Starting phenix.real_space_refine on Thu Sep 18 00:35:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdd_52061/09_2025/9hdd_52061.cif" } resolution = 3.62 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 3902 2.51 5 N 1062 2.21 5 O 1304 1.98 5 H 6260 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12556 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6278 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 395} Chain: "B" Number of atoms: 6278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 6278 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 395} Time building chain proxies: 2.42, per 1000 atoms: 0.19 Number of scatterers: 12556 At special positions: 0 Unit cell: (80.24, 93.84, 96.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1304 8.00 N 1062 7.00 C 3902 6.00 H 6260 1.00 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: 1.16 Conformation dependent library (CDL) restraints added in 359.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 560 through 594 removed outlier: 3.749A pdb=" N GLN A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Proline residue: A 572 - end of helix removed outlier: 3.938A pdb=" N SER A 588 " --> pdb=" O THR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 632 removed outlier: 3.550A pdb=" N SER A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 668 Processing helix chain 'A' and resid 669 through 693 Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.669A pdb=" N ILE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 734 through 741 removed outlier: 4.270A pdb=" N SER A 737 " --> pdb=" O ASN A 734 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 739 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN A 741 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 762 removed outlier: 3.590A pdb=" N GLU A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 801 removed outlier: 3.820A pdb=" N GLN A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 812 through 838 Processing helix chain 'A' and resid 839 through 841 No H-bonds generated for 'chain 'A' and resid 839 through 841' Processing helix chain 'A' and resid 850 through 874 removed outlier: 3.650A pdb=" N VAL A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 913 removed outlier: 4.180A pdb=" N ASP A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 958 removed outlier: 3.609A pdb=" N LEU A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 939 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 940 " --> pdb=" O GLN A 936 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 954 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'B' and resid 561 through 594 removed outlier: 4.523A pdb=" N ASP B 568 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Proline residue: B 572 - end of helix removed outlier: 3.880A pdb=" N SER B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 633 removed outlier: 3.554A pdb=" N SER B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 668 Processing helix chain 'B' and resid 669 through 695 removed outlier: 3.504A pdb=" N LEU B 679 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.166A pdb=" N LEU B 699 " --> pdb=" O MET B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 730 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 745 through 762 removed outlier: 3.670A pdb=" N GLU B 749 " --> pdb=" O ASN B 745 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 801 removed outlier: 3.722A pdb=" N GLN B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 795 " --> pdb=" O ILE B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 812 through 838 Processing helix chain 'B' and resid 838 through 843 removed outlier: 4.141A pdb=" N THR B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 843 " --> pdb=" O LYS B 839 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 838 through 843' Processing helix chain 'B' and resid 850 through 874 removed outlier: 4.173A pdb=" N PHE B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 913 removed outlier: 4.110A pdb=" N ASP B 911 " --> pdb=" O MET B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 958 removed outlier: 3.776A pdb=" N MET B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 938 " --> pdb=" O MET B 934 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 940 " --> pdb=" O GLN B 936 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 944 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS B 952 " --> pdb=" O SER B 948 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 953 " --> pdb=" O ASN B 949 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 954 " --> pdb=" O ALA B 950 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 955 " --> pdb=" O ARG B 951 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 957 " --> pdb=" O ARG B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 968 removed outlier: 3.711A pdb=" N GLN