Starting phenix.real_space_refine on Thu Jul 2 22:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzb_42838/07_2026/8uzb_42838.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 19 5.16 5 C 6286 2.51 5 N 1973 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7485 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 39, 'TRANS': 870} Chain breaks: 3 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2267 Classifications: {'RNA': 107} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 97} Chain breaks: 2 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.81, per 1000 atoms: 0.26 Number of scatterers: 10882 At special positions: 0 Unit cell: (97.65, 123.69, 132.99, 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 19 16.00 P 162 15.00 O 2442 8.00 N 1973 7.00 C 6286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 302.4 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 45.1% alpha, 14.5% beta 68 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 47 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.539A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.777A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.699A pdb=" N SER A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.184A pdb=" N SER A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.534A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 422 through 434 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 503 through 506 removed outlier: 4.097A pdb=" N SER A 506 " --> pdb=" O ARG A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 667 through 679 Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.816A pdb=" N THR A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.673A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.610A pdb=" N ILE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 736 " --> pdb=" O PRO A 732 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 774 removed outlier: 4.557A pdb=" N ARG A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.502A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 860 through 874 removed outlier: 3.565A pdb=" N TYR A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.286A pdb=" N ILE A 497 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 14 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A 31 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP A 16 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 29 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 18 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.784A pdb=" N ILE A 297 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 388 removed outlier: 4.110A pdb=" N TYR A 387 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 826 removed outlier: 5.818A pdb=" N TYR A 823 " --> pdb=" O VAL A 836 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 836 " --> pdb=" O TYR A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AA7, first strand: chain 'A' and resid 911 through 914 removed outlier: 4.370A pdb=" N THR A 919 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 937 through 944 removed outlier: 6.394A pdb=" N VAL A 929 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 979 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 957 removed outlier: 3.843A pdb=" N LYS A 968 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1033 through 1038 removed outlier: 5.318A pdb=" N LEU A1023 " --> pdb=" O GLY A1036 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1015 " --> pdb=" O GLU A1024 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A1026 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A1013 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP A1008 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N ARG A 992 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N PHE A1010 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N LEU A 990 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N TYR A1012 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N ILE A 988 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N LYS A1014 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 986 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N ILE A1016 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP A 984 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1044 " --> pdb=" O GLU A 989 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 326 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 109 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2984 1.46 - 1.58: 5187 1.58 - 1.70: 319 1.70 - 1.82: 33 Bond restraints: 11431 Sorted by residual: bond pdb=" C3' DC D 40 " pdb=" C2' DC D 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT C 6 " pdb=" C2' DT C 6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.39e+00 bond pdb=" C3' DA C 22 " pdb=" C2' DA C 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.98e+00 bond pdb=" C3' DC C 24 " pdb=" C2' DC C 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.34e+00 bond pdb=" C3' DG C 16 " pdb=" C2' DG C 16 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.86e+00 ... (remaining 