Starting phenix.real_space_refine on Fri Jul 3 03:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_19850.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_19850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_19850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_19850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2026/9eoa_19850.map" } 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-dev-6108/lib/python3.11/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: 2.73, per 1000 atoms: 0.23 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: 0.96 Conformation dependent library (CDL) restraints added in 560.0 milliseconds 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: 1.35 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: 2.50 Time building geometry restraints manager: 1.30 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=" C3' DC B 4 " pdb=" C2' DC B 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+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 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15671 1.81 - 3.63: 857 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: 1436 0.055 - 0.110: 376 0.110 - 0.164: 76 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: 2.390 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: 13.180 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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= 0.424 Angle : 0.885 9.073 16670 Z= 0.612 Chirality : 0.057 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 are 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/Z covalent geometry : bond 0.00598 / 0.42 (12136) covalent geometry : angle 0.88414 / 0.61 (16668) SS BOND : bond 0.02797 / 1.47 ( 1) SS BOND : angle 3.34981 / 1.90 ( 2) hydrogen bonds : bond 0.17757 / 11.15 ( 646) hydrogen bonds : angle 7.24017 / 5.12 ( 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 : 0.398 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: 0.7367 (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: 0.1041 time to fit residues: 52.2665 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 : 0.346 ------------------------------------------------------------------------------- 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... A 389 ASN A 490 ASN A 495 GLN ** A 718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS A 861 ASN A 929 GLN G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133144 restraints weight = 18340.436| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.56 r_work: 0.3584 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12137 Z= 0.219 Angle : 0.659 7.077 16670 Z= 0.361 Chirality : 0.046 0.227 1923 Planarity : 0.004 0.046 1906 Dihedral : 19.248 65.476 2148 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.92 % Allowed : 22.42 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1317 helix: 1.02 (0.23), residues: 504 sheet: 0.67 (0.28), residues: 351 loop : -0.39 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 952 TYR 0.016 0.002 TYR A 418 PHE 0.021 0.002 PHE F 169 TRP 0.013 0.002 TRP A 664 HIS 0.004 0.001 HIS H 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (12136) covalent geometry : angle 0.65945 / 0.36 (16668) SS BOND : bond 0.00876 / 0.46 ( 1) SS BOND : angle 0.80641 / 0.45 ( 2) hydrogen bonds : bond 0.05021 / 3.31 ( 646) hydrogen bonds : angle 5.75352 / 4.02 ( 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 359 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8564 (tttt) cc_final: 0.8268 (ttpp) REVERT: A 628 LYS cc_start: 0.7499 (tmtt) cc_final: 0.7114 (tmtt) REVERT: A 632 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7284 (tp-100) REVERT: A 842 TYR cc_start: 0.8476 (t80) cc_final: 0.8165 (t80) REVERT: A 888 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7291 (mm-40) REVERT: A 889 LEU cc_start: 0.8132 (tp) cc_final: 0.7892 (tp) REVERT: A 929 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7548 (mm-40) REVERT: A 932 VAL cc_start: 0.8489 (t) cc_final: 0.8250 (p) REVERT: A 947 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 950 ASP cc_start: 0.7435 (p0) cc_final: 0.7012 (p0) REVERT: A 1002 GLU cc_start: 0.8351 (pt0) cc_final: 0.7859 (pt0) REVERT: F 16 LEU cc_start: 0.8241 (mm) cc_final: 0.8002 (mm) REVERT: F 167 VAL cc_start: 0.7525 (OUTLIER) cc_final: 0.7276 (m) REVERT: F 193 GLU cc_start: 0.7436 (mp0) cc_final: 0.7214 (mp0) REVERT: G 29 ASP cc_start: 0.7101 (t0) cc_final: 0.6736 (t0) REVERT: G 138 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7226 (tmtt) REVERT: G 168 