B 965 " --> pdb=" O ALA B 961 " (cutoff:3.500A) 505 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 6250 1.13 - 1.30: 1163 1.30 - 1.47: 2243 1.47 - 1.64: 2936 1.64 - 1.82: 46 Bond restraints: 12638 Sorted by residual: bond pdb=" NE2 GLN A 688 " pdb="HE22 GLN A 688 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL B 783 " pdb=" H VAL B 783 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS B 739 " pdb=" H LYS B 739 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU A 935 " pdb=" H GLU A 935 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 PHE B 649 " pdb=" HD1 PHE B 649 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 12633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 19215 2.42 - 4.84: 2688 4.84 - 7.26: 895 7.26 - 9.68: 109 9.68 - 12.10: 7 Bond angle restraints: 22914 Sorted by residual: angle pdb=" CA ASP B 895 " pdb=" CB ASP B 895 " pdb=" CG ASP B 895 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA ASP A 895 " pdb=" CB ASP A 895 " pdb=" CG ASP A 895 " ideal model delta sigma weight residual 112.60 117.98 -5.38 1.00e+00 1.00e+00 2.89e+01 angle pdb=" CA PHE A 691 " pdb=" CB PHE A 691 " pdb=" CG PHE A 691 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA PHE B 691 " pdb=" CB PHE B 691 " pdb=" CG PHE B 691 " ideal model delta sigma weight residual 113.80 119.08 -5.28 1.00e+00 1.00e+00 2.79e+01 angle pdb=" CA ASP B 922 " pdb=" CB ASP B 922 " pdb=" CG ASP B 922 " ideal model delta sigma weight residual 112.60 117.67 -5.07 1.00e+00 1.00e+00 2.57e+01 ... (remaining 22909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5314 17.63 - 35.27: 424 35.27 - 52.90: 100 52.90 - 70.53: 105 70.53 - 88.17: 11 Dihedral angle restraints: 5954 sinusoidal: 3308 harmonic: 2646 Sorted by residual: dihedral pdb=" CA MET A 695 " pdb=" C MET A 695 " pdb=" N SER A 696 " pdb=" CA SER A 696 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA MET B 695 " pdb=" C MET B 695 " pdb=" N SER B 696 " pdb=" CA SER B 696 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA THR B 876 " pdb=" C THR B 876 " pdb=" N SER B 877 " pdb=" CA SER B 877 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 5951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 610 0.070 - 0.140: 350 0.140 - 0.210: 88 0.210 - 0.280: 6 0.280 - 0.350: 4 Chirality restraints: 1058 Sorted by residual: chirality pdb=" CA HIS A 912 " pdb=" N HIS A 912 " pdb=" C HIS A 912 " pdb=" CB HIS A 912 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA HIS B 912 " pdb=" N HIS B 912 " pdb=" C HIS B 912 " pdb=" CB HIS B 912 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ASN B 745 " pdb=" N ASN B 745 " pdb=" C ASN B 745 " pdb=" CB ASN B 745 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 1055 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 622 " -0.076 2.00e-02 2.50e+03 5.56e-02 9.28e+01 pdb=" CG PHE A 622 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE A 622 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 622 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 622 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE A 622 " -0.048 2.00e-02 2.50e+03 pdb=" CZ PHE A 622 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE A 622 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE A 622 " 0.134 2.00e-02 2.50e+03 pdb=" HE1 PHE A 622 " 0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 622 " -0.073 2.00e-02 2.50e+03 pdb=" HZ PHE A 622 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 622 " 0.051 2.00e-02 2.50e+03 4.08e-02 5.00e+01 pdb=" CG PHE B 622 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE B 622 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 622 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 622 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE B 622 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE B 622 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE B 622 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE B 622 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 PHE B 622 " -0.051 2.00e-02 2.50e+03 pdb=" HE2 PHE B 622 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE B 622 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 937 " -0.038 2.00e-02 2.50e+03 5.76e-02 4.98e+01 pdb=" CD GLN A 937 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 937 " 0.061 2.00e-02 2.50e+03 pdb=" NE2 GLN A 937 " -0.067 2.00e-02 2.50e+03 pdb="HE21 GLN A 937 " 0.093 2.00e-02 2.50e+03 pdb="HE22 GLN A 937 " -0.039 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 726 2.19 - 2.79: 22817 2.79 - 3.40: 34819 3.40 - 4.00: 42112 4.00 - 4.60: 63881 Nonbonded interactions: 164355 Sorted by model distance: nonbonded pdb=" OE1 GLU A 796 " pdb=" HG SER A 880 " model vdw 1.588 2.450 nonbonded pdb=" O ILE A 585 " pdb=" HG SER A 588 " model vdw 1.592 2.450 nonbonded pdb=" O VAL A 646 " pdb=" HG SER A 650 " model vdw 1.598 2.450 nonbonded pdb=" O ILE B 585 " pdb=" HG SER B 588 " model vdw 1.602 2.450 nonbonded pdb=" HG SER A 726 " pdb=" OE2 GLU A 730 " model vdw 1.609 2.450 ... (remaining 164350 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.060 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.011 0.047 6378 Z= 0.673 Angle : 1.796 9.951 8666 Z= 1.208 Chirality : 0.085 0.350 1058 Planarity : 0.011 0.064 1128 Dihedral : 14.686 88.166 2370 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.24), residues: 814 helix: -1.25 (0.16), residues: 652 sheet: None (None), residues: 0 loop : -2.62 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 958 TYR 0.060 0.016 TYR B 809 PHE 0.057 0.014 PHE A 622 TRP 0.031 0.008 TRP A 815 HIS 0.014 0.004 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.01052 ( 6378) covalent geometry : angle 1.79644 ( 8666) hydrogen bonds : bond 0.15739 ( 505) hydrogen bonds : angle 7.40197 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8242 (mtp) cc_final: 0.7909 (tmm) REVERT: A 729 ILE cc_start: 0.9798 (mt) cc_final: 0.9474 (tp) REVERT: A 814 ARG cc_start: 0.9015 (mtt180) cc_final: 0.8501 (mmt180) REVERT: A 845 ASP cc_start: 0.9571 (m-30) cc_final: 0.9348 (t70) REVERT: A 889 CYS cc_start: 0.9224 (m) cc_final: 0.8976 (t) REVERT: B 663 TYR cc_start: 0.9327 (t80) cc_final: 0.9094 (t80) REVERT: B 779 ILE cc_start: 0.9730 (mt) cc_final: 0.9528 (mm) REVERT: B 814 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8432 (mmt180) REVERT: B 934 MET cc_start: 0.9446 (tpt) cc_final: 0.8959 (tmm) REVERT: B 962 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8945 (t80) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2593 time to fit residues: 36.1025 Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 GLN B 628 ASN B 659 ASN B 867 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.060375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.044278 restraints weight = 108468.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045907 restraints weight = 73982.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047141 restraints weight = 56162.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.048106 restraints weight = 45766.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.048880 restraints weight = 39024.368| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6378 Z= 0.185 Angle : 0.653 7.586 8666 Z= 0.363 Chirality : 0.036 0.133 1058 Planarity : 0.004 0.033 1128 Dihedral : 6.389 50.641 852 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.39 % Allowed : 9.00 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.28), residues: 814 helix: 0.93 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -2.42 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 953 TYR 0.006 0.002 TYR B 689 PHE 0.011 0.002 PHE B 622 TRP 0.011 0.001 TRP A 815 HIS 0.004 0.001 HIS A 960 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6378) covalent geometry : angle 0.65345 ( 8666) hydrogen bonds : bond 0.06229 ( 505) hydrogen bonds : angle 4.56747 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 MET cc_start: 0.8356 (mtp) cc_final: 0.7972 (mtp) REVERT: A 729 ILE cc_start: 0.9651 (mt) cc_final: 0.9371 (tp) REVERT: A 814 ARG cc_start: 0.9182 (mtt180) cc_final: 0.8762 (mmt180) REVERT: A 889 CYS cc_start: 0.9109 (m) cc_final: 0.8566 (t) REVERT: A 934 MET cc_start: 0.9317 (tpt) cc_final: 0.8865 (tmm) REVERT: B 814 ARG cc_start: 0.9039 (mtt180) cc_final: 0.8511 (mmt180) REVERT: B 934 MET cc_start: 0.9311 (tpt) cc_final: 0.8995 (tmm) REVERT: B 962 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8761 (t80) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.2896 time to fit residues: 27.2592 Evaluate side-chains 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 956 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN A 794 GLN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.060199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044217 restraints weight = 111435.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.045869 restraints weight = 76192.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.047117 restraints weight = 57754.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.048101 restraints weight = 46844.