061 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.190961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.133567 restraints weight = 20811.384| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.93 r_work: 0.3042 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18708 Z= 0.158 Angle : 0.560 8.855 25364 Z= 0.289 Chirality : 0.040 0.150 2988 Planarity : 0.004 0.039 3120 Dihedral : 3.699 20.250 2448 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 2.04 % Allowed : 26.02 % Favored : 71.93 % 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: 1.48 (0.18), residues: 2272 helix: 1.79 (0.13), residues: 1668 sheet: -1.65 (0.88), residues: 48 loop : -1.27 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 975 TYR 0.011 0.001 TYR A 456 PHE 0.010 0.001 PHE D 841 TRP 0.009 0.001 TRP A 832 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00387 (18708) covalent geometry : angle 0.55979 (25364) hydrogen bonds : bond 0.04720 ( 1177) hydrogen bonds : angle 4.00240 ( 3483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.654 Fit side-chains REVERT: B 486 LEU cc_start: 0.8869 (tp) cc_final: 0.8636 (tp) REVERT: B 499 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8207 (tp40) REVERT: B 691 GLN cc_start: 0.8277 (mt0) cc_final: 0.7924 (mt0) REVERT: B 721 MET cc_start: 0.7734 (tpt) cc_final: 0.7009 (mmt) REVERT: B 723 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7858 (mp) REVERT: B 785 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6676 (t80) REVERT: B 911 MET cc_start: 0.9131 (ptp) cc_final: 0.8771 (ptm) REVERT: B 981 GLU cc_start: 0.8033 (tp30) cc_final: 0.7738 (tp30) REVERT: A 486 LEU cc_start: 0.8871 (tp) cc_final: 0.8647 (tp) REVERT: A 499 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8208 (tp40) REVERT: A 515 TRP cc_start: 0.8359 (m-10) cc_final: 0.7909 (m-10) REVERT: A 531 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (pttm) REVERT: A 691 GLN cc_start: 0.8276 (mt0) cc_final: 0.7916 (mt0) REVERT: A 721 MET cc_start: 0.7731 (tpt) cc_final: 0.7016 (mmt) REVERT: A 723 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 785 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6678 (t80) REVERT: A 911 MET cc_start: 0.9137 (ptp) cc_final: 0.8773 (ptm) REVERT: A 981 GLU cc_start: 0.7997 (tp30) cc_final: 0.7721 (tp30) REVERT: A 1061 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: C 486 LEU cc_start: 0.8863 (tp) cc_final: 0.8633 (tp) REVERT: C 499 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8225 (tp40) REVERT: C 515 TRP cc_start: 0.8357 (m-10) cc_final: 0.7909 (m-10) REVERT: C 691 GLN cc_start: 0.8272 (mt0) cc_final: 0.7913 (mt0) REVERT: C 721 MET cc_start: 0.7750 (tpt) cc_final: 0.7021 (mmt) REVERT: C 723 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7795 (mp) REVERT: C 785 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6664 (t80) REVERT: C 911 MET cc_start: 0.9130 (ptp) cc_final: 0.8763 (ptm) REVERT: C 981 GLU cc_start: 0.7979 (tp30) cc_final: 0.7722 (tp30) REVERT: C 1061 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: D 486 LEU cc_start: 0.8863 (tp) cc_final: 0.8642 (tp) REVERT: D 499 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8110 (tp40) REVERT: D 515 TRP cc_start: 0.8357 (m-10) cc_final: 0.7903 (m-10) REVERT: D 691 GLN cc_start: 0.8272 (mt0) cc_final: 0.7915 (mt0) REVERT: D 721 MET cc_start: 0.7753 (tpt) cc_final: 0.7028 (mmt) REVERT: D 723 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 785 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6668 (t80) REVERT: D 911 MET cc_start: 0.9134 (ptp) cc_final: 0.8766 (ptm) REVERT: D 981 GLU cc_start: 0.8011 (tp30) cc_final: 0.7736 (tp30) outliers start: 40 outliers final: 25 residues processed: 334 average time/residue: 0.1404 time to fit residues: 71.7838 Evaluate side-chains 334 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1061 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 10 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 216 optimal weight: 0.4980 chunk 170 optimal weight: 0.6980 chunk 201 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1061 GLN C 512 