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (mttt) REVERT: G 222 SER cc_start: 0.7894 (t) cc_final: 0.7542 (p) REVERT: G 229 MET cc_start: 0.5061 (mtm) cc_final: 0.4725 (mtm) REVERT: G 232 ASP cc_start: 0.7854 (m-30) cc_final: 0.7625 (m-30) REVERT: G 244 MET cc_start: 0.8118 (tmm) cc_final: 0.7775 (tmm) REVERT: H 227 LEU cc_start: 0.7222 (mp) cc_final: 0.6936 (mp) outliers start: 46 outliers final: 27 residues processed: 337 average time/residue: 0.1023 time to fit residues: 48.8798 Evaluate side-chains 342 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 929 GLN Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 70 VAL 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 203 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE 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: 0.9990 chunk 124 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 ASN A 779 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133178 restraints weight = 18552.116| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.66 r_work: 0.3589 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12137 Z= 0.166 Angle : 0.612 7.000 16670 Z= 0.334 Chirality : 0.043 0.244 1923 Planarity : 0.004 0.057 1906 Dihedral : 19.155 65.806 2108 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.01 % Allowed : 22.42 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1317 helix: 1.14 (0.23), residues: 504 sheet: 0.52 (0.28), residues: 347 loop : -0.29 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 61 TYR 0.027 0.002 TYR A 375 PHE 0.018 0.001 PHE F 215 TRP 0.010 0.002 TRP A 847 HIS 0.006 0.001 HIS H 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12136) covalent geometry : angle 0.61210 / 0.33 (16668) SS BOND : bond 0.00499 / 0.26 ( 1) SS BOND : angle 0.31858 / 0.18 ( 2) hydrogen bonds : bond 0.04291 / 2.82 ( 646) hydrogen bonds : angle 5.46158 / 3.81 ( 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 367 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8585 (tttt) cc_final: 0.8285 (ttpp) REVERT: A 457 GLN cc_start: 0.7563 (mt0) cc_final: 0.7289 (mt0) REVERT: A 605 TYR cc_start: 0.8597 (t80) cc_final: 0.8305 (t80) REVERT: A 628 LYS cc_start: 0.7379 (tmtt) cc_final: 0.7042 (tmtt) REVERT: A 632 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7264 (tp-100) REVERT: A 689 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6301 (mm-30) REVERT: A 722 LEU cc_start: 0.7984 (mp) cc_final: 0.7747 (mt) REVERT: A 723 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: A 910 GLU cc_start: 0.7772 (tp30) cc_final: 0.7422 (tp30) REVERT: A 929 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: A 932 VAL cc_start: 0.8513 (t) cc_final: 0.8248 (p) REVERT: A 950 ASP cc_start: 0.7377 (p0) cc_final: 0.6900 (p0) REVERT: F 16 LEU cc_start: 0.8249 (mm) cc_final: 0.7996 (mm) REVERT: F 85 GLU cc_start: 0.7519 (pm20) cc_final: 0.7206 (pm20) REVERT: F 193 GLU cc_start: 0.7460 (mp0) cc_final: 0.7184 (mp0) REVERT: F 214 PHE cc_start: 0.7575 (m-10) cc_final: 0.7198 (m-10) REVERT: G 77 LYS cc_start: 0.8477 (mptt) cc_final: 0.8016 (mptt) REVERT: G 80 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7795 (mmmm) REVERT: G 116 MET cc_start: 0.5769 (mmp) cc_final: 0.5078 (mmp) REVERT: G 119 MET cc_start: 0.5710 (mmt) cc_final: 0.5418 (mmp) REVERT: G 124 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7622 (tm-30) REVERT: G 138 LYS cc_start: 0.7674 (tmtt) cc_final: 0.7161 (tmtt) REVERT: G 222 SER cc_start: 0.7896 (t) cc_final: 0.7529 (p) REVERT: G 229 MET cc_start: 0.5090 (mtm) cc_final: 0.4756 (mtm) REVERT: G 232 ASP cc_start: 0.7869 (m-30) cc_final: 0.7659 (m-30) REVERT: G 244 MET cc_start: 0.8125 (tmm) cc_final: 0.7715 (tmm) REVERT: H 130 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7163 (tm-30) outliers start: 47 outliers final: 28 residues processed: 343 average time/residue: 0.0998 time to fit residues: 47.8264 Evaluate side-chains 345 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 224 THR 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 F residue 255 ILE Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 158 VAL 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 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** A 929 GLN ** 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 = 0.4102 r_free = 0.4102 target = 0.162840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133758 restraints weight = 18565.348| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.66 r_work: 0.3594 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12137 Z= 0.145 