11426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15630 1.46 - 2.92: 453 2.92 - 4.39: 54 4.39 - 5.85: 8 5.85 - 7.31: 5 Bond angle restraints: 16150 Sorted by residual: angle pdb=" N3 DT C 15 " pdb=" C4 DT C 15 " pdb=" O4 DT C 15 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 30 " pdb=" C4 DT C 30 " pdb=" O4 DT C 30 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 31 " pdb=" C4 DT D 31 " pdb=" O4 DT D 31 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" O4' DA D 43 " pdb=" C4' DA D 43 " pdb=" C3' DA D 43 " ideal model delta sigma weight residual 106.00 103.55 2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT C 35 " pdb=" C4 DT C 35 " pdb=" O4 DT C 35 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 16145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 6437 33.01 - 66.02: 539 66.02 - 99.03: 41 99.03 - 132.04: 0 132.04 - 165.05: 3 Dihedral angle restraints: 7020 sinusoidal: 4348 harmonic: 2672 Sorted by residual: dihedral pdb=" C4' DT C 6 " pdb=" C3' DT C 6 " pdb=" O3' DT C 6 " pdb=" P DG C 7 " ideal model delta sinusoidal sigma weight residual 220.00 54.95 165.05 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' C B 77 " pdb=" C3' C B 77 " pdb=" O3' C B 77 " pdb=" P A B 78 " ideal model delta sinusoidal sigma weight residual -110.00 55.03 -165.03 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DG C 17 " ideal model delta sinusoidal sigma weight residual 220.00 61.09 158.91 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1365 0.038 - 0.075: 355 0.075 - 0.113: 108 0.113 - 0.150: 22 0.150 - 0.188: 4 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C3' C B 77 " pdb=" C4' C B 77 " pdb=" O3' C B 77 " pdb=" C2' C B 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB THR A 416 " pdb=" CA THR A 416 " pdb=" OG1 THR A 416 " pdb=" CG2 THR A 416 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA TRP A 763 " pdb=" N TRP A 763 " pdb=" C TRP A 763 " pdb=" CB TRP A 763 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1851 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 777 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO A 778 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 778 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 778 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 13 " 0.024 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" N1 DT C 13 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT C 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT C 13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT C 13 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT C 13 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT C 13 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT C 13 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT C 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 13 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 93 " -0.020 2.00e-02 2.50e+03 8.95e-03 2.40e+00 pdb=" N9 G B 93 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 93 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 93 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 93 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 93 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 93 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 93 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 396 2.70 - 3.25: 9681 3.25 - 3.80: 19056 3.80 - 4.35: 25439 4.35 - 4.90: 37296 Nonbonded interactions: 91868 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" O GLU A 386 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR A 12 " pdb=" O PHE A 34 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 768 " pdb=" NH2 ARG A 771 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASP A 337 " pdb=" NE2 GLN A 341 " model vdw 2.243 3.120 nonbonded pdb=" OD2 ASP A 28 " pdb=" OH TYR A 491 " model vdw 2.254 3.040 ... (remaining 91863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.650 Find NCS groups from input model: 0.050 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.004 0.075 11431 Z= 0.286 Angle : 0.571 7.309 16150 Z= 0.448 Chirality : 0.039 0.188 1854 Planarity : 0.004 0.062 1494 Dihedral : 20.256 165.051 5292 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 902 helix: 1.28 (0.27), residues: 375 sheet: -0.76 (0.47), residues: 120 loop : -0.12 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 503 TYR 0.020 0.001 TYR A 864 PHE 0.009 0.001 PHE A 759 TRP 0.013 0.001 TRP A 763 HIS 0.002 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.29 (11431) covalent geometry : angle 0.57144 / 0.45 (16150) hydrogen bonds : bond 0.15725 / 10.57 ( 480) hydrogen bonds : angle 5.45626 / 4.09 ( 1214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.7844 time to fit residues: 88.8208 Evaluate side-chains 80 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114931 restraints weight = 11141.287| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.66 r_work: 0.3146 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11431 Z= 0.218 Angle : 0.600 6.751 16150 Z= 0.341 Chirality : 0.044 0.291 1854 Planarity : 0.005 0.054 1494 Dihedral : 22.290 170.469 3337 