Starting phenix.real_space_refine on Wed Jun 11 08:22:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdd_52061/06_2025/9hdd_52061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdd_52061/06_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_52061/06_2025/9hdd_52061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdd_52061/06_2025/9hdd_52061.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdd_52061/06_2025/9hdd_52061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdd_52061/06_2025/9hdd_52061.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.76, per 1000 atoms: 0.54 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: 3.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 4.49 Time building geometry restraints manager: 4.13 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: 0.02 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: 0.620 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: 0.240 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 30.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.008 TRP A 815 HIS 0.014 0.004 HIS A 912 PHE 0.057 0.014 PHE A 622 TYR 0.060 0.016 TYR B 809 ARG 0.022 0.002 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.15739 ( 505) hydrogen bonds : angle 7.40197 ( 1509) covalent geometry : bond 0.01052 ( 6378) covalent geometry : angle 1.79644 ( 8666) *********************** 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 : 0.995 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: A 565 MET cc_start: 0.8242 (mtp) cc_final: 0.7909 (tmm) REVERT: A 663 TYR cc_start: 0.9331 (t80) cc_final: 0.8899 (t80) REVERT: A 729 ILE cc_start: 0.9798 (mt) cc_final: 0.9483 (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: 0.9099 (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 960 HIS cc_start: 0.9482 (m90) cc_final: 0.9079 (m170) REVERT: B 962 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8943 (t80) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.5277 time to fit residues: 74.0361 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 : 0.951 ------------------------------------------------------------------------------- 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 67 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.061082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.044980 restraints weight = 108554.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046611 restraints weight = 73875.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047882 restraints weight = 56015.759| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6378 Z= 0.191 Angle : 0.655 7.928 8666 Z= 0.361 Chirality : 0.036 0.161 1058 Planarity : 0.004 0.035 1128 Dihedral : 6.368 50.620 852 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.52 % Allowed : 8.73 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 814 helix: 0.96 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -2.41 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 815 HIS 0.004 0.001 HIS A 960 PHE 0.012 0.001 PHE B 626 TYR 0.008 0.001 TYR B 689 ARG 0.003 0.001 ARG B 953 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 505) hydrogen bonds : angle 4.50868 ( 1509) covalent geometry : bond 0.00355 ( 6378) covalent geometry : angle 0.65492 ( 8666) *********************** 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 83 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.032 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: A 663 TYR cc_start: 0.9237 (t80) cc_final: 0.8917 (t80) REVERT: A 695 MET cc_start: 0.8261 (mtp) cc_final: 0.7895 (mtp) REVERT: A 697 GLU cc_start: 0.8922 (tt0) cc_final: 0.8697 (tm-30) REVERT: A 729 ILE cc_start: 0.9677 (mt) cc_final: 0.9374 (tp) REVERT: A 814 ARG cc_start: 0.9158 (mtt180) cc_final: 0.8722 (mmt180) REVERT: A 845 ASP cc_start: 0.9274 (m-30) cc_final: 0.9047 (t70) REVERT: A 889 CYS cc_start: 0.9176 (m) cc_final: 0.8636 (t) REVERT: A 934 MET cc_start: 0.9333 (tpt) cc_final: 0.8873 (tmm) REVERT: B 814 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8290 (mmt180) REVERT: B 934 MET cc_start: 0.9318 (tpt) cc_final: 0.8997 (tmm) REVERT: B 962 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8765 (t80) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.6130 time to fit residues: 61.5865 Evaluate side-chains 69 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 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 0 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 688 GLN ** B 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.041908 restraints weight = 119339.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.043357 restraints weight = 82638.