Angle : 0.589 7.218 16670 Z= 0.320 Chirality : 0.043 0.237 1923 Planarity : 0.004 0.060 1906 Dihedral : 19.141 66.185 2101 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.75 % Allowed : 23.61 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1317 helix: 1.33 (0.23), residues: 504 sheet: 0.42 (0.28), residues: 347 loop : -0.26 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 952 TYR 0.028 0.002 TYR A 375 PHE 0.050 0.001 PHE F 215 TRP 0.014 0.002 TRP A 901 HIS 0.006 0.001 HIS H 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12136) covalent geometry : angle 0.58925 / 0.32 (16668) SS BOND : bond 0.00417 / 0.22 ( 1) SS BOND : angle 0.19762 / 0.12 ( 2) hydrogen bonds : bond 0.03868 / 2.56 ( 646) hydrogen bonds : angle 5.21599 / 3.65 ( 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 357 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6797 (tp30) cc_final: 0.6567 (mm-30) REVERT: A 425 LYS cc_start: 0.8585 (tttt) cc_final: 0.8353 (ttpp) REVERT: A 459 GLU cc_start: 0.7317 (pm20) cc_final: 0.7102 (pm20) REVERT: A 628 LYS cc_start: 0.7333 (tmtt) cc_final: 0.7005 (tmtt) REVERT: A 632 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7245 (tp-100) REVERT: A 932 VAL cc_start: 0.8472 (t) cc_final: 0.8233 (p) REVERT: A 950 ASP cc_start: 0.7297 (p0) cc_final: 0.6864 (p0) REVERT: A 982 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: A 1002 GLU cc_start: 0.8352 (pt0) cc_final: 0.8009 (pt0) REVERT: F 16 LEU cc_start: 0.8249 (mm) cc_final: 0.8023 (mm) REVERT: F 80 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8268 (mtmt) REVERT: F 167 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7183 (m) REVERT: F 193 GLU cc_start: 0.7441 (mp0) cc_final: 0.7143 (mp0) REVERT: F 214 PHE cc_start: 0.7560 (m-10) cc_final: 0.7287 (m-10) REVERT: F 248 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7903 (mtmt) REVERT: G 40 MET cc_start: 0.7039 (mtt) cc_final: 0.6723 (ttt) REVERT: G 80 LYS cc_start: 0.8045 (mmtp) cc_final: 0.7801 (mmmm) REVERT: G 116 MET cc_start: 0.5837 (mmp) cc_final: 0.5047 (mmp) REVERT: G 119 MET cc_start: 0.5682 (mmt) cc_final: 0.5447 (mmp) REVERT: G 124 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7398 (tm-30) REVERT: G 138 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7155 (tmtt) REVERT: G 222 SER cc_start: 0.7896 (t) cc_final: 0.7560 (p) REVERT: G 229 MET cc_start: 0.5120 (mtm) cc_final: 0.4765 (mtm) REVERT: G 244 MET cc_start: 0.8145 (tmm) cc_final: 0.7716 (tmm) REVERT: H 130 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7268 (tm-30) REVERT: H 237 VAL cc_start: 0.6303 (OUTLIER) cc_final: 0.6086 (p) outliers start: 44 outliers final: 27 residues processed: 335 average time/residue: 0.0953 time to fit residues: 44.8487 Evaluate side-chains 334 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 662 VAL Chi-restraints excluded: chain A residue 675 GLU 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 F residue 3 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 11 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 Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 25 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 0.0370 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 929 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 = 0.4105 r_free = 0.4105 target = 0.162994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134232 restraints weight = 18603.114| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.63 r_work: 0.3595 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12137 Z= 0.150 Angle : 0.593 6.853 16670 Z= 0.321 Chirality : 0.043 0.235 1923 Planarity : 0.004 0.045 1906 Dihedral : 18.999 66.050 2093 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.09 % Allowed : 23.44 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1317 helix: 1.37 (0.23), residues: 505 sheet: 0.39 (0.28), residues: 347 loop : -0.26 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 61 TYR 0.030 0.002 TYR A 375 PHE 0.080 0.002 PHE F 215 TRP 0.013 0.002 TRP A 901 HIS 0.006 0.001 HIS H 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12136) covalent geometry : angle 0.59289 / 0.32 (16668) SS BOND : bond 0.00412 / 0.22 ( 1) SS BOND : angle 0.14281 / 0.08 ( 2) hydrogen bonds : bond 0.03789 / 2.53 ( 646) hydrogen bonds : angle 5.13895 / 3.61 ( 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 353 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8593 (tttt) cc_final: 0.8358 (ttpp) REVERT: A 459 GLU cc_start: 0.7358 (pm20) cc_final: 0.7085 (pm20) REVERT: A 591 