Starting phenix.real_space_refine on Sat Aug 23 11:35:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.map" model { file = "/net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eoa_19850/08_2025/9eoa_19850.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 63 5.49 5 S 72 5.16 5 C 7262 2.51 5 N 2033 2.21 5 O 2377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11807 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4782 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 21, 'TRANS': 570} Chain breaks: 3 Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 605 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "C" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 434 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "G" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "H" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1817 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain breaks: 3 Time building chain proxies: 3.33, per 1000 atoms: 0.28 Number of scatterers: 11807 At special positions: 0 Unit cell: (97.8194, 106.961, 145.358, 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 72 16.00 P 63 15.00 O 2377 8.00 N 2033 7.00 C 7262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 162 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 618.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2542 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 41.7% alpha, 21.6% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.596A pdb=" N ASN A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.836A pdb=" N LYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 538 through 556 removed outlier: 4.402A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 598 through 622 Processing helix chain 'A' and resid 623 through 641 Processing helix chain 'A' and resid 644 through 651 removed outlier: 3.950A pdb=" N ARG A 648 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.825A pdb=" N CYS A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 683 through 695 Processing helix chain 'A' and resid 703 through 718 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.543A pdb=" N ALA A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 756 Processing helix chain 'A' and resid 757 through 760 Processing helix chain 'A' and resid 813 through 825 Processing helix chain 'A' and resid 835 through 851 removed outlier: 6.128A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 879 removed outlier: 3.938A pdb=" N THR A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 879 " --> pdb=" O PHE A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 894 through 909 removed outlier: 3.566A pdb=" N THR A 905 " --> pdb=" O TRP A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 removed outlier: 3.608A pdb=" N PHE A 922 " --> pdb=" O TRP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 Processing helix chain 'A' and resid 936 through 949 removed outlier: 3.636A pdb=" N LEU A 940 " --> pdb=" O GLY A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 984 through 997 Processing helix chain 'F' and resid 8 through 21 removed outlier: 4.232A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 removed outlier: 3.871A pdb=" N ALA F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'G' and resid 8 through 21 removed outlier: 4.150A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.333A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 9 through 23 removed outlier: 3.667A pdb=" N ASP H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 81 removed outlier: 3.729A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.700A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 783 removed outlier: 4.271A pdb=" N LYS A 778 " --> pdb=" O VAL A1001 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU A1002 " --> pdb=" O PHE A 971 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 973 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A1004 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU A 975 " --> pdb=" O CYS A1004 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A1006 " --> pdb=" O GLU A 975 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS A 977 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS A 970 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 963 " --> pdb=" O LYS A 972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 58 through 62 removed outlier: 5.238A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG F 5 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 4 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AA5, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AA6, first strand: chain 'F' and resid 29 through 30 removed outlier: 5.789A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.972A pdb=" N VAL F 203 " --> pdb=" O CYS F 162 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.821A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.544A pdb=" N LEU G 251 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 157 through 159 Processing sheet with id=AB2, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.502A pdb=" N ALA H 26 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.554A pdb=" N LEU H 47 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR H 249 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER H 230 " --> pdb=" O VAL H 233 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU H 235 