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.048874 restraints weight = 39862.112| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6378 Z= 0.162 Angle : 0.542 5.884 8666 Z= 0.309 Chirality : 0.033 0.129 1058 Planarity : 0.004 0.036 1128 Dihedral : 5.464 48.740 852 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.25 % Allowed : 9.28 % Favored : 89.47 % 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 aren not related in a simple way. whole: 1.74 (0.29), residues: 814 helix: 1.92 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.17 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 765 TYR 0.007 0.001 TYR A 809 PHE 0.009 0.002 PHE A 626 TRP 0.008 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6378) covalent geometry : angle 0.54235 ( 8666) hydrogen bonds : bond 0.05053 ( 505) hydrogen bonds : angle 4.08647 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 729 ILE cc_start: 0.9630 (mt) cc_final: 0.9407 (tp) REVERT: A 814 ARG cc_start: 0.9361 (mtt180) cc_final: 0.8897 (mmt180) REVERT: A 889 CYS cc_start: 0.9127 (m) cc_final: 0.8591 (t) REVERT: A 934 MET cc_start: 0.9430 (tpt) cc_final: 0.9053 (tmm) REVERT: B 814 ARG cc_start: 0.9241 (mtt180) cc_final: 0.8783 (mmt180) REVERT: B 934 MET cc_start: 0.9390 (tpt) cc_final: 0.9170 (tmm) REVERT: B 962 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8666 (t80) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.2430 time to fit residues: 21.4051 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 overall best weight: 2.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.059305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.043375 restraints weight = 110880.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044895 restraints weight = 77594.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.046067 restraints weight = 59886.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.046922 restraints weight = 49433.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.047661 restraints weight = 42625.262| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6378 Z= 0.170 Angle : 0.529 4.881 8666 Z= 0.299 Chirality : 0.033 0.115 1058 Planarity : 0.004 0.052 1128 Dihedral : 5.129 47.931 852 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 9.56 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.30), residues: 814 helix: 2.36 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.03 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 685 TYR 0.006 0.001 TYR A 809 PHE 0.017 0.002 PHE B 607 TRP 0.006 0.001 TRP B 815 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6378) covalent geometry : angle 0.52909 ( 8666) hydrogen bonds : bond 0.04677 ( 505) hydrogen bonds : angle 3.91144 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9427 (mtt180) cc_final: 0.8986 (mmt180) REVERT: A 889 CYS cc_start: 0.9103 (m) cc_final: 0.8594 (t) REVERT: A 934 MET cc_start: 0.9392 (tpt) cc_final: 0.9169 (tmm) REVERT: B 814 ARG cc_start: 0.9275 (mtt180) cc_final: 0.8803 (mmt180) REVERT: B 934 MET cc_start: 0.9479 (tpt) cc_final: 0.9187 (tmm) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.2348 time to fit residues: 19.8483 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.059657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.043903 restraints weight = 114971.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045593 restraints weight = 77824.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046822 restraints weight = 58554.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.047789 restraints weight = 47354.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.048536 restraints weight = 40196.340| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6378 Z= 0.167 Angle : 0.522 6.177 8666 Z= 0.296 Chirality : 0.033 0.113 1058 Planarity : 0.004 0.039 1128 Dihedral : 4.920 47.281 852 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Rotamer: Outliers : 2.08 % Allowed : 10.11 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.30), residues: 814 helix: 2.61 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.95 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 685 TYR 0.008 0.001 TYR B 689 PHE 0.013 0.002 PHE A 607 TRP 0.005 0.001 TRP B 815 HIS 0.005 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6378) covalent geometry : angle 0.52209 ( 8666) hydrogen bonds : bond 0.04489 ( 505) hydrogen bonds : angle 3.83516 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9448 (mtt180) cc_final: 0.9001 (mmt180) REVERT: A 889 CYS cc_start: 0.9235 (m) cc_final: 0.8647 (t) REVERT: A 934 MET cc_start: 0.9338 (tpt) cc_final: 0.9134 (tmm) REVERT: B 688 GLN cc_start: 0.9604 (OUTLIER) cc_final: 0.9208 (tm-30) REVERT: B 814 ARG cc_start: 0.9319 (mtt180) cc_final: 0.8852 (mmt180) REVERT: B 934 MET cc_start: 0.9482 (tpt) cc_final: 0.9186 (tmm) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.2441 time to fit residues: 21.0679 Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 688 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.058997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.043489 restraints weight = 116598.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.045090 restraints weight = 79751.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.046306 restraints weight = 60573.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.047282 restraints weight = 48967.