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7764 (ttp-110) REVERT: A 722 LEU cc_start: 0.8021 (mp) cc_final: 0.7807 (mt) REVERT: A 834 GLU cc_start: 0.7065 (tp30) cc_final: 0.6759 (tp30) REVERT: A 929 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7578 (mm-40) REVERT: A 932 VAL cc_start: 0.8468 (t) cc_final: 0.8221 (p) REVERT: A 947 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 950 ASP cc_start: 0.7319 (p0) cc_final: 0.6854 (p0) REVERT: A 982 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8260 (mtm-85) REVERT: F 16 LEU cc_start: 0.8244 (mm) cc_final: 0.8033 (mm) REVERT: F 80 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8300 (mtpt) REVERT: F 167 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7132 (m) REVERT: F 193 GLU cc_start: 0.7406 (mp0) cc_final: 0.7121 (mp0) REVERT: F 214 PHE cc_start: 0.7482 (m-10) cc_final: 0.7279 (m-10) REVERT: G 40 MET cc_start: 0.7055 (mtt) cc_final: 0.6726 (ttt) REVERT: G 77 LYS cc_start: 0.8539 (mptt) cc_final: 0.8122 (mmtm) REVERT: G 80 LYS cc_start: 0.8064 (mmtp) cc_final: 0.7824 (mmmm) REVERT: G 116 MET cc_start: 0.5776 (mmp) cc_final: 0.4978 (mmp) REVERT: G 119 MET cc_start: 0.5654 (mmt) cc_final: 0.5438 (mmp) REVERT: G 124 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7273 (tm-30) REVERT: G 138 LYS cc_start: 0.7701 (tmtt) cc_final: 0.7169 (tmtt) REVERT: G 222 SER cc_start: 0.7983 (t) cc_final: 0.7649 (p) REVERT: G 229 MET cc_start: 0.5062 (mtm) cc_final: 0.4704 (mtm) REVERT: G 244 MET cc_start: 0.8160 (tmm) cc_final: 0.7895 (tmm) REVERT: H 80 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8022 (ttmm) REVERT: H 130 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7343 (tm-30) outliers start: 48 outliers final: 29 residues processed: 330 average time/residue: 0.0944 time to fit residues: 44.1293 Evaluate side-chains 330 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 237 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 832 HIS A 929 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133059 restraints weight = 18556.378| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.61 r_work: 0.3583 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12137 Z= 0.197 Angle : 0.618 7.044 16670 Z= 0.333 Chirality : 0.044 0.230 1923 Planarity : 0.004 0.041 1906 Dihedral : 19.000 65.963 2093 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.35 % Allowed : 24.47 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1317 helix: 1.29 (0.23), residues: 504 sheet: 0.45 (0.28), residues: 345 loop : -0.32 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 61 TYR 0.031 0.003 TYR A 375 PHE 0.094 0.002 PHE F 215 TRP 0.010 0.002 TRP A 906 HIS 0.011 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (12136) covalent geometry : angle 0.61845 / 0.33 (16668) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 0.16184 / 0.09 ( 2) hydrogen bonds : bond 0.03988 / 2.67 ( 646) hydrogen bonds : angle 5.14024 / 3.62 ( 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 352 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8599 (tttt) cc_final: 0.8379 (ttpp) REVERT: A 459 GLU cc_start: 0.7344 (pm20) cc_final: 0.7061 (pm20) REVERT: A 476 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7145 (mt-10) REVERT: A 591 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7810 (ttp-110) REVERT: A 628 LYS cc_start: 0.7346 (tmtt) cc_final: 0.7113 (tmtt) REVERT: A 834 GLU cc_start: 0.7066 (tp30) cc_final: 0.6810 (tp30) REVERT: A 929 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: A 932 VAL cc_start: 0.8490 (t) cc_final: 0.8224 (p) REVERT: A 947 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7983 (mp) REVERT: F 16 LEU cc_start: 0.8280 (mm) cc_final: 0.8053 (mm) REVERT: F 80 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8315 (mtpt) REVERT: F 193 GLU cc_start: 0.7439 (mp0) cc_final: 0.7107 (mp0) REVERT: G 40 MET cc_start: 0.7083 (mtt) cc_final: 0.6749 (ttt) REVERT: G 80 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7820 (mmmm) REVERT: G 116 MET cc_start: 0.5818 (mmp) cc_final: 0.5113 (mmp) REVERT: G 119 MET cc_start: 0.5684 (mmt) cc_final: 0.5478 (mmp) REVERT: G 124 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7471 (tm-30) REVERT: G 138 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7190 (tmtt) REVERT: G 222 SER cc_start: 0.8028 (t) cc_final: 0.7708 (p) REVERT: G 229 MET cc_start: 0.5087 (mtm) cc_final: 0.4732 (mtm) REVERT: G 244 MET cc_start: 0.8167 (tmm) cc_final: 0.7878 (tmm) REVERT: H 80 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8027 (ttmm) REVERT: H 130 