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER H 228 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL H 237 " --> pdb=" O THR H 226 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR H 226 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR H 239 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR H 224 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS H 135 " --> pdb=" O MET H 229 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2640 1.33 - 1.45: 2692 1.45 - 1.57: 6570 1.57 - 1.69: 123 1.69 - 1.81: 111 Bond restraints: 12136 Sorted by residual: bond pdb=" N VAL F 233 " pdb=" CA VAL F 233 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.32e+01 bond pdb=" N MET H 139 " pdb=" CA MET H 139 " ideal model delta sigma weight residual 1.453 1.484 -0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" N THR H 219 " pdb=" CA THR H 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.04e-02 9.25e+03 1.07e+01 bond pdb=" N VAL H 48 " pdb=" CA VAL H 48 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N CYS G 135 " pdb=" CA CYS G 135 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.24e-02 6.50e+03 1.04e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15747 1.81 - 3.63: 781 3.63 - 5.44: 114 5.44 - 7.26: 21 7.26 - 9.07: 5 Bond angle restraints: 16668 Sorted by residual: angle pdb=" N PRO A 856 " pdb=" CA PRO A 856 " pdb=" C PRO A 856 " ideal model delta sigma weight residual 111.32 119.79 -8.47 1.71e+00 3.42e-01 2.45e+01 angle pdb=" C GLY A 854 " pdb=" N ILE A 855 " pdb=" CA ILE A 855 " ideal model delta sigma weight residual 123.04 118.60 4.44 9.20e-01 1.18e+00 2.33e+01 angle pdb=" N TYR A 683 " pdb=" CA TYR A 683 " pdb=" C TYR A 683 " ideal model delta sigma weight residual 114.64 107.45 7.19 1.52e+00 4.33e-01 2.23e+01 angle pdb=" N LEU A 462 " pdb=" CA LEU A 462 " pdb=" C LEU A 462 " ideal model delta sigma weight residual 109.54 103.08 6.46 1.37e+00 5.33e-01 2.22e+01 angle pdb=" C PRO A 770 " pdb=" N GLU A 771 " pdb=" CA GLU A 771 " ideal model delta sigma weight residual 122.77 116.57 6.20 1.33e+00 5.65e-01 2.17e+01 ... (remaining 16663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5932 17.92 - 35.85: 837 35.85 - 53.77: 338 53.77 - 71.70: 75 71.70 - 89.62: 10 Dihedral angle restraints: 7192 sinusoidal: 3289 harmonic: 3903 Sorted by residual: dihedral pdb=" CB CYS G 135 " pdb=" SG CYS G 135 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual -86.00 -133.08 47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA ARG A 739 " pdb=" C ARG A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C CYS G 135 " pdb=" N CYS G 135 " pdb=" CA CYS G 135 " pdb=" CB CYS G 135 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1489 0.055 - 0.110: 334 0.110 - 0.164: 65 0.164 - 0.219: 25 0.219 - 0.274: 10 Chirality restraints: 1923 Sorted by residual: chirality pdb=" CA CYS G 135 " pdb=" N CYS G 135 " pdb=" C CYS G 135 " pdb=" CB CYS G 135 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE H 147 " pdb=" CA ILE H 147 " pdb=" CG1 ILE H 147 " pdb=" CG2 ILE H 147 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1920 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 768 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLN A 768 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 768 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 769 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 46 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C SER H 46 " 0.050 2.00e-02 2.50e+03 pdb=" O SER H 46 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU H 47 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 42 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C SER H 42 " 0.048 2.00e-02 2.50e+03 pdb=" O SER H 42 " -0.019 2.00e-02 2.50e+03 pdb=" N SER H 43 " -0.016 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1203 2.74 - 3.28: 11914 3.28 - 3.82: 20843 3.82 - 4.36: 24428 4.36 - 4.90: 39583 Nonbonded interactions: 97971 Sorted by model distance: nonbonded pdb=" OH TYR A 822 " pdb=" OE2 GLU A1002 " model vdw 2.201 3.040 nonbonded pdb=" O THR G 73 " pdb=" OG SER G 76 " model vdw 2.221 3.040 nonbonded pdb=" O SER A 836 " pdb=" OG1 THR A 840 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 895 " pdb=" OG SER A 933 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR A 555 " pdb=" OD1 ASN A 861 " model vdw 2.287 3.040 ... (remaining 97966 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 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 119 or resid 128 through 163 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'G' and (resid 1 through 119 or resid 128 through 163 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'H' and resid 1 through 253) } 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=0.00 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: 3.420 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.006 0.078 12137 Z= 0.347 Angle : 0.857 9.073 16670 Z= 0.552 Chirality : 0.055 0.274 1923 Planarity : 0.005 0.061 1906 Dihedral : 19.327 89.622 4647 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.84 % Allowed : 23.27 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.23), residues: 1317 helix: 1.08 (0.24), residues: 483 sheet: 0.83 (0.29), residues: 350 loop : -0.26 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 146 TYR 0.038 0.002 TYR A 375 PHE 0.019 0.002 PHE A 971 TRP 0.023 0.003 TRP A 664 HIS 0.003 