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.044555 restraints weight = 63685.803| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6378 Z= 0.332 Angle : 0.688 6.751 8666 Z= 0.416 Chirality : 0.036 0.156 1058 Planarity : 0.005 0.050 1128 Dihedral : 5.822 47.320 852 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Rotamer: Outliers : 2.08 % Allowed : 10.66 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 814 helix: 1.27 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -2.20 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 815 HIS 0.012 0.002 HIS B 903 PHE 0.019 0.002 PHE A 649 TYR 0.010 0.002 TYR A 809 ARG 0.008 0.001 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.06301 ( 505) hydrogen bonds : angle 4.61841 ( 1509) covalent geometry : bond 0.00559 ( 6378) covalent geometry : angle 0.68785 ( 8666) *********************** 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: 15 poor density : 56 time to evaluate : 1.040 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: A 663 TYR cc_start: 0.9214 (t80) cc_final: 0.8904 (t80) REVERT: A 814 ARG cc_start: 0.9465 (mtt180) cc_final: 0.9104 (mmt180) REVERT: A 845 ASP cc_start: 0.9319 (m-30) cc_final: 0.9092 (t70) REVERT: A 889 CYS cc_start: 0.9171 (m) cc_final: 0.8616 (t) REVERT: A 934 MET cc_start: 0.9403 (tpt) cc_final: 0.9188 (tmm) REVERT: B 814 ARG cc_start: 0.9389 (mtt180) cc_final: 0.8972 (mmt180) REVERT: B 934 MET cc_start: 0.9438 (tpt) cc_final: 0.9176 (tmm) REVERT: B 962 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8715 (t80) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.5057 time to fit residues: 45.7399 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 956 GLU 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 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 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 688 GLN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.058814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.043255 restraints weight = 113540.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.044859 restraints weight = 78243.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046086 restraints weight = 59617.089| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6378 Z= 0.124 Angle : 0.536 5.804 8666 Z= 0.293 Chirality : 0.033 0.116 1058 Planarity : 0.004 0.056 1128 Dihedral : 5.316 46.297 852 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.54 % Rotamer: Outliers : 1.39 % Allowed : 11.22 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 814 helix: 2.17 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 815 HIS 0.006 0.001 HIS B 763 PHE 0.008 0.001 PHE A 808 TYR 0.010 0.001 TYR A 689 ARG 0.008 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 505) hydrogen bonds : angle 3.96844 ( 1509) covalent geometry : bond 0.00231 ( 6378) covalent geometry : angle 0.53590 ( 8666) *********************** 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 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.957 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 663 TYR cc_start: 0.9085 (t80) cc_final: 0.8783 (t80) REVERT: A 695 MET cc_start: 0.8426 (mtp) cc_final: 0.8117 (mtp) REVERT: A 697 GLU cc_start: 0.8845 (tt0) cc_final: 0.8627 (tm-30) REVERT: A 814 ARG cc_start: 0.9376 (mtt180) cc_final: 0.8975 (mmt180) REVERT: A 845 ASP cc_start: 0.9340 (m-30) cc_final: 0.9138 (t70) REVERT: A 934 MET cc_start: 0.9390 (tpt) cc_final: 0.9148 (tmm) REVERT: B 814 ARG cc_start: 0.9312 (mtt180) cc_final: 0.8835 (mmt180) REVERT: B 934 MET cc_start: 0.9407 (tpt) cc_final: 0.9189 (tmm) outliers start: 10 outliers final: 10 residues processed: 66 average time/residue: 0.5204 time to fit residues: 43.1496 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 786 LEU Chi-restraints excluded: chain A residue 923 PHE 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 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 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.059407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.043871 restraints weight = 113288.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.045604 restraints weight = 75922.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046853 restraints weight = 56829.749| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6378 Z= 0.146 Angle : 0.513 4.633 8666 Z= 0.288 Chirality : 0.033 0.113 1058 Planarity : 0.004 0.033 1128 Dihedral : 5.008 45.894 852 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.46 % Favored : 97.30 % Rotamer: Outliers : 1.11 % Allowed : 11.36 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.30), residues: 814 helix: 2.53 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.12 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 815 HIS 0.005 0.001 HIS B 763 PHE 0.012 0.001 PHE A 607 TYR 0.006 0.001 TYR B 809 ARG 0.002 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 505) hydrogen bonds : angle 3.84163 ( 1509) covalent geometry : bond 0.00253 ( 6378) covalent geometry : angle 0.51339 ( 8666) *********************** 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 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 1.010 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 663 TYR cc_start: 0.9076 (t80) cc_final: 0.8797 (t80) REVERT: A 697 GLU cc_start: 0.8874 (tt0) cc_final: 0.8654 (tm-30) REVERT: A 814 ARG cc_start: 0.9405 (mtt180) cc_final: 0.9014 (mmt180) REVERT: A 934 MET cc_start: 0.9382 (tpt) cc_final: 0.9155 (tmm) REVERT: B 814 ARG cc_start: 0.9347 (mtt180) cc_final: 0.8902 (mmt180) REVERT: B 934 MET cc_start: 0.9497 (tpt) cc_final: 0.9207 (tmm) outliers start: 8 outliers final: 8 residues processed: 67 average time/residue: 0.5496 time to fit residues: 46.0522 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 786 LEU Chi-restraints excluded: chain A residue 923 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.059997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.044307 restraints weight = 113453.