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7340 (tm-30) outliers start: 51 outliers final: 34 residues processed: 328 average time/residue: 0.0955 time to fit residues: 44.6474 Evaluate side-chains 332 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 522 VAL 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 772 MET Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 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 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 6 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 101 LEU 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: 0.5980 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 632 GLN A 929 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132130 restraints weight = 18383.151| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.68 r_work: 0.3574 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12137 Z= 0.206 Angle : 0.645 9.236 16670 Z= 0.344 Chirality : 0.045 0.243 1923 Planarity : 0.004 0.076 1906 Dihedral : 19.036 66.082 2091 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.18 % Allowed : 25.23 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.23), residues: 1317 helix: 1.18 (0.23), residues: 503 sheet: 0.46 (0.28), residues: 345 loop : -0.31 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 899 TYR 0.034 0.003 TYR A 375 PHE 0.099 0.002 PHE F 215 TRP 0.012 0.002 TRP A 906 HIS 0.010 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (12136) covalent geometry : angle 0.64486 / 0.34 (16668) SS BOND : bond 0.00426 / 0.22 ( 1) SS BOND : angle 0.15854 / 0.08 ( 2) hydrogen bonds : bond 0.04026 / 2.69 ( 646) hydrogen bonds : angle 5.15699 / 3.62 ( 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 357 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8615 (tttt) cc_final: 0.8396 (ttpp) REVERT: A 459 GLU cc_start: 0.7376 (pm20) cc_final: 0.7125 (pm20) REVERT: A 476 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 723 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: A 752 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7953 (mtp85) REVERT: A 895 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: A 929 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: A 932 VAL cc_start: 0.8485 (t) cc_final: 0.8229 (p) REVERT: A 947 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8013 (mp) REVERT: F 16 LEU cc_start: 0.8282 (mm) cc_final: 0.8057 (mm) REVERT: F 80 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8325 (mtpt) REVERT: F 193 GLU cc_start: 0.7463 (mp0) cc_final: 0.7132 (mp0) REVERT: G 40 MET cc_start: 0.7088 (mtt) cc_final: 0.6765 (ttt) REVERT: G 68 MET cc_start: 0.7135 (tpp) cc_final: 0.6896 (mpp) REVERT: G 116 MET cc_start: 0.5824 (mmp) cc_final: 0.5220 (mmp) REVERT: G 124 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7479 (tm-30) REVERT: G 138 LYS cc_start: 0.7773 (tmtt) cc_final: 0.7246 (tmtt) REVERT: G 222 SER cc_start: 0.8048 (t) cc_final: 0.7719 (p) REVERT: G 229 MET cc_start: 0.5103 (mtm) cc_final: 0.4766 (mtm) REVERT: G 244 MET cc_start: 0.8169 (tmm) cc_final: 0.7866 (tmm) REVERT: H 17 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7044 (mt-10) REVERT: H 25 GLU cc_start: 0.7935 (mp0) cc_final: 0.7442 (mp0) REVERT: H 80 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8031 (ttmm) REVERT: H 130 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7333 (tm-30) REVERT: H 180 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7153 (tt) outliers start: 49 outliers final: 39 residues processed: 331 average time/residue: 0.0964 time to fit residues: 45.2712 Evaluate side-chains 348 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 522 VAL 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 772 MET Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 SER 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 235 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 6 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 101 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 40 optimal weight: 0.0470 chunk 110 optimal weight: 0.0980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 632 GLN ** A 929 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.162318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133890 restraints weight = 18523.755| |-----------------------------------------------------------------------------| 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: 0.7400 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12137 Z= 0.147 Angle : 0.631 7.700 16670 Z= 0.335 Chirality : 