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00558 (12136) covalent geometry : angle 0.85645 (16668) SS BOND : bond 0.02797 ( 1) SS BOND : angle 3.34981 ( 2) hydrogen bonds : bond 0.17757 ( 646) hydrogen bonds : angle 7.24017 ( 1778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 332 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8427 (tttt) cc_final: 0.8165 (ttpp) REVERT: A 522 VAL cc_start: 0.7714 (t) cc_final: 0.7499 (m) REVERT: A 632 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7436 (tp-100) REVERT: A 889 LEU cc_start: 0.8233 (tp) cc_final: 0.7965 (tp) REVERT: A 947 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 950 ASP cc_start: 0.7724 (p0) cc_final: 0.7368 (p0) REVERT: A 970 HIS cc_start: 0.7280 (m90) cc_final: 0.7052 (m90) REVERT: F 6 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7881 (tp) REVERT: F 16 LEU cc_start: 0.8241 (mm) cc_final: 0.8039 (mm) REVERT: F 80 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8270 (mtpt) REVERT: G 115 GLU cc_start: 0.7242 (pt0) cc_final: 0.6981 (pt0) REVERT: G 222 SER cc_start: 0.7608 (t) cc_final: 0.7134 (p) REVERT: G 229 MET cc_start: 0.5207 (mtm) cc_final: 0.4831 (mtm) REVERT: G 232 ASP cc_start: 0.7919 (m-30) cc_final: 0.7711 (m-30) outliers start: 45 outliers final: 33 residues processed: 353 average time/residue: 0.1132 time to fit residues: 56.2181 Evaluate side-chains 360 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 495 GLN A 506 GLN A 779 HIS A 929 GLN G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.160658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131475 restraints weight = 18369.278| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.64 r_work: 0.3570 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12137 Z= 0.223 Angle : 0.629 7.760 16670 Z= 0.340 Chirality : 0.044 0.298 1923 Planarity : 0.004 0.044 1906 Dihedral : 19.006 65.157 2148 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.84 % Allowed : 21.82 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1317 helix: 1.05 (0.23), residues: 505 sheet: 0.75 (0.28), residues: 350 loop : -0.35 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 952 TYR 0.018 0.002 TYR A 699 PHE 0.013 0.002 PHE A 673 TRP 0.014 0.002 TRP A 664 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00490 (12136) covalent geometry : angle 0.62868 (16668) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.18479 ( 2) hydrogen bonds : bond 0.04321 ( 646) hydrogen bonds : angle 5.41026 ( 1778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8655 (tttt) cc_final: 0.8421 (ttpp) REVERT: A 628 LYS cc_start: 0.7388 (tmtt) cc_final: 0.7175 (tmtt) REVERT: A 778 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7637 (mmmt) REVERT: A 889 LEU cc_start: 0.8088 (tp) cc_final: 0.7873 (tp) REVERT: A 929 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7639 (mm-40) REVERT: A 932 VAL cc_start: 0.8423 (t) cc_final: 0.8215 (p) REVERT: A 950 ASP cc_start: 0.7216 (p0) cc_final: 0.6793 (p0) REVERT: A 1002 GLU cc_start: 0.8383 (pt0) cc_final: 0.8147 (pt0) REVERT: F 16 LEU cc_start: 0.8265 (mm) cc_final: 0.8019 (mm) REVERT: F 81 CYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8480 (t) REVERT: F 85 GLU cc_start: 0.7543 (pm20) cc_final: 0.7194 (pm20) REVERT: F 193 GLU cc_start: 0.7511 (mp0) cc_final: 0.7212 (mp0) REVERT: G 29 ASP cc_start: 0.7272 (t0) cc_final: 0.6884 (t0) REVERT: G 77 LYS cc_start: 0.8485 (mptt) cc_final: 0.8059 (mmtm) REVERT: G 80 LYS cc_start: 0.8071 (mmtp) cc_final: 0.7810 (mmmm) REVERT: G 138 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7209 (tmtt) REVERT: G 168 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (mttt) REVERT: G 222 SER cc_start: 0.8070 (t) cc_final: 0.7740 (p) REVERT: G 229 MET cc_start: 0.5107 (mtm) cc_final: 0.4738 (mtm) REVERT: G 232 ASP cc_start: 0.7866 (m-30) cc_final: 0.7650 (m-30) REVERT: H 227 LEU cc_start: 0.7251 (mp) cc_final: 0.6980 (mp) REVERT: H 237 VAL cc_start: 0.6400 (OUTLIER) cc_final: 0.6138 (p) outliers start: 45 outliers final: 22 residues processed: 352 average time/residue: 0.1140 time to fit residues: 56.4143 Evaluate side-chains 345 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 319 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 81 CYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 104 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN F 71 ASN G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133354 restraints weight = 18506.727| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.67 r_work: 0.3587 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 0.037 12137 Z= 0.154 Angle : 0.584 8.078 16670 Z= 0.311 Chirality : 0.042 0.270 1923 Planarity : 0.004 0.041 1906 Dihedral : 18.672 66.048 2096 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.84 % Allowed : 22.17 % Favored : 74.00 % 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 aren not related in a simple way. whole: 0.78 (0.23), residues: 1317 helix: 1.27 (0.23), residues: 505 sheet: 0.60 (0.28), residues: 344 loop : -0.26 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 952 TYR 0.017 0.002 TYR A 375 PHE 0.015 0.001 PHE F 215 TRP 0.011 0.002 TRP A 664 HIS 0.006 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00342 (12136) covalent geometry : angle 0.58427 (16668) SS BOND : bond 0.00395 ( 1) SS BOND : angle 0.17634 ( 2) hydrogen bonds : bond 0.03742 ( 646) hydrogen bonds : angle 5.10217 ( 