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.179778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132868 restraints weight = 20758.808| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.40 r_work: 0.3196 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18708 Z= 0.153 Angle : 0.562 9.022 25364 Z= 0.289 Chirality : 0.039 0.151 2988 Planarity : 0.004 0.040 3120 Dihedral : 3.725 20.366 2448 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.96 % Favored : 95.69 % Rotamer: Outliers : 2.20 % Allowed : 25.92 % Favored : 71.88 % 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: 1.45 (0.18), residues: 2272 helix: 1.79 (0.13), residues: 1668 sheet: -1.73 (0.87), residues: 48 loop : -1.34 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 975 TYR 0.011 0.001 TYR A 456 PHE 0.009 0.001 PHE B 841 TRP 0.009 0.001 TRP A 832 HIS 0.003 0.001 HIS D 983 Details of bonding type rmsd covalent geometry : bond 0.00371 (18708) covalent geometry : angle 0.56215 (25364) hydrogen bonds : bond 0.04681 ( 1177) hydrogen bonds : angle 3.98779 ( 3483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 313 time to evaluate : 0.838 Fit side-chains REVERT: B 486 LEU cc_start: 0.8971 (tp) cc_final: 0.8734 (tp) REVERT: B 499 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8232 (tp40) REVERT: B 691 GLN cc_start: 0.8334 (mt0) cc_final: 0.7953 (mt0) REVERT: B 721 MET cc_start: 0.7808 (tpt) cc_final: 0.7187 (mmt) REVERT: B 723 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 785 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6727 (t80) REVERT: A 486 LEU cc_start: 0.8980 (tp) cc_final: 0.8743 (tp) REVERT: A 499 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8228 (tp40) REVERT: A 515 TRP cc_start: 0.8376 (m-10) cc_final: 0.7947 (m-10) REVERT: A 691 GLN cc_start: 0.8342 (mt0) cc_final: 0.7974 (mt0) REVERT: A 721 MET cc_start: 0.7785 (tpt) cc_final: 0.7181 (mmt) REVERT: A 723 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 785 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 981 GLU cc_start: 0.7997 (tp30) cc_final: 0.7750 (tp30) REVERT: C 486 LEU cc_start: 0.8970 (tp) cc_final: 0.8727 (tp) REVERT: C 499 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8202 (tp40) REVERT: C 504 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7628 (pttt) REVERT: C 515 TRP cc_start: 0.8379 (m-10) cc_final: 0.7950 (m-10) REVERT: C 691 GLN cc_start: 0.8334 (mt0) cc_final: 0.7956 (mt0) REVERT: C 721 MET cc_start: 0.7824 (tpt) cc_final: 0.7186 (mmt) REVERT: C 723 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8015 (mp) REVERT: C 785 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6723 (t80) REVERT: C 981 GLU cc_start: 0.7941 (tp30) cc_final: 0.7698 (tp30) REVERT: C 1061 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8655 (tt0) REVERT: D 486 LEU cc_start: 0.8965 (tp) cc_final: 0.8729 (tp) REVERT: D 499 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8203 (tp40) REVERT: D 515 TRP cc_start: 0.8375 (m-10) cc_final: 0.7947 (m-10) REVERT: D 691 GLN cc_start: 0.8335 (mt0) cc_final: 0.7969 (mt0) REVERT: D 721 MET cc_start: 0.7790 (tpt) cc_final: 0.7186 (mmt) REVERT: D 723 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8022 (mp) REVERT: D 785 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6701 (t80) REVERT: D 981 GLU cc_start: 0.7988 (tp30) cc_final: 0.7744 (tp30) outliers start: 43 outliers final: 24 residues processed: 346 average time/residue: 0.1430 time to fit residues: 75.1694 Evaluate side-chains 340 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1061 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 184 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 0.0010 chunk 195 optimal weight: 5.