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048060 restraints weight = 41436.184| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6378 Z= 0.196 Angle : 0.528 4.727 8666 Z= 0.304 Chirality : 0.033 0.112 1058 Planarity : 0.004 0.045 1128 Dihedral : 4.869 46.699 852 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.97 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 10.11 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.29), residues: 814 helix: 2.68 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.93 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 898 TYR 0.007 0.001 TYR A 809 PHE 0.008 0.001 PHE B 607 TRP 0.005 0.001 TRP A 815 HIS 0.005 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6378) covalent geometry : angle 0.52750 ( 8666) hydrogen bonds : bond 0.04544 ( 505) hydrogen bonds : angle 3.85917 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9385 (mtt180) cc_final: 0.9050 (mmt180) REVERT: A 889 CYS cc_start: 0.9117 (m) cc_final: 0.8508 (t) REVERT: A 934 MET cc_start: 0.9370 (tpt) cc_final: 0.9152 (tmm) REVERT: B 814 ARG cc_start: 0.9378 (mtt180) cc_final: 0.9008 (mmt180) REVERT: B 934 MET cc_start: 0.9472 (tpt) cc_final: 0.9186 (tmm) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.2618 time to fit residues: 21.9536 Evaluate side-chains 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.059272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.043632 restraints weight = 115776.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.045290 restraints weight = 78867.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.046540 restraints weight = 59687.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047471 restraints weight = 48342.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.048237 restraints weight = 41175.192| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6378 Z= 0.151 Angle : 0.517 7.136 8666 Z= 0.286 Chirality : 0.032 0.116 1058 Planarity : 0.004 0.047 1128 Dihedral : 4.748 46.475 852 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.84 % Favored : 97.79 % Rotamer: Outliers : 1.94 % Allowed : 11.08 % Favored : 86.98 % 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 aren not related in a simple way. whole: 3.07 (0.30), residues: 814 helix: 2.87 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.84 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 898 TYR 0.006 0.001 TYR A 663 PHE 0.012 0.001 PHE B 690 TRP 0.005 0.001 TRP A 815 HIS 0.005 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6378) covalent geometry : angle 0.51686 ( 8666) hydrogen bonds : bond 0.04202 ( 505) hydrogen bonds : angle 3.72655 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9400 (mtt180) cc_final: 0.9041 (mmt180) REVERT: A 889 CYS cc_start: 0.9128 (m) cc_final: 0.8513 (t) REVERT: A 934 MET cc_start: 0.9347 (tpt) cc_final: 0.9131 (tmm) REVERT: B 796 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: B 814 ARG cc_start: 0.9396 (mtt180) cc_final: 0.9011 (mmt180) REVERT: B 934 MET cc_start: 0.9476 (tpt) cc_final: 0.9178 (tmm) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.2467 time to fit residues: 20.7893 Evaluate side-chains 65 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.059545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.043827 restraints weight = 113871.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045436 restraints weight = 77820.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046763 restraints weight = 59227.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047686 restraints weight = 47656.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.048487 restraints weight = 40482.671| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6378 Z= 0.127 Angle : 0.508 8.245 8666 Z= 0.273 Chirality : 0.033 0.221 1058 Planarity : 0.004 0.047 1128 Dihedral : 4.571 45.860 852 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.09 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 11.36 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.30), residues: 814 helix: 3.14 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.70 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 898 TYR 0.006 0.001 TYR A 809 PHE 0.013 0.001 PHE B 607 TRP 0.006 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6378) covalent geometry : angle 0.50841 ( 8666) hydrogen bonds : bond 0.03870 ( 505) hydrogen bonds : angle 3.54112 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9410 (mtt180) cc_final: 0.9046 (mmt180) REVERT: A 889 CYS cc_start: 0.9159 (m) cc_final: 0.8594 (t) REVERT: A 934 MET cc_start: 0.9355 (tpt) cc_final: 0.9120 (tmm) REVERT: B 796 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: B 814 ARG cc_start: 0.9381 (mtt180) cc_final: 0.9014 (mmt180) REVERT: B 934 MET cc_start: 0.9478 (tpt) cc_final: 0.9171 (tmm) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.2413 time to fit residues: 20.5738 Evaluate side-chains 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.059612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.044186 restraints weight = 115302.