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.10 % Allowed : 9.37 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.28), residues: 902 helix: 1.28 (0.27), residues: 387 sheet: -0.75 (0.45), residues: 125 loop : -0.23 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 698 TYR 0.022 0.002 TYR A 491 PHE 0.014 0.002 PHE A 932 TRP 0.009 0.001 TRP A 763 HIS 0.008 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (11431) covalent geometry : angle 0.59975 / 0.34 (16150) hydrogen bonds : bond 0.06054 / 4.05 ( 480) hydrogen bonds : angle 4.20435 / 3.07 ( 1214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.335 Fit side-chains REVERT: A 28 ASP cc_start: 0.8407 (m-30) cc_final: 0.7940 (m-30) REVERT: A 335 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: A 437 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: A 460 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8219 (ttt) REVERT: A 696 ASN cc_start: 0.7990 (t0) cc_final: 0.7728 (t0) outliers start: 17 outliers final: 3 residues processed: 95 average time/residue: 0.7220 time to fit residues: 72.8948 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 795 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115207 restraints weight = 11234.092| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.60 r_work: 0.3195 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11431 Z= 0.144 Angle : 0.517 6.758 16150 Z= 0.301 Chirality : 0.040 0.262 1854 Planarity : 0.004 0.033 1494 Dihedral : 22.320 169.176 3337 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 11.10 % Favored : 86.81 % 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 are not related in a simple way. whole: 0.61 (0.28), residues: 902 helix: 1.50 (0.27), residues: 387 sheet: -1.11 (0.44), residues: 122 loop : -0.08 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.013 0.001 TYR A 491 PHE 0.009 0.001 PHE A 932 TRP 0.007 0.001 TRP A 763 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11431) covalent geometry : angle 0.51696 / 0.30 (16150) hydrogen bonds : bond 0.05237 / 3.49 ( 480) hydrogen bonds : angle 3.99316 / 2.91 ( 1214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.287 Fit side-chains REVERT: A 28 ASP cc_start: 0.8383 (m-30) cc_final: 0.7881 (m-30) REVERT: A 335 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: A 337 ASP cc_start: 0.8223 (t70) cc_final: 0.7810 (t0) REVERT: A 457 GLN cc_start: 0.7605 (tp40) cc_final: 0.7359 (tp-100) REVERT: A 500 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: A 696 ASN cc_start: 0.7986 (t0) cc_final: 0.7679 (t0) REVERT: A 869 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7416 (mm-40) REVERT: A 1044 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7735 (ttm-80) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 0.7456 time to fit residues: 80.1012 Evaluate side-chains 90 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113076 restraints weight = 11261.002| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.60 r_work: 0.3163 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11431 Z= 0.188 Angle : 0.554 6.872 16150 Z= 0.316 Chirality : 0.042 0.291 1854 Planarity : 0.005 0.038 1494 Dihedral : 22.310 169.294 3337 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.47 % Allowed : 11.47 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.28), residues: 902 helix: 1.47 (0.27), residues: 387 sheet: -1.05 (0.45), residues: 115 loop : -0.16 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1060 TYR 0.012 0.001 TYR A 864 PHE 0.013 0.001 PHE A 932 TRP 0.008 0.001 TRP A 763 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (11431) covalent geometry : angle 0.55396 / 0.32 (16150) hydrogen bonds : bond 0.05400 / 3.61 ( 480) hydrogen bonds : angle 3.92306 / 2.87 ( 1214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.393 Fit side-chains REVERT: A 28 ASP cc_start: 0.8416 (m-30) cc_final: 0.7870 (m-30) REVERT: A 335 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: A 337 ASP cc_start: 0.8205 (t70) cc_final: 0.7772 (t0) REVERT: A 457 GLN cc_start: 0.7660 (tp40) cc_final: 0.7430 (tp-100) REVERT: A 500 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 696 ASN cc_start: 0.8140 (t0) cc_final: 0.7786 (t0) REVERT: A 798 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7065 (mp) REVERT: A 869 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7428 (mm-40) REVERT: A 948 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 1044 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7700 (ttm-80) outliers start: 20 outliers final: 7 residues processed: 97 average time/residue: 0.7078 time to fit residues: 73.1784 Evaluate side-chains 93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 98 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN A 793 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125081 restraints weight = 11203.353| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.20 r_work: 0.3137 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11431 Z= 0.141 Angle : 0.522 6.910 16150 Z= 0.300 Chirality : 0.040 0.271 1854 Planarity : 0.004 0.034 1494 Dihedral : 22.323 169.310 3337 