Starting phenix.real_space_refine on Fri Jan 17 10:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_42838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_42838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_42838.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_42838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzb_42838/01_2025/8uzb_42838.cif" } resolution = 2.63 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.69, per 1000 atoms: 0.61 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: 3.05 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.01 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: 6.12 Time building geometry restraints manager: 3.28 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=" CB PRO A 778 " pdb=" CG PRO A 778 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C3' C B 77 " pdb=" O3' C B 77 " ideal model delta sigma weight residual 1.427 1.442 -0.015 1.50e-02 4.44e+03 1.03e+00 bond pdb=" CG PRO A 778 " pdb=" CD PRO A 778 " ideal model delta sigma weight residual 1.503 1.470 0.033 3.40e-02 8.65e+02 9.58e-01 bond pdb=" CA THR A 416 " pdb=" CB THR A 416 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.48e-02 4.57e+03 9.16e-01 ... (remaining 11426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15774 1.46 - 2.92: 314 2.92 - 4.39: 49 4.39 - 5.85: 8 5.85 - 7.31: 5 Bond angle restraints: 16150 Sorted by residual: angle pdb=" C THR A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 121.91 128.69 -6.78 2.03e+00 2.43e-01 1.11e+01 angle pdb=" C3' C B 77 " pdb=" O3' C B 77 " pdb=" P A B 78 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.75e+00 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 107.20 111.47 -4.27 1.70e+00 3.46e-01 6.32e+00 angle pdb=" CB MET A 207 " pdb=" CG MET A 207 " pdb=" SD MET A 207 " ideal model delta sigma weight residual 112.70 120.01 -7.31 3.00e+00 1.11e-01 5.94e+00 angle pdb=" N PRO A 778 " pdb=" CD PRO A 778 " pdb=" CG PRO A 778 " ideal model delta sigma weight residual 103.20 99.67 3.53 1.50e+00 4.44e-01 5.53e+00 ... (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: 1417 0.038 - 0.075: 329 0.075 - 0.113: 85 0.113 - 0.150: 20 0.150 - 0.188: 3 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: 0.920 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:14.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11431 Z= 0.194 Angle : 0.528 7.309 16150 Z= 0.284 Chirality : 0.037 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 (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: 0.49 (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 TRP 0.013 0.001 TRP A 763 HIS 0.002 0.001 HIS A1028 PHE 0.009 0.001 PHE A 759 TYR 0.020 0.001 TYR A 864 ARG 0.007 0.000 ARG A 503 *********************** 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 : 1.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.6984 time to fit residues: 192.6098 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 : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.166342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114991 restraints weight = 11064.814| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.59 r_work: 0.3191 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11431 Z= 0.234 Angle : 0.555 6.830 16150 Z= 0.299 Chirality : 0.039 0.176 1854 Planarity : 0.004 0.035 1494 Dihedral : 22.135 165.805 3337 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.73 % Allowed : 9.74 % 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 (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: 0.72 (0.28), residues: 902 helix: 1.52 (0.27), residues: 386 sheet: -0.86 (0.45), residues: 121 loop : -0.02 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 763 HIS 0.003 0.001 HIS A 720 PHE 0.010 0.001 PHE A 932 TYR 0.016 0.001 TYR A 491 ARG 0.006 0.000 ARG A 908 *********************** 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 104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.961 Fit side-chains REVERT: A 28 ASP cc_start: 0.8363 (m-30) cc_final: 0.7748 (m-30) REVERT: A 335 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 1060 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7726 (ttp80) outliers start: 14 outliers final: 3 residues processed: 97 average time/residue: 1.6943 time to fit residues: 174.7659 Evaluate side-chains 89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 795 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.171228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129286 restraints weight = 11215.599| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.98 r_work: 0.3224 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11431 Z= 0.152 Angle : 0.502 6.842 16150 Z= 0.270 Chirality : 0.036 0.175 1854 Planarity : 0.004 0.033 1494 Dihedral : 22.043 165.449 3337 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.73 % Allowed : 10.97 % Favored : 87.30 % 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: 0.98 (0.29), residues: 902 helix: 1.79 (0.27), residues: 386 sheet: -0.59 (0.46), residues: 116 loop : -0.00 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 763 HIS 0.004 0.001 HIS A1028 PHE 0.008 0.001 PHE A 882 TYR 0.013 0.001 TYR A 864 ARG 0.004 0.000 ARG A1060 *********************** 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 107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.930 Fit side-chains REVERT: A 28 ASP cc_start: 0.8391 (m-30) cc_final: 0.7942 (m-30) REVERT: A 162 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: A 337 ASP cc_start: 0.8206 (t70) cc_final: 0.7836 (t0) REVERT: A 457 GLN cc_start: 0.7684 (tp40) cc_final: 0.7449 (tp-100) REVERT: A 500 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: A 817 ARG cc_start: 0.8917 (mmp-170) cc_final: 0.8697 (mmm160) outliers start: 14 outliers final: 4 residues processed: 102 average time/residue: 1.6293 time to fit residues: 176.7929 Evaluate side-chains 85 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER 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 10 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 0.0030 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.165263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113783 restraints weight = 11102.270| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.59 r_work: 0.3172 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11431 Z= 0.265 Angle : 0.560 6.995 16150 Z= 0.302 Chirality : 0.040 0.206 1854 Planarity : 0.004 0.033 1494 Dihedral : 22.118 166.698 3337 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.59 % Allowed : 11.59 % Favored : 85.82 % 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: 0.83 (0.28), residues: 902 helix: 1.73 (0.27), residues: 386 sheet: -0.98 (0.44), residues: 122 loop : -0.02 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 763 HIS 0.004 0.001 HIS A 300 PHE 0.014 0.001 PHE A 932 TYR 0.013 0.001 TYR A 864 ARG 0.004 0.000 ARG A 698 *********************** 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 111 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.910 Fit side-chains REVERT: A 28 ASP cc_start: 0.8387 (m-30) cc_final: 0.7814 (m-30) REVERT: A 306 LEU cc_start: 0.7207 (mp) cc_final: 0.6807 (mt) REVERT: A 335 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: A 337 ASP cc_start: 0.8137 (t70) cc_final: 0.7746 (t0) REVERT: A 500 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 706 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6800 (mmt90) REVERT: A 869 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7477 (mm-40) REVERT: A 948 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 1044 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7626 (ttm-80) outliers start: 21 outliers final: 7 residues processed: 100 average time/residue: 1.7700 time to fit residues: 187.8594 Evaluate side-chains 92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 706 ARG Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1029 ASP 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 33 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123003 restraints weight = 11132.361| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.23 r_work: 0.3111 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11431 Z= 0.262 Angle : 0.562 7.019 16150 Z= 0.302 Chirality : 0.040 0.194 1854 Planarity : 0.004 0.034 1494 Dihedral : 22.089 166.941 3337 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.21 % Allowed : 13.07 % 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 (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: 0.80 (0.28), residues: 902 helix: 1.65 (0.27), residues: 388 sheet: -0.77 (0.45), residues: 120 loop : -0.08 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.002 0.001 HIS A 300 PHE 0.014 0.001 PHE A 932 TYR 0.013 0.001 TYR A 864 ARG 0.007 0.000 ARG A1060 *********************** 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 111 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.954 Fit side-chains REVERT: A 28 ASP cc_start: 0.8482 (m-30) cc_final: 0.8254 (m-30) REVERT: A 335 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: A 337 ASP cc_start: 0.8158 (t70) cc_final: 0.7738 (t0) REVERT: A 392 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8118 (mmmt) REVERT: A 500 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: A 706 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6844 (mmt90) REVERT: A 798 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7077 (mp) REVERT: A 869 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7500 (mm-40) REVERT: A 948 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8351 (mt) REVERT: A 1044 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7569 (ttm-80) outliers start: 26 outliers final: 10 residues processed: 100 average time/residue: 1.6954 time to fit residues: 180.1277 Evaluate side-chains 96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG 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 1029 ASP 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 