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046036 restraints weight = 76756.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.047325 restraints weight = 57517.262| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6378 Z= 0.123 Angle : 0.491 4.736 8666 Z= 0.271 Chirality : 0.032 0.113 1058 Planarity : 0.004 0.034 1128 Dihedral : 4.789 45.662 852 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.09 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 10.94 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.30), residues: 814 helix: 2.79 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.99 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 815 HIS 0.005 0.001 HIS B 763 PHE 0.010 0.001 PHE A 607 TYR 0.005 0.001 TYR B 809 ARG 0.003 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 505) hydrogen bonds : angle 3.67346 ( 1509) covalent geometry : bond 0.00217 ( 6378) covalent geometry : angle 0.49093 ( 8666) *********************** 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 68 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.032 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 663 TYR cc_start: 0.9035 (t80) cc_final: 0.8765 (t80) REVERT: A 697 GLU cc_start: 0.8891 (tt0) cc_final: 0.8663 (tm-30) REVERT: A 814 ARG cc_start: 0.9386 (mtt180) cc_final: 0.9002 (mmt180) REVERT: A 934 MET cc_start: 0.9370 (tpt) cc_final: 0.9125 (tmm) REVERT: B 814 ARG cc_start: 0.9368 (mtt180) cc_final: 0.8934 (mmt180) REVERT: B 934 MET cc_start: 0.9495 (tpt) cc_final: 0.9181 (tmm) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.5538 time to fit residues: 47.3696 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.058966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.043091 restraints weight = 113589.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.044769 restraints weight = 77682.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.045996 restraints weight = 58797.744| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6378 Z= 0.166 Angle : 0.520 6.732 8666 Z= 0.291 Chirality : 0.033 0.171 1058 Planarity : 0.004 0.032 1128 Dihedral : 4.699 45.053 852 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.09 % Favored : 97.54 % Rotamer: Outliers : 1.39 % Allowed : 11.22 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.30), residues: 814 helix: 2.86 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.98 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 815 HIS 0.005 0.001 HIS B 763 PHE 0.009 0.001 PHE B 607 TYR 0.007 0.001 TYR A 809 ARG 0.002 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 505) hydrogen bonds : angle 3.70606 ( 1509) covalent geometry : bond 0.00286 ( 6378) covalent geometry : angle 0.51982 ( 8666) *********************** 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 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.066 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 663 TYR cc_start: 0.9092 (t80) cc_final: 0.8823 (t80) REVERT: A 697 GLU cc_start: 0.8870 (tt0) cc_final: 0.8656 (tm-30) REVERT: A 814 ARG cc_start: 0.9418 (mtt180) cc_final: 0.9055 (mmt180) REVERT: A 934 MET cc_start: 0.9366 (tpt) cc_final: 0.9131 (tmm) REVERT: B 796 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: B 814 ARG cc_start: 0.9385 (mtt180) cc_final: 0.9013 (mmt180) REVERT: B 934 MET cc_start: 0.9497 (tpt) cc_final: 0.9188 (tmm) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.5316 time to fit residues: 44.0674 Evaluate side-chains 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE 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 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 66 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.059918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.044126 restraints weight = 113935.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.045824 restraints weight = 77815.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.047122 restraints weight = 58772.196| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6378 Z= 0.121 Angle : 0.500 7.209 8666 Z= 0.269 Chirality : 0.032 0.121 1058 Planarity : 0.004 0.032 1128 Dihedral : 4.565 45.274 852 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.84 % Favored : 97.79 % Rotamer: Outliers : 1.39 % Allowed : 11.77 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.30), residues: 814 helix: 3.09 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.89 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 815 HIS 0.005 0.001 HIS B 763 PHE 0.011 0.001 PHE B 626 TYR 0.006 0.001 TYR A 809 ARG 0.002 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 505) hydrogen bonds : angle 3.55167 ( 1509) covalent geometry : bond 0.00223 ( 6378) covalent geometry : angle 0.49997 ( 8666) *********************** 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 67 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.065 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 663 TYR cc_start: 0.9107 (t80) cc_final: 0.8873 (t80) REVERT: A 814 ARG cc_start: 0.9407 (mtt180) cc_final: 0.9056 (mmt180) REVERT: A 934 MET cc_start: 0.9356 (tpt) cc_final: 0.9115 (tmm) REVERT: B 796 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: B 814 ARG cc_start: 0.9381 (mtt180) cc_final: 0.9028 (mmt180) REVERT: B 934 MET cc_start: 0.9477 (tpt) cc_final: 0.9169 (tmm) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.5048 time to fit residues: 42.7059 Evaluate side-chains 63 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE 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 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 12 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.061366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.045188 restraints weight = 109510.