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1061 GLN C 512 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.182698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152987 restraints weight = 20741.234| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.27 r_work: 0.3141 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18708 Z= 0.164 Angle : 0.581 9.037 25364 Z= 0.299 Chirality : 0.040 0.151 2988 Planarity : 0.004 0.041 3120 Dihedral : 3.776 20.519 2448 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer: Outliers : 2.30 % Allowed : 25.82 % Favored : 71.88 % 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 (0.18), residues: 2272 helix: 1.68 (0.13), residues: 1672 sheet: -1.80 (0.86), residues: 48 loop : -1.31 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 975 TYR 0.011 0.001 TYR B 456 PHE 0.010 0.001 PHE A 841 TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00403 (18708) covalent geometry : angle 0.58090 (25364) hydrogen bonds : bond 0.04856 ( 1177) hydrogen bonds : angle 4.06351 ( 3483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 486 LEU cc_start: 0.8932 (tp) cc_final: 0.8694 (tp) REVERT: B 499 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8159 (tp40) REVERT: B 691 GLN cc_start: 0.8249 (mt0) cc_final: 0.7894 (mt0) REVERT: B 721 MET cc_start: 0.7610 (tpt) cc_final: 0.7007 (mmt) REVERT: B 723 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7889 (mp) REVERT: B 785 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6703 (t80) REVERT: B 808 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 911 MET cc_start: 0.9115 (ptp) cc_final: 0.8726 (ptm) REVERT: A 486 LEU cc_start: 0.8932 (tp) cc_final: 0.8689 (tp) REVERT: A 499 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8130 (tp40) REVERT: A 691 GLN cc_start: 0.8240 (mt0) cc_final: 0.7878 (mt0) REVERT: A 721 MET cc_start: 0.7616 (tpt) cc_final: 0.7012 (mmt) REVERT: A 723 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 785 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6700 (t80) REVERT: A 808 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 911 MET cc_start: 0.9115 (ptp) cc_final: 0.8727 (ptm) REVERT: A 981 GLU cc_start: 0.7941 (tp30) cc_final: 0.7682 (tp30) REVERT: A 1061 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: C 486 LEU cc_start: 0.8925 (tp) cc_final: 0.8689 (tp) REVERT: C 499 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8305 (tp40) REVERT: C 691 GLN cc_start: 0.8256 (mt0) cc_final: 0.7896 (mt0) REVERT: C 721 MET cc_start: 0.7623 (tpt) cc_final: 0.7002 (mmt) REVERT: C 723 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7803 (mp) REVERT: C 785 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6692 (t80) REVERT: C 808 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7678 (mm-30) REVERT: C 911 MET cc_start: 0.9110 (ptp) cc_final: 0.8718 (ptm) REVERT: C 981 GLU cc_start: 0.7922 (tp30) cc_final: 0.7662 (tp30) REVERT: C 1061 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: D 486 LEU cc_start: 0.8924 (tp) cc_final: 0.8687 (tp) REVERT: D 499 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8336 (tp40) REVERT: D 691 GLN cc_start: 0.8242 (mt0) cc_final: 0.7883 (mt0) REVERT: D 721 MET cc_start: 0.7609 (tpt) cc_final: 0.6999 (mmt) REVERT: D 723 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7810 (mp) REVERT: D 785 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6712 (t80) REVERT: D 808 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 911 MET cc_start: 0.9118 (ptp) cc_final: 0.8731 (ptm) outliers start: 45 outliers final: 23 residues processed: 346 average time/residue: 0.1291 time to fit residues: 67.8875 Evaluate side-chains 336 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 303 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 1061 GLN Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 214 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 222 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.186154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153140 restraints weight = 20806.800| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.40 r_work: 0.3171 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18708 Z= 0.119 Angle : 0.552 9.335 25364 Z= 0.281 Chirality : 0.038 0.151 2988 Planarity : 0.004 0.041 3120 Dihedral : 3.660 20.676 2448 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.92 % Favored : 95.73 % Rotamer: Outliers : 1.89 % Allowed : 26.12 % Favored : 71.98 % 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: 1.64 (0.18), residues: 2272 helix: 1.93 (0.13), residues: 1660 sheet: -1.93 (0.87), residues: 48 