104 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116799 restraints weight = 11296.817| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.59 r_work: 0.3211 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11431 Z= 0.173 Angle : 0.510 6.936 16150 Z= 0.275 Chirality : 0.036 0.174 1854 Planarity : 0.004 0.033 1494 Dihedral : 21.968 166.527 3337 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.47 % Allowed : 14.30 % Favored : 83.23 % 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: 0.97 (0.29), residues: 902 helix: 1.85 (0.27), residues: 388 sheet: -0.89 (0.45), residues: 122 loop : 0.04 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 763 HIS 0.002 0.000 HIS A1028 PHE 0.008 0.001 PHE A 932 TYR 0.012 0.001 TYR A 864 ARG 0.007 0.000 ARG A1060 *********************** 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 110 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.975 Fit side-chains REVERT: A 28 ASP cc_start: 0.8367 (m-30) cc_final: 0.8036 (m-30) REVERT: A 290 GLN cc_start: 0.6192 (mt0) cc_final: 0.5843 (mm-40) REVERT: A 337 ASP cc_start: 0.8003 (t70) cc_final: 0.7638 (t0) REVERT: A 706 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6792 (mmt90) REVERT: A 798 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6995 (mp) REVERT: A 869 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7442 (mm-40) REVERT: A 948 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8183 (mt) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 1.7637 time to fit residues: 190.8813 Evaluate side-chains 96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 181 TYR Chi-restraints excluded: chain A residue 355 SER 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 706 ARG 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 1046 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123169 restraints weight = 11339.773| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.20 r_work: 0.3112 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11431 Z= 0.254 Angle : 0.559 7.021 16150 Z= 0.300 Chirality : 0.039 0.237 1854 Planarity : 0.004 0.035 1494 Dihedral : 22.043 167.641 3337 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.96 % Allowed : 14.18 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 902 helix: 1.74 (0.27), residues: 387 sheet: -0.88 (0.44), residues: 127 loop : -0.05 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 763 HIS 0.002 0.001 HIS A 93 PHE 0.012 0.001 PHE A 932 TYR 0.015 0.001 TYR A 864 ARG 0.007 0.000 ARG A1060 *********************** 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 106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.995 Fit side-chains REVERT: A 290 GLN cc_start: 0.6301 (mt0) cc_final: 0.5879 (mm-40) REVERT: A 337 ASP cc_start: 0.8097 (t70) cc_final: 0.7716 (t0) REVERT: A 500 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: A 706 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6758 (mmt90) REVERT: A 798 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7041 (mp) REVERT: A 869 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7489 (mm-40) REVERT: A 948 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 966 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: A 1044 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7576 (ttm-80) outliers start: 24 outliers final: 12 residues processed: 97 average time/residue: 1.6911 time to fit residues: 174.2449 Evaluate side-chains 95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 500 GLU 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 706 ARG 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 966 GLU Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1029 ASP 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 103 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116916 restraints weight = 11149.659| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.58 r_work: 0.3213 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11431 Z= 0.170 Angle : 0.514 6.932 16150 Z= 0.277 Chirality : 0.036 0.174 1854 Planarity : 0.004 0.037 1494 Dihedral : 21.953 167.368 3337 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 15.54 % Favored : 82.37 % 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: 1.01 (0.29), residues: 902 helix: 1.90 (0.27), residues: 388 sheet: -0.79 (0.45), residues: 127 loop : 0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 763 HIS 0.002 0.000 HIS A 380 PHE 0.007 0.001 PHE A 852 TYR 0.014 0.001 TYR A 864 ARG 0.008 0.000 ARG A1060 *********************** 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: 17 poor density : 85 time to evaluate : 1.043 Fit side-chains REVERT: A 162 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: A 290 GLN cc_start: 0.6298 (mt0) cc_final: 0.5820 (mm-40) REVERT: A 337 ASP cc_start: 0.7967 (t70) cc_final: 0.7580 (t0) REVERT: A 706 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6862 (mmt90) REVERT: A 798 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6985 (mp) REVERT: A 869 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: A 948 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8165 (mt) REVERT: A 1044 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7656 (ttm-80) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 1.7381 time to fit residues: 173.3459 Evaluate side-chains 96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 181 TYR Chi-restraints excluded: chain A residue 355 SER 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 706 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.0370 chunk 102 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120465 restraints weight = 11222.170| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.28 r_work: 0.3069 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11431 Z= 0.398 Angle : 0.648 8.564 16150 Z= 0.345 Chirality : 0.044 0.193 1854 Planarity : 0.006 0.054 1494 Dihedral : 22.203 169.882 3337 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.96 % Allowed : 15.17 % Favored : 81.87 % 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: 0.56 (0.28), residues: 902 helix: 1.51 (0.27), residues: 382 sheet: -0.90 (0.43), residues: 124 loop : -0.24 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 763 HIS 0.005 0.001 HIS A1028 PHE 0.019 0.002 PHE A 932 TYR 0.020 0.002 TYR A 864 ARG 0.013 0.001 ARG A1031 *********************** 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 104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.973 Fit side-chains REVERT: A 290 GLN cc_start: 0.6508 (mt0) cc_final: 0.5964 (mm-40) REVERT: A 335 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: A 337 ASP cc_start: 0.8166 (t70) cc_final: 0.7792 (t0) REVERT: A 706 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6789 (mmt90) REVERT: A 798 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7116 (mp) REVERT: A 869 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7452 (mm-40) REVERT: A 948 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8477 (mt) REVERT: A 1044 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7588 (ttm-80) outliers start: 24 outliers final: 9 residues processed: 98 average time/residue: 1.6652 time to fit residues: 173.7285 Evaluate side-chains 91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG 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 1003 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 63 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.165995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123508 restraints weight = 11161.136| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.06 r_work: 0.3124 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11431 Z= 0.224 Angle : 0.562 9.979 16150 Z= 0.300 Chirality : 0.038 0.174 1854 Planarity : 0.004 0.047 1494 Dihedral : 22.056 168.586 3337 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.10 % Allowed : 16.40 % Favored : 81.50 % 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: 0.79 (0.28), residues: 902 helix: 1.71 (0.27), residues: 387 sheet: -0.81 (0.45), residues: 120 loop : -0.14 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.005 0.001 HIS A1028 PHE 0.010 0.001 PHE A 932 TYR 0.017 0.001 TYR A 864 ARG 0.010 0.000 ARG A1031 ********************** 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 96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.932 Fit side-chains REVERT: A 337 ASP cc_start: 0.8001 (t70) cc_final: 0.7618 (t0) REVERT: A 706 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6749 (mmt90) REVERT: A 869 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7435 (mm-40) REVERT: A 1044 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7604 (ttm-80) REVERT: A 1060 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7512 (ttp-170) outliers start: 17 outliers final: 7 residues processed: 90 average time/residue: 1.8453 time to fit residues: 175.8498 Evaluate side-chains 86 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 1003 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 71 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 0.0170 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120776 restraints weight = 11067.275| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.21 r_work: 0.3084 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11431 Z= 0.325 Angle : 0.614 8.118 16150 Z= 0.327 Chirality : 0.042 0.175 1854 Planarity : 0.005 0.041 1494 Dihedral : 22.169 170.026 3337 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.10 % Allowed : 16.28 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.28), residues: 902 helix: 1.46 (0.27), residues: 389 sheet: -0.92 (0.44), residues: 120 loop : -0.21 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 763 HIS 0.007 0.001 HIS A1028 PHE 0.015 0.002 PHE A 932 TYR 0.022 0.001 TYR A 864 ARG 0.007 0.001 ARG A1060 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8796.27 seconds wall clock time: 155 minutes 30.32 seconds (9330.32 seconds total)