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047149 restraints weight = 67718.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.048586 restraints weight = 48915.383| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6378 Z= 0.105 Angle : 0.503 6.704 8666 Z= 0.267 Chirality : 0.032 0.118 1058 Planarity : 0.004 0.039 1128 Dihedral : 4.415 45.219 852 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.72 % Favored : 97.91 % Rotamer: Outliers : 1.25 % Allowed : 12.05 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.30), residues: 814 helix: 3.26 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -1.77 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 815 HIS 0.004 0.000 HIS B 763 PHE 0.008 0.001 PHE A 607 TYR 0.005 0.001 TYR A 809 ARG 0.003 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 505) hydrogen bonds : angle 3.43917 ( 1509) covalent geometry : bond 0.00203 ( 6378) covalent geometry : angle 0.50299 ( 8666) *********************** 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 66 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.913 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 663 TYR cc_start: 0.9075 (t80) cc_final: 0.8845 (t80) REVERT: A 814 ARG cc_start: 0.9404 (mtt180) cc_final: 0.9020 (mmt180) REVERT: A 934 MET cc_start: 0.9321 (tpt) cc_final: 0.9118 (tmm) REVERT: B 796 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: B 814 ARG cc_start: 0.9375 (mtt180) cc_final: 0.8991 (mmt180) REVERT: B 934 MET cc_start: 0.9484 (tpt) cc_final: 0.9165 (tmm) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.6031 time to fit residues: 51.0180 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 923 PHE 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 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 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.059254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.043441 restraints weight = 112973.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.045142 restraints weight = 77048.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.046420 restraints weight = 58303.095| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6378 Z= 0.162 Angle : 0.528 5.825 8666 Z= 0.292 Chirality : 0.033 0.118 1058 Planarity : 0.004 0.043 1128 Dihedral : 4.373 44.556 852 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.72 % Favored : 97.91 % Rotamer: Outliers : 1.52 % Allowed : 12.19 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.30), residues: 814 helix: 3.19 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 PHE 0.009 0.001 PHE B 607 TYR 0.005 0.001 TYR A 809 ARG 0.002 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 505) hydrogen bonds : angle 3.55688 ( 1509) covalent geometry : bond 0.00281 ( 6378) covalent geometry : angle 0.52793 ( 8666) ********************** 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 64 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.912 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: A 663 TYR cc_start: 0.9082 (t80) cc_final: 0.8853 (t80) REVERT: A 814 ARG cc_start: 0.9419 (mtt180) cc_final: 0.9010 (mmt180) REVERT: A 934 MET cc_start: 0.9344 (tpt) cc_final: 0.9105 (tmm) REVERT: B 796 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: B 814 ARG cc_start: 0.9402 (mtt180) cc_final: 0.9005 (mmt180) REVERT: B 934 MET cc_start: 0.9473 (tpt) cc_final: 0.9162 (tmm) outliers start: 11 outliers final: 10 residues processed: 63 average time/residue: 0.4952 time to fit residues: 39.5600 Evaluate side-chains 62 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 923 PHE Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 745 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.059691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.043141 restraints weight = 112372.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.045026 restraints weight = 73430.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046423 restraints weight = 54112.930| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6378 Z= 0.112 Angle : 0.511 8.725 8666 Z= 0.268 Chirality : 0.032 0.123 1058 Planarity : 0.004 0.045 1128 Dihedral : 4.026 19.151 850 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.47 % Favored : 98.16 % Rotamer: Outliers : 1.52 % Allowed : 12.33 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.30), residues: 814 helix: 3.33 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.62 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 815 HIS 0.004 0.001 HIS B 763 PHE 0.009 0.001 PHE A 607 TYR 0.005 0.001 TYR A 809 ARG 0.002 0.000 ARG A 873 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 505) hydrogen bonds : angle 3.43993 ( 1509) covalent geometry : bond 0.00213 ( 6378) covalent geometry : angle 0.51060 ( 8666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.69 seconds wall clock time: 71 minutes 49.81 seconds (4309.81 seconds total)