1778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.7924 (t80) cc_final: 0.7677 (t80) REVERT: A 425 LYS cc_start: 0.8585 (tttt) cc_final: 0.8349 (ttpp) REVERT: A 605 TYR cc_start: 0.8601 (t80) cc_final: 0.8316 (t80) REVERT: A 632 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7521 (tp-100) REVERT: A 651 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 778 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7607 (mmmt) REVERT: A 932 VAL cc_start: 0.8497 (t) cc_final: 0.8285 (p) REVERT: A 950 ASP cc_start: 0.7186 (p0) cc_final: 0.6698 (p0) REVERT: A 1002 GLU cc_start: 0.8390 (pt0) cc_final: 0.8061 (pt0) REVERT: F 16 LEU cc_start: 0.8253 (mm) cc_final: 0.8026 (mm) REVERT: F 60 TYR cc_start: 0.7421 (t80) cc_final: 0.7180 (t80) REVERT: F 80 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8337 (mtpt) REVERT: F 193 GLU cc_start: 0.7450 (mp0) cc_final: 0.7101 (mp0) REVERT: F 214 PHE cc_start: 0.7588 (m-10) cc_final: 0.7169 (m-10) REVERT: G 29 ASP cc_start: 0.7204 (t0) cc_final: 0.6800 (t0) REVERT: G 47 LEU cc_start: 0.8009 (tp) cc_final: 0.7799 (tp) REVERT: G 116 MET cc_start: 0.5747 (mmp) cc_final: 0.5145 (mmp) REVERT: G 124 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 138 LYS cc_start: 0.7685 (tmtt) cc_final: 0.7138 (tmtt) REVERT: G 168 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7866 (mttt) REVERT: G 175 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7672 (pt) REVERT: G 222 SER cc_start: 0.8035 (t) cc_final: 0.7676 (p) REVERT: G 229 MET cc_start: 0.5247 (mtm) cc_final: 0.4872 (mtm) REVERT: G 232 ASP cc_start: 0.7844 (m-30) cc_final: 0.7638 (m-30) REVERT: H 130 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7297 (tm-30) REVERT: H 237 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.6144 (p) outliers start: 45 outliers final: 20 residues processed: 355 average time/residue: 0.1221 time to fit residues: 60.6909 Evaluate side-chains 348 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 72 optimal weight: 0.2980 chunk 48 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 632 GLN A 832 HIS G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133411 restraints weight = 18626.173| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.58 r_work: 0.3595 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12137 Z= 0.159 Angle : 0.577 7.243 16670 Z= 0.308 Chirality : 0.042 0.259 1923 Planarity : 0.004 0.044 1906 Dihedral : 18.651 66.072 2090 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.01 % Allowed : 23.44 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.23), residues: 1317 helix: 1.37 (0.23), residues: 505 sheet: 0.56 (0.29), residues: 343 loop : -0.26 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 697 TYR 0.031 0.002 TYR A 375 PHE 0.045 0.002 PHE F 215 TRP 0.010 0.002 TRP A 708 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00354 (12136) covalent geometry : angle 0.57694 (16668) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.16656 ( 2) hydrogen bonds : bond 0.03601 ( 646) hydrogen bonds : angle 5.00131 ( 1778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6784 (tp30) cc_final: 0.6540 (mm-30) REVERT: A 422 PHE cc_start: 0.7909 (t80) cc_final: 0.7673 (t80) REVERT: A 425 LYS cc_start: 0.8633 (tttt) cc_final: 0.8410 (ttpp) REVERT: A 632 GLN cc_start: 0.8005 (tp40) cc_final: 0.7743 (mm110) REVERT: A 722 LEU cc_start: 0.8063 (mp) cc_final: 0.7855 (mt) REVERT: A 778 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7581 (mmmt) REVERT: A 834 GLU cc_start: 0.7057 (tp30) cc_final: 0.6841 (tp30) REVERT: A 888 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7144 (mm-40) REVERT: A 889 LEU cc_start: 0.8121 (tp) cc_final: 0.7846 (tp) REVERT: A 910 GLU cc_start: 0.7847 (tp30) cc_final: 0.7496 (tp30) REVERT: A 932 VAL cc_start: 0.8464 (t) cc_final: 0.8258 (p) REVERT: A 950 ASP cc_start: 0.7275 (p0) cc_final: 0.6820 (p0) REVERT: F 16 LEU cc_start: 0.8276 (mm) cc_final: 0.8058 (mm) REVERT: F 193 GLU cc_start: 0.7456 (mp0) cc_final: 0.7111 (mp0) REVERT: F 214 PHE cc_start: 0.7578 (m-10) cc_final: 0.7233 (m-10) REVERT: G 40 MET cc_start: 0.7029 (mtt) cc_final: 0.6694 (ttt) REVERT: G 77 LYS cc_start: 0.8578 (mptt) cc_final: 0.8230 (mmtm) REVERT: G 116 MET cc_start: 0.5788 (mmp) cc_final: 0.5272 (mmp) REVERT: G 124 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7320 (tm-30) REVERT: G 168 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7861 (mttt) REVERT: G 175 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7629 (pt) REVERT: G 222 SER cc_start: 0.8035 (t) cc_final: 0.7709 (p) REVERT: G 229 MET cc_start: 0.5116 (mtm) cc_final: 0.4758 (mtm) REVERT: H 80 LYS cc_start: 0.8259 (tttt) cc_final: 0.7931 (ttmm) REVERT: H 130 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7317 (tm-30) outliers start: 47 outliers final: 31 residues processed: 343 average time/residue: 0.1185 time to fit residues: 57.2318 Evaluate side-chains 344 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 chunk 133 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 490 ASN A 861 ASN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.161882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133343 restraints weight = 18589.233| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.58 r_work: 0.3595 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12137 Z= 0.160 Angle : 0.583 8.622 16670 Z= 0.309 Chirality : 0.042 0.250 1923 Planarity : 0.004 0.043 1906 Dihedral : 18.683 