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.96 % Allowed : 11.34 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.28), residues: 902 helix: 1.61 (0.27), residues: 385 sheet: -1.03 (0.45), residues: 115 loop : -0.11 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1060 TYR 0.012 0.001 TYR A 864 PHE 0.011 0.001 PHE A 932 TRP 0.007 0.001 TRP A 763 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11431) covalent geometry : angle 0.52184 / 0.30 (16150) hydrogen bonds : bond 0.04993 / 3.34 ( 480) hydrogen bonds : angle 3.81098 / 2.78 ( 1214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.272 Fit side-chains REVERT: A 28 ASP cc_start: 0.8461 (m-30) cc_final: 0.7909 (m-30) REVERT: A 337 ASP cc_start: 0.8188 (t70) cc_final: 0.7798 (t0) REVERT: A 457 GLN cc_start: 0.7686 (tp-100) cc_final: 0.7449 (tp-100) REVERT: A 500 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: A 696 ASN cc_start: 0.8215 (t0) cc_final: 0.7871 (t0) REVERT: A 798 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7013 (mp) REVERT: A 869 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7449 (mm-40) REVERT: A 966 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: A 1044 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7695 (ttm-80) outliers start: 24 outliers final: 8 residues processed: 105 average time/residue: 0.7557 time to fit residues: 84.1780 Evaluate side-chains 95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120432 restraints weight = 11232.722| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.17 r_work: 0.3091 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11431 Z= 0.240 Angle : 0.609 8.012 16150 Z= 0.342 Chirality : 0.046 0.316 1854 Planarity : 0.005 0.050 1494 Dihedral : 22.350 169.794 3337 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.47 % Allowed : 13.07 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.28), residues: 902 helix: 1.40 (0.27), residues: 381 sheet: -1.05 (0.44), residues: 120 loop : -0.31 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1060 TYR 0.015 0.002 TYR A 864 PHE 0.017 0.002 PHE A 932 TRP 0.008 0.001 TRP A 763 HIS 0.009 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (11431) covalent geometry : angle 0.60915 / 0.34 (16150) hydrogen bonds : bond 0.05833 / 3.92 ( 480) hydrogen bonds : angle 3.89167 / 2.84 ( 1214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.356 Fit side-chains REVERT: A 290 GLN cc_start: 0.6895 (tt0) cc_final: 0.5868 (mp10) REVERT: A 305 LEU cc_start: 0.7451 (tt) cc_final: 0.7131 (tp) REVERT: A 335 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: A 337 ASP cc_start: 0.8189 (t70) cc_final: 0.7777 (t0) REVERT: A 457 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7527 (tp-100) REVERT: A 500 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: A 798 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7064 (mp) REVERT: A 869 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7457 (mm-40) REVERT: A 966 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: A 1044 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7737 (ttm-80) outliers start: 20 outliers final: 8 residues processed: 98 average time/residue: 0.7824 time to fit residues: 81.5414 Evaluate side-chains 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124897 restraints weight = 11229.734| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.01 r_work: 0.3152 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11431 Z= 0.128 Angle : 0.515 6.961 16150 Z= 0.298 Chirality : 0.040 0.263 1854 Planarity : 0.004 0.034 1494 Dihedral : 22.346 169.475 3337 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.47 % Allowed : 13.81 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.28), residues: 902 helix: 1.60 (0.27), residues: 387 sheet: -1.02 (0.46), residues: 115 loop : -0.15 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1060 TYR 0.012 0.001 TYR A 864 PHE 0.008 0.001 PHE A 932 TRP 0.008 0.001 TRP A 763 HIS 0.003 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (11431) covalent geometry : angle 0.51507 / 0.30 (16150) hydrogen bonds : bond 0.04891 / 3.28 ( 480) hydrogen bonds : angle 3.75593 / 2.73 ( 1214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.342 Fit side-chains REVERT: A 81 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 337 ASP cc_start: 0.8117 (t70) cc_final: 0.7733 (t0) REVERT: A 500 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: A 798 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 1044 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7654 (ttm-80) outliers start: 20 outliers final: 10 residues processed: 102 average time/residue: 0.7719 time to fit residues: 83.6884 Evaluate side-chains 98 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114354 restraints weight = 11254.227| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.73 r_work: 0.3125 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11431 Z= 0.180 Angle : 0.559 7.675 16150 Z= 0.315 Chirality : 0.042 0.291 1854 Planarity : 0.005 0.039 1494 Dihedral : 22.318 169.270 3337 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.34 % Allowed : 15.17 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 