loop : -1.23 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 975 TYR 0.011 0.001 TYR B 456 PHE 0.008 0.001 PHE A 877 TRP 0.010 0.001 TRP A 832 HIS 0.003 0.000 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00273 (18708) covalent geometry : angle 0.55167 (25364) hydrogen bonds : bond 0.04114 ( 1177) hydrogen bonds : angle 3.91336 ( 3483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 309 time to evaluate : 0.647 Fit side-chains REVERT: B 486 LEU cc_start: 0.8891 (tp) cc_final: 0.8658 (tp) REVERT: B 499 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8139 (tp40) REVERT: B 515 TRP cc_start: 0.8369 (m-10) cc_final: 0.8083 (m-10) REVERT: B 691 GLN cc_start: 0.8231 (mt0) cc_final: 0.7883 (mt0) REVERT: B 721 MET cc_start: 0.7599 (tpt) cc_final: 0.6951 (mmt) REVERT: B 723 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 785 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6766 (t80) REVERT: A 486 LEU cc_start: 0.8889 (tp) cc_final: 0.8656 (tp) REVERT: A 499 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8146 (tp40) REVERT: A 515 TRP cc_start: 0.8327 (m-10) cc_final: 0.7971 (m-10) REVERT: A 691 GLN cc_start: 0.8214 (mt0) cc_final: 0.7860 (mt0) REVERT: A 721 MET cc_start: 0.7598 (tpt) cc_final: 0.6951 (mmt) REVERT: A 723 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 785 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 1061 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: C 486 LEU cc_start: 0.8873 (tp) cc_final: 0.8644 (tp) REVERT: C 499 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8334 (tp40) REVERT: C 504 LYS cc_start: 0.7693 (tttt) cc_final: 0.7488 (pttt) REVERT: C 515 TRP cc_start: 0.8324 (m-10) cc_final: 0.7957 (m-10) REVERT: C 691 GLN cc_start: 0.8244 (mt0) cc_final: 0.7900 (mt0) REVERT: C 721 MET cc_start: 0.7603 (tpt) cc_final: 0.6956 (mmt) REVERT: C 723 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7824 (mp) REVERT: C 785 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6771 (t80) REVERT: D 486 LEU cc_start: 0.8880 (tp) cc_final: 0.8648 (tp) REVERT: D 499 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8293 (tp40) REVERT: D 515 TRP cc_start: 0.8330 (m-10) cc_final: 0.7963 (m-10) REVERT: D 691 GLN cc_start: 0.8246 (mt0) cc_final: 0.7897 (mt0) REVERT: D 721 MET cc_start: 0.7606 (tpt) cc_final: 0.6961 (mmt) REVERT: D 723 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7831 (mp) REVERT: D 785 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6721 (t80) outliers start: 37 outliers final: 19 residues processed: 333 average time/residue: 0.1189 time to fit residues: 61.0949 Evaluate side-chains 339 residues out of total 2084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1061 GLN Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1061 GLN Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 874 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 186 optimal weight: 0.0010 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 0.6980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.187964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155448 restraints weight = 20832.174| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.53 r_work: 0.3163 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18708 Z= 0.114 Angle : 0.536 9.067 25364 Z= 0.274 Chirality : 0.038 0.151 2988 Planarity : 0.004 0.041 3120 Dihedral : 3.591 20.258 2448 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.09 % Favored : 95.69 % Rotamer: Outliers : 1.89 % Allowed : 25.77 % Favored : 72.34 % 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 (0.18), residues: 2272 helix: 1.98 (0.13), residues: 1672 sheet: -1.99 (0.88), residues: 48 loop : -1.11 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 975 TYR 0.010 0.001 TYR B 456 PHE 0.008 0.001 PHE D 877 TRP 0.010 0.001 TRP C 832 HIS 0.002 0.000 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00259 (18708) covalent geometry : angle 0.53616 (25364) hydrogen bonds : bond 0.03985 ( 1177) hydrogen bonds : angle 3.84447 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5703.33 seconds wall clock time: 98 minutes 6.18 seconds (5886.18 seconds total)