66.557 2090 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.01 % Allowed : 24.13 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.23), residues: 1317 helix: 1.37 (0.23), residues: 506 sheet: 0.64 (0.29), residues: 346 loop : -0.38 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 952 TYR 0.032 0.002 TYR A 375 PHE 0.074 0.002 PHE F 215 TRP 0.010 0.002 TRP A 708 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00360 (12136) covalent geometry : angle 0.58321 (16668) SS BOND : bond 0.00328 ( 1) SS BOND : angle 0.12277 ( 2) hydrogen bonds : bond 0.03562 ( 646) hydrogen bonds : angle 4.91305 ( 1778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6725 (tp30) cc_final: 0.6471 (mm-30) REVERT: A 422 PHE cc_start: 0.7852 (t80) cc_final: 0.7610 (t80) REVERT: A 425 LYS cc_start: 0.8642 (tttt) cc_final: 0.8343 (ttpp) REVERT: A 591 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7739 (ttp-110) REVERT: A 632 GLN cc_start: 0.8030 (tp40) cc_final: 0.7766 (mm-40) REVERT: A 723 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 778 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7549 (mmmt) REVERT: A 888 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7129 (mm-40) REVERT: A 889 LEU cc_start: 0.8113 (tp) cc_final: 0.7848 (tp) REVERT: A 932 VAL cc_start: 0.8462 (t) cc_final: 0.8257 (p) REVERT: A 947 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7972 (mp) REVERT: F 16 LEU cc_start: 0.8292 (mm) cc_final: 0.8064 (mm) REVERT: F 85 GLU cc_start: 0.7440 (pm20) cc_final: 0.7131 (pm20) REVERT: F 193 GLU cc_start: 0.7394 (mp0) cc_final: 0.7033 (mp0) REVERT: F 214 PHE cc_start: 0.7493 (m-10) cc_final: 0.7277 (m-10) REVERT: G 13 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7728 (ttmt) REVERT: G 40 MET cc_start: 0.6973 (mtt) cc_final: 0.6697 (ttt) REVERT: G 68 MET cc_start: 0.7192 (tpp) cc_final: 0.6984 (mpp) REVERT: G 77 LYS cc_start: 0.8524 (mptt) cc_final: 0.8171 (mttp) REVERT: G 80 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7837 (mmmm) REVERT: G 112 SER cc_start: 0.7261 (m) cc_final: 0.6709 (p) REVERT: G 116 MET cc_start: 0.5546 (mmp) cc_final: 0.5060 (mmp) REVERT: G 124 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7496 (tm-30) REVERT: G 168 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7878 (mttt) REVERT: G 175 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7561 (pt) REVERT: G 222 SER cc_start: 0.8099 (t) cc_final: 0.7740 (p) REVERT: G 229 MET cc_start: 0.5131 (mtm) cc_final: 0.4806 (mtm) REVERT: H 25 GLU cc_start: 0.7941 (mp0) cc_final: 0.7475 (mp0) REVERT: H 80 LYS cc_start: 0.8236 (tttt) cc_final: 0.7908 (ttmm) REVERT: H 130 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7323 (tm-30) outliers start: 47 outliers final: 31 residues processed: 346 average time/residue: 0.1179 time to fit residues: 57.9779 Evaluate side-chains 348 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 313 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** G 213 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.160652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132223 restraints weight = 18583.651| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.58 r_work: 0.3578 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12137 Z= 0.189 Angle : 0.603 7.819 16670 Z= 0.320 Chirality : 0.043 0.217 1923 Planarity : 0.004 0.045 1906 Dihedral : 18.723 67.140 2090 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.03 % Allowed : 23.96 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.23), residues: 1317 helix: 1.31 (0.23), residues: 505 sheet: 0.62 (0.29), residues: 346 loop : -0.39 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 146 TYR 0.036 0.003 TYR A 375 PHE 0.090 0.002 PHE F 215 TRP 0.010 0.002 TRP A 708 HIS 0.007 0.001 HIS F 246 Details of bonding type rmsd covalent geometry : bond 0.00424 (12136) covalent geometry : angle 0.60289 (16668) SS BOND : bond 0.00347 ( 1) SS BOND : angle 0.16479 ( 2) hydrogen bonds : bond 0.03751 ( 646) hydrogen bonds : angle 4.91994 ( 1778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 324 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6796 (tp30) cc_final: 0.6559 (mm-30) REVERT: A 425 LYS cc_start: 0.8658 (tttt) cc_final: 0.8442 (ttpp) REVERT: A 591 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7759 (ttp-110) REVERT: A 632 GLN cc_start: 0.8028 (tp40) cc_final: 0.7789 (mm-40) REVERT: A 869 ASP cc_start: 0.7415 (m-30) cc_final: 0.7155 (m-30) REVERT: A 884 GLU cc_start: 0.7941 (tp30) cc_final: 0.7719 (tp30) REVERT: A 889 LEU cc_start: 0.8153 (tp) cc_final: 0.7911 (tp) REVERT: A 910 GLU cc_start: 0.7859 (tp30) cc_final: 0.7610 (tp30) REVERT: A 947 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 961 LEU cc_start: 0.8003 (mt) cc_final: 0.7793 (mt) REVERT: A 970 HIS cc_start: 0.7216 (m-70) cc_final: 0.6990 (m90) REVERT: F 16 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8060 (mm) REVERT: F 135 CYS cc_start: 0.7738 (p) cc_final: 0.7498 (t) REVERT: F 193 GLU cc_start: 0.7396 (mp0) cc_final: 0.7016 (mp0) REVERT: G 12 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (tt) REVERT: G 13 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7730 (ttmt) REVERT: G 40 MET cc_start: 0.7008 (mtt) cc_final: 0.6732 (ttt) REVERT: G 68 MET cc_start: 0.7326 (tpp) cc_final: 0.7088 (mpp) REVERT: G 77 LYS cc_start: 0.8589 (mptt) cc_final: 0.8319 (mttp) REVERT: G 116 MET cc_start: 0.5568 (mmp) cc_final: 