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.045821 restraints weight = 76886.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.047057 restraints weight = 57899.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047989 restraints weight = 46917.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048743 restraints weight = 39928.346| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6378 Z= 0.147 Angle : 0.497 5.884 8666 Z= 0.278 Chirality : 0.032 0.120 1058 Planarity : 0.004 0.047 1128 Dihedral : 4.475 46.435 852 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.21 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 11.36 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.30), residues: 814 helix: 3.14 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -1.54 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.006 0.001 TYR A 663 PHE 0.010 0.001 PHE B 607 TRP 0.005 0.001 TRP B 815 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6378) covalent geometry : angle 0.49737 ( 8666) hydrogen bonds : bond 0.03887 ( 505) hydrogen bonds : angle 3.52698 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9421 (mtt180) cc_final: 0.9073 (mmt180) REVERT: A 889 CYS cc_start: 0.9063 (m) cc_final: 0.8470 (t) REVERT: B 796 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: B 814 ARG cc_start: 0.9398 (mtt180) cc_final: 0.9053 (mmt180) REVERT: B 934 MET cc_start: 0.9475 (tpt) cc_final: 0.9178 (tmm) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.2584 time to fit residues: 20.8208 Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.059617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.043562 restraints weight = 113560.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.045226 restraints weight = 76773.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046487 restraints weight = 58068.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.047444 restraints weight = 47080.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.048249 restraints weight = 40076.031| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6378 Z= 0.126 Angle : 0.506 6.014 8666 Z= 0.277 Chirality : 0.032 0.113 1058 Planarity : 0.004 0.047 1128 Dihedral : 4.446 46.176 852 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.09 % Favored : 97.54 % Rotamer: Outliers : 1.94 % Allowed : 11.63 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.30), residues: 814 helix: 3.18 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -1.83 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.005 0.001 TYR A 809 PHE 0.010 0.001 PHE B 607 TRP 0.006 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6378) covalent geometry : angle 0.50565 ( 8666) hydrogen bonds : bond 0.03749 ( 505) hydrogen bonds : angle 3.48985 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 814 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8979 (mmt180) REVERT: B 796 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: B 814 ARG cc_start: 0.9375 (mtt180) cc_final: 0.8965 (mmt180) REVERT: B 905 MET cc_start: 0.8606 (ppp) cc_final: 0.8396 (ppp) REVERT: B 934 MET cc_start: 0.9461 (tpt) cc_final: 0.9154 (tmm) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.2370 time to fit residues: 20.8485 Evaluate side-chains 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 860 GLU Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 860 GLU Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 962 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 0.0570 chunk 58 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 659 ASN B 688 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.059980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.043791 restraints weight = 111401.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045461 restraints weight = 74961.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046795 restraints weight = 56749.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047830 restraints weight = 45747.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048648 restraints weight = 38449.954| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6378 Z= 0.102 Angle : 0.491 6.084 8666 Z= 0.262 Chirality : 0.032 0.119 1058 Planarity : 0.004 0.047 1128 Dihedral : 4.314 46.146 852 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.84 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 12.47 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.30), residues: 814 helix: 3.29 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.89 (0.44), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.005 0.001 TYR A 809 PHE 0.012 0.001 PHE B 607 TRP 0.006 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 6378) covalent geometry : angle 0.49135 ( 8666) hydrogen bonds : bond 0.03433 ( 505) hydrogen bonds : angle 3.37956 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.53 seconds wall clock time: 38 minutes 17.49 seconds (2297.49 seconds total)