902 helix: 1.53 (0.27), residues: 387 sheet: -1.02 (0.46), residues: 115 loop : -0.20 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1031 TYR 0.015 0.001 TYR A 864 PHE 0.013 0.001 PHE A 932 TRP 0.007 0.001 TRP A 763 HIS 0.006 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (11431) covalent geometry : angle 0.55896 / 0.31 (16150) hydrogen bonds : bond 0.05231 / 3.51 ( 480) hydrogen bonds : angle 3.79560 / 2.77 ( 1214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.377 Fit side-chains REVERT: A 335 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: A 337 ASP cc_start: 0.8074 (t70) cc_final: 0.7662 (t0) REVERT: A 500 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 798 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6961 (mp) REVERT: A 869 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7420 (mm-40) REVERT: A 966 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: A 1044 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7638 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.8100 time to fit residues: 83.1049 Evaluate side-chains 97 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114379 restraints weight = 11187.662| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.59 r_work: 0.3181 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11431 Z= 0.135 Angle : 0.531 7.930 16150 Z= 0.302 Chirality : 0.040 0.268 1854 Planarity : 0.004 0.039 1494 Dihedral : 22.334 169.462 3337 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.28), residues: 902 helix: 1.62 (0.27), residues: 387 sheet: -0.98 (0.46), residues: 115 loop : -0.13 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.018 0.001 TYR A 864 PHE 0.008 0.001 PHE A 932 TRP 0.007 0.001 TRP A 763 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11431) covalent geometry : angle 0.53075 / 0.30 (16150) hydrogen bonds : bond 0.04905 / 3.29 ( 480) hydrogen bonds : angle 3.76552 / 2.74 ( 1214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.263 Fit side-chains REVERT: A 335 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: A 337 ASP cc_start: 0.8052 (t70) cc_final: 0.7627 (t0) REVERT: A 500 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: A 798 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6964 (mp) REVERT: A 869 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: A 1044 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7640 (ttm-80) outliers start: 20 outliers final: 10 residues processed: 95 average time/residue: 0.7423 time to fit residues: 74.5624 Evaluate side-chains 96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129931 restraints weight = 11133.614| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.01 r_work: 0.3183 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11431 Z= 0.148 Angle : 0.539 9.012 16150 Z= 0.305 Chirality : 0.041 0.276 1854 Planarity : 0.004 0.038 1494 Dihedral : 22.297 169.130 3337 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.34 % Allowed : 15.66 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.28), residues: 902 helix: 1.62 (0.27), residues: 387 sheet: -0.95 (0.46), residues: 115 loop : -0.14 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.018 0.001 TYR A 864 PHE 0.010 0.001 PHE A 932 TRP 0.007 0.001 TRP A 763 HIS 0.005 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (11431) covalent geometry : angle 0.53867 / 0.30 (16150) hydrogen bonds : bond 0.04926 / 3.31 ( 480) hydrogen bonds : angle 3.74652 / 2.73 ( 1214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.291 Fit side-chains REVERT: A 337 ASP cc_start: 0.8198 (t70) cc_final: 0.7876 (t0) REVERT: A 500 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: A 798 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 869 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: A 966 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: A 1044 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7937 (ttm-80) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 0.8028 time to fit residues: 80.5944 Evaluate side-chains 94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129883 restraints weight = 11203.843| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.02 r_work: 0.3186 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11431 Z= 0.146 Angle : 0.543 8.872 16150 Z= 0.307 Chirality : 0.040 0.274 1854 Planarity : 0.004 0.037 1494 Dihedral : 22.294 169.244 3337 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.10 % Allowed : 16.65 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.28), residues: 902 helix: 1.64 (0.27), residues: 387 sheet: -0.94 (0.46), residues: 115 loop : -0.13 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1060 TYR 0.021 0.001 TYR A 864 PHE 0.010 0.001 PHE A 932 TRP 0.008 0.001 TRP A 763 HIS 0.004 0.001 HIS A1028 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (11431) covalent geometry : angle 0.54340 / 0.31 (16150) hydrogen bonds : bond 0.04888 / 3.28 ( 480) hydrogen bonds : angle 3.73702 / 2.72 ( 1214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.63 seconds wall clock time: 73 minutes 10.95 seconds (4390.95 seconds total)