0.5086 (mmp) REVERT: G 124 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7503 (tm-30) REVERT: G 168 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: G 175 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7569 (pt) REVERT: G 199 MET cc_start: 0.7182 (tmm) cc_final: 0.6800 (ttp) REVERT: G 222 SER cc_start: 0.8159 (t) cc_final: 0.7792 (p) REVERT: G 229 MET cc_start: 0.5106 (mtm) cc_final: 0.4796 (mtm) REVERT: H 25 GLU cc_start: 0.7955 (mp0) cc_final: 0.7473 (mp0) REVERT: H 80 LYS cc_start: 0.8283 (tttt) cc_final: 0.7956 (ttmm) REVERT: H 119 MET cc_start: 0.4303 (OUTLIER) cc_final: 0.2515 (tmm) REVERT: H 130 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7331 (tm-30) REVERT: H 148 CYS cc_start: 0.8106 (m) cc_final: 0.7639 (m) REVERT: H 169 PHE cc_start: 0.7500 (m-80) cc_final: 0.7290 (m-80) outliers start: 59 outliers final: 37 residues processed: 353 average time/residue: 0.1204 time to fit residues: 60.3008 Evaluate side-chains 354 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 116 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.0470 chunk 125 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN G 184 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.162583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134227 restraints weight = 18461.128| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.58 r_work: 0.3603 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12137 Z= 0.151 Angle : 0.600 7.384 16670 Z= 0.315 Chirality : 0.043 0.221 1923 Planarity : 0.004 0.049 1906 Dihedral : 18.692 67.586 2090 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.75 % Allowed : 24.64 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.23), residues: 1317 helix: 1.37 (0.23), residues: 505 sheet: 0.64 (0.29), residues: 346 loop : -0.38 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 752 TYR 0.036 0.002 TYR A 375 PHE 0.025 0.001 PHE F 215 TRP 0.010 0.002 TRP A 708 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00340 (12136) covalent geometry : angle 0.59963 (16668) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.15395 ( 2) hydrogen bonds : bond 0.03488 ( 646) hydrogen bonds : angle 4.83701 ( 1778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 325 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8663 (tttt) cc_final: 0.8442 (ttpp) REVERT: A 632 GLN cc_start: 0.8018 (tp40) cc_final: 0.7805 (mm-40) REVERT: A 697 ARG cc_start: 0.7234 (ttm-80) cc_final: 0.6968 (mtp85) REVERT: A 834 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6674 (mm-30) REVERT: A 869 ASP cc_start: 0.7347 (m-30) cc_final: 0.7104 (m-30) REVERT: A 889 LEU cc_start: 0.8104 (tp) cc_final: 0.7883 (tp) REVERT: A 947 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 967 GLN cc_start: 0.7882 (tp40) cc_final: 0.7448 (tp40) REVERT: A 970 HIS cc_start: 0.7157 (m-70) cc_final: 0.6929 (m90) REVERT: A 1002 GLU cc_start: 0.8323 (pt0) cc_final: 0.7914 (pt0) REVERT: F 16 LEU cc_start: 0.8278 (mm) cc_final: 0.8044 (mm) REVERT: F 85 GLU cc_start: 0.7408 (pm20) cc_final: 0.7161 (pm20) REVERT: F 159 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (m) REVERT: F 193 GLU cc_start: 0.7358 (mp0) cc_final: 0.6966 (mp0) REVERT: F 214 PHE cc_start: 0.7379 (m-10) cc_final: 0.7069 (m-10) REVERT: G 12 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8630 (tt) REVERT: G 13 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7739 (ttmt) REVERT: G 40 MET cc_start: 0.6972 (mtt) cc_final: 0.6709 (ttt) REVERT: G 68 MET cc_start: 0.7310 (tpp) cc_final: 0.7029 (mpp) REVERT: G 116 MET cc_start: 0.5462 (mmp) cc_final: 0.5041 (mmp) REVERT: G 122 ASP cc_start: 0.6694 (t0) cc_final: 0.6311 (t0) REVERT: G 124 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7516 (tm-30) REVERT: G 151 LEU cc_start: 0.8539 (mp) cc_final: 0.8160 (mt) REVERT: G 168 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7875 (mttt) REVERT: G 199 MET cc_start: 0.7269 (tmm) cc_final: 0.6898 (ttp) REVERT: G 222 SER cc_start: 0.8165 (t) cc_final: 0.7799 (p) REVERT: G 229 MET cc_start: 0.5099 (mtm) cc_final: 0.4768 (mtm) REVERT: H 25 GLU cc_start: 0.7947 (mp0) cc_final: 0.7442 (mp0) REVERT: H 80 LYS cc_start: 0.8242 (tttt) cc_final: 0.7913 (ttmm) REVERT: H 119 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.2759 (tmm) REVERT: H 130 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7375 (tm-30) REVERT: H 148 CYS cc_start: 0.8107 (m) cc_final: 0.7639 (m) REVERT: H 169 PHE cc_start: 0.7498 (m-80) cc_final: 0.7294 (m-80) REVERT: H 199 MET cc_start: 0.4490 (mtt) cc_final: 0.4046 (mmm) outliers start: 44 outliers final: 31 residues processed: 348 average time/residue: 0.1268 time to fit residues: 62.5642 Evaluate side-chains 352 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** 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 = 0.4100 r_free = 0.4100 target = 0.162162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133696 restraints weight = 18526.042| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.59 r_work: 0.3589 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12137 Z= 0.164 Angle : 0.618 8.064 16670 Z= 0.323 Chirality : 0.043 0.225 1923 Planarity : 0.004 0.039 1906 Dihedral : 18.710 67.707 2090 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.67 % Allowed : 25.32 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.23), residues: 1317 helix: 1.36 (0.23), residues: 506 sheet: 0.62 (0.29), residues: 346 loop : -0.42 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 752 TYR 0.038 0.002 TYR A 375 PHE 0.029 0.002 PHE F 215 TRP 0.010 0.002 TRP A 708 HIS 0.006 0.001 HIS F 246 Details of bonding type rmsd covalent geometry : bond 0.00372 (12136) covalent geometry : angle 0.61823 (16668) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.16502 ( 2) hydrogen bonds : bond 0.03528 ( 646) hydrogen bonds : angle 4.79946 ( 1778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6703 (tp30) cc_final: 0.6493 (mm-30) REVERT: A 632 GLN cc_start: 0.7973 (tp40) cc_final: 0.7750 (mm-40) REVERT: A 723 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: A 834 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 869 ASP cc_start: 0.7382 (m-30) cc_final: 0.7113 (m-30) REVERT: A 884 GLU cc_start: 0.7933 (tp30) cc_final: 0.7711 (tp30) REVERT: A 889 LEU cc_start: 0.8131 (tp) cc_final: 0.7910 (tp) REVERT: A 947 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 967 GLN cc_start: 0.7790 (tp40) cc_final: 0.7361 (tp40) REVERT: F 16 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (mm) REVERT: F 85 GLU cc_start: 0.7431 (pm20) cc_final: 0.7109 (pm20) REVERT: F 159 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8162 (m) REVERT: F 193 GLU cc_start: 0.7370 (mp0) cc_final: 0.6973 (mp0) REVERT: F 214 PHE cc_start: 0.7422 (m-10) cc_final: 0.7118 (m-10) REVERT: G 13 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7641 (ttmt) REVERT: G 40 MET cc_start: 0.7026 (mtt) cc_final: 0.6755 (ttt) REVERT: G 78 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7095 (mm) REVERT: G 116 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.5080 (mmp) REVERT: G 122 ASP cc_start: 0.6719 (t0) cc_final: 0.6353 (t0) REVERT: G 124 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7529 (tm-30) REVERT: G 138 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7459 (tmtt) REVERT: G 164 LYS cc_start: 0.8568 (mttt) cc_final: 0.8353 (mttt) REVERT: G 168 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7919 (mttt) REVERT: G 199 MET cc_start: 0.7287 (tmm) cc_final: 0.6923 (ttp) REVERT: G 222 SER cc_start: 0.8205 (t) cc_final: 0.7842 (p) REVERT: G 229 MET cc_start: 0.5246 (mtm) cc_final: 0.4910 (mtm) REVERT: G 247 LEU cc_start: 0.7859 (tp) cc_final: 0.7564 (tt) REVERT: H 25 GLU cc_start: 0.7944 (mp0) cc_final: 0.7421 (mp0) REVERT: H 80 LYS cc_start: 0.8239 (tttt) cc_final: 0.7921 (ttmm) REVERT: H 119 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.2750 (tmm) REVERT: H 130 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7358 (tm-30) REVERT: H 148 CYS cc_start: 0.8068 (m) cc_final: 0.7606 (m) outliers start: 43 outliers final: 30 residues processed: 348 average time/residue: 0.1243 time to fit residues: 60.7885 Evaluate side-chains 359 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 55 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** 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 = 0.4100 r_free = 0.4100 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133692 restraints weight = 18376.130| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.56 r_work: 0.3581 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12137 Z= 0.168 Angle : 0.630 9.322 16670 Z= 0.328 Chirality : 0.043 0.229 1923 Planarity : 0.004 0.049 1906 Dihedral : 18.747 68.227 2090 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.84 % Allowed : 25.83 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.23), residues: 1317 helix: 1.34 (0.23), residues: 505 sheet: 0.60 (0.29), residues: 346 loop : -0.47 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 752 TYR 0.034 0.002 TYR A 375 PHE 0.029 0.001 PHE F 215 TRP 0.010 0.002 TRP A 847 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00382 (12136) covalent geometry : angle 0.63053 (16668) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.16158 ( 2) hydrogen bonds : bond 0.03576 ( 646) hydrogen bonds : angle 4.82744 ( 1778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6849 (tp30) cc_final: 0.6626 (mm-30) REVERT: A 632 GLN cc_start: 0.7962 (tp40) cc_final: 0.7749 (mm-40) REVERT: A 778 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7575 (mmmt) REVERT: A 834 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6661 (mm-30) REVERT: A 869 ASP cc_start: 0.7444 (m-30) cc_final: 0.7170 (m-30) REVERT: A 884 GLU cc_start: 0.7943 (tp30) cc_final: 0.7718 (tp30) REVERT: A 889 LEU cc_start: 0.8141 (tp) cc_final: 0.7925 (tp) REVERT: A 947 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 967 GLN cc_start: 0.7767 (tp40) cc_final: 0.7349 (tp40) REVERT: F 16 LEU cc_start: 0.8269 (mm) cc_final: 0.8056 (mm) REVERT: F 85 GLU cc_start: 0.7567 (pm20) cc_final: 0.7191 (pm20) REVERT: F 135 CYS cc_start: 0.7754 (p) cc_final: 0.7338 (t) REVERT: F 159 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8154 (m) REVERT: F 193 GLU cc_start: 0.7371 (mp0) cc_final: 0.6955 (mp0) REVERT: F 214 PHE cc_start: 0.7363 (m-10) cc_final: 0.7073 (m-10) REVERT: G 12 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8765 (tp) REVERT: G 13 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7666 (ttmt) REVERT: G 40 MET cc_start: 0.7015 (mtt) cc_final: 0.6738 (ttt) REVERT: G 78 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7074 (mm) REVERT: G 116 MET cc_start: 0.5503 (OUTLIER) cc_final: 0.5121 (mmp) REVERT: G 122 ASP cc_start: 0.6743 (t0) cc_final: 0.6377 (t0) REVERT: G 124 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7514 (tm-30) REVERT: G 138 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7443 (tmtt) REVERT: G 164 LYS cc_start: 0.8579 (mttt) cc_final: 0.8332 (mttt) REVERT: G 168 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7932 (mttt) REVERT: G 199 MET cc_start: 0.7298 (tmm) cc_final: 0.6954 (ttp) REVERT: G 222 SER cc_start: 0.8221 (t) cc_final: 0.7846 (p) REVERT: G 229 MET cc_start: 0.5226 (mtm) cc_final: 0.4913 (mtm) REVERT: H 25 GLU cc_start: 0.7933 (mp0) cc_final: 0.7409 (mp0) REVERT: H 80 LYS cc_start: 0.8237 (tttt) cc_final: 0.7918 (ttmm) REVERT: H 119 MET cc_start: 0.4454 (OUTLIER) cc_final: 0.2695 (tmm) REVERT: H 130 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7352 (tm-30) REVERT: H 148 CYS cc_start: 0.8061 (m) cc_final: 0.7599 (m) outliers start: 45 outliers final: 29 residues processed: 338 average time/residue: 0.1262 time to fit residues: 59.5190 Evaluate side-chains 345 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 0.0060 chunk 30 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.0370 chunk 90 optimal weight: 0.8980 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134437 restraints weight = 18567.549| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.59 r_work: 0.3596 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12137 Z= 0.147 Angle : 0.625 8.010 16670 Z= 0.326 Chirality : 0.043 0.229 1923 Planarity : 0.004 0.059 1906 Dihedral : 18.685 68.483 2090 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.41 % Allowed : 26.34 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.23), residues: 1317 helix: 1.36 (0.23), residues: 507 sheet: 0.56 (0.29), residues: 347 loop : -0.47 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.035 0.002 TYR A 375 PHE 0.026 0.002 PHE F 215 TRP 0.010 0.002 TRP A 847 HIS 0.005 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00334 (12136) covalent geometry : angle 0.62471 (16668) SS BOND : bond 0.00318 ( 1) SS BOND : angle 0.08636 ( 2) hydrogen bonds : bond 0.03430 ( 646) hydrogen bonds : angle 4.77630 ( 1778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 632 GLN cc_start: 0.7923 (tp40) cc_final: 0.7719 (mm-40) REVERT: A 778 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7579 (mmmt) REVERT: A 869 ASP cc_start: 0.7411 (m-30) cc_final: 0.7139 (m-30) REVERT: A 895 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 896 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7717 (mm-30) REVERT: A 947 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 967 GLN cc_start: 0.7915 (tp40) cc_final: 0.7444 (tp40) REVERT: F 16 LEU cc_start: 0.8279 (mm) cc_final: 0.8067 (mm) REVERT: F 85 GLU cc_start: 0.7601 (pm20) cc_final: 0.7080 (pm20) REVERT: F 193 GLU cc_start: 0.7329 (mp0) cc_final: 0.6912 (mp0) REVERT: F 214 PHE cc_start: 0.7305 (m-10) cc_final: 0.7027 (m-10) REVERT: G 12 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8742 (tp) REVERT: G 13 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7622 (ttmt) REVERT: G 40 MET cc_start: 0.6979 (mtt) cc_final: 0.6701 (ttt) REVERT: G 68 MET cc_start: 0.7469 (tpp) cc_final: 0.7156 (mpp) REVERT: G 78 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7051 (mm) REVERT: G 116 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5065 (mmp) REVERT: G 122 ASP cc_start: 0.6706 (t0) cc_final: 0.6358 (t0) REVERT: G 124 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7573 (tm-30) REVERT: G 138 LYS cc_start: 0.7735 (tmtt) cc_final: 0.7449 (tmtt) REVERT: G 164 LYS cc_start: 0.8586 (mttt) cc_final: 0.8337 (mttt) REVERT: G 168 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (mttt) REVERT: G 199 MET cc_start: 0.7288 (tmm) cc_final: 0.7016 (ttp) REVERT: G 222 SER cc_start: 0.8193 (t) cc_final: 0.7808 (p) REVERT: G 229 MET cc_start: 0.5233 (mtm) cc_final: 0.4915 (mtm) REVERT: H 25 GLU cc_start: 0.7900 (mp0) cc_final: 0.7402 (mp0) REVERT: H 80 LYS cc_start: 0.8208 (tttt) cc_final: 0.7853 (ttmm) REVERT: H 119 MET cc_start: 0.4437 (OUTLIER) cc_final: 0.2504 (tmm) REVERT: H 130 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7362 (tm-30) REVERT: H 148 CYS cc_start: 0.8088 (m) cc_final: 0.7624 (m) outliers start: 40 outliers final: 29 residues processed: 327 average time/residue: 0.1279 time to fit residues: 58.2555 Evaluate side-chains 333 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.161781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133325 restraints weight = 18659.543| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.59 r_work: 0.3572 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12137 Z= 0.183 Angle : 0.653 8.733 16670 Z= 0.340 Chirality : 0.044 0.231 1923 Planarity : 0.004 0.038 1906 Dihedral : 18.716 68.588 2089 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.15 % Allowed : 26.34 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1317 helix: 1.24 (0.23), residues: 506 sheet: 0.59 (0.29), residues: 346 loop : -0.55 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.036 0.002 TYR A 375 PHE 0.031 0.002 PHE F 215 TRP 0.011 0.002 TRP A 919 HIS 0.004 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00416 (12136) covalent geometry : angle 0.65275 (16668) SS BOND : bond 0.00335 ( 1) SS BOND : angle 0.13950 ( 2) hydrogen bonds : bond 0.03677 ( 646) hydrogen bonds : angle 4.84467 ( 1778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3043.18 seconds wall clock time: 53 minutes 11.81 seconds (3191.81 seconds total)