0.044 0.263 1923 Planarity : 0.004 0.072 1906 Dihedral : 19.033 66.297 2091 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.58 % Allowed : 26.26 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1317 helix: 1.28 (0.23), residues: 503 sheet: 0.51 (0.29), residues: 343 loop : -0.32 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 146 TYR 0.034 0.002 TYR A 375 PHE 0.092 0.002 PHE F 215 TRP 0.011 0.002 TRP A 708 HIS 0.008 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (12136) covalent geometry : angle 0.63065 / 0.33 (16668) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 0.13561 / 0.07 ( 2) hydrogen bonds : bond 0.03750 / 2.51 ( 646) hydrogen bonds : angle 5.06770 / 3.56 ( 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 347 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 399 GLN cc_start: 0.6685 (tm-30) cc_final: 0.6415 (tt0) REVERT: A 403 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 425 LYS cc_start: 0.8608 (tttt) cc_final: 0.8392 (ttpp) REVERT: A 459 GLU cc_start: 0.7302 (pm20) cc_final: 0.7030 (pm20) REVERT: A 591 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7761 (ttp-110) REVERT: A 752 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7979 (mtp180) REVERT: A 910 GLU cc_start: 0.7789 (tp30) cc_final: 0.7454 (tp30) REVERT: A 932 VAL cc_start: 0.8488 (t) cc_final: 0.8234 (p) REVERT: A 947 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8008 (mp) REVERT: F 16 LEU cc_start: 0.8286 (mm) cc_final: 0.8056 (mm) REVERT: F 85 GLU cc_start: 0.7442 (pm20) cc_final: 0.7175 (pm20) REVERT: F 134 SER cc_start: 0.5882 (OUTLIER) cc_final: 0.5272 (p) REVERT: F 193 GLU cc_start: 0.7426 (mp0) cc_final: 0.7086 (mp0) REVERT: F 214 PHE cc_start: 0.7466 (m-10) cc_final: 0.7082 (m-10) REVERT: G 40 MET cc_start: 0.7033 (mtt) cc_final: 0.6731 (ttt) REVERT: G 68 MET cc_start: 0.7081 (tpp) cc_final: 0.6861 (mpp) REVERT: G 112 SER cc_start: 0.7260 (m) cc_final: 0.6562 (p) REVERT: G 116 MET cc_start: 0.5797 (mmp) cc_final: 0.5156 (mmp) REVERT: G 124 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7502 (tm-30) REVERT: G 138 LYS cc_start: 0.7810 (tmtt) cc_final: 0.7256 (tmtt) REVERT: G 222 SER cc_start: 0.8036 (t) cc_final: 0.7718 (p) REVERT: G 229 MET cc_start: 0.5019 (mtm) cc_final: 0.4713 (mtm) REVERT: G 244 MET cc_start: 0.8226 (tmm) cc_final: 0.7935 (tmm) REVERT: H 25 GLU cc_start: 0.7934 (mp0) cc_final: 0.7456 (mp0) REVERT: H 80 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7985 (ttmm) REVERT: H 130 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7280 (tm-30) outliers start: 42 outliers final: 29 residues processed: 329 average time/residue: 0.0933 time to fit residues: 44.1730 Evaluate side-chains 330 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE 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 662 VAL 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 3 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 6 LEU Chi-restraints excluded: chain H residue 101 LEU 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: 0.8980 chunk 133 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 GLN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** A 929 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.162174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133709 restraints weight = 18424.014| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.57 r_work: 0.3599 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12137 Z= 0.160 Angle : 0.648 8.487 16670 Z= 0.343 Chirality : 0.045 0.278 1923 Planarity : 0.004 0.076 1906 Dihedral : 19.003 66.053 2090 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.07 % Allowed : 27.11 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1317 helix: 1.26 (0.23), residues: 507 sheet: 0.53 (0.29), residues: 348 loop : -0.41 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 146 TYR 0.037 0.003 TYR A 375 PHE 0.030 0.002 PHE F 215 TRP 0.011 0.002 TRP A 901 HIS 0.008 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (12136) covalent geometry : angle 0.64818 / 0.34 (16668) SS BOND : bond 0.00397 / 0.21 ( 1) SS BOND : angle 0.15761 / 0.08 ( 2) hydrogen bonds : bond 0.03812 / 2.54 ( 646) hydrogen bonds : angle 5.01578 / 3.53 ( 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 337 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8632 (tttt) cc_final: 0.8427 (ttpp) REVERT: A 459 GLU cc_start: 0.7286 (pm20) cc_final: 0.7028 (pm20) REVERT: A 752 ARG cc_start: 0.8252 (mtp85) cc_final: 0.8003 (mtp180) REVERT: A 932 VAL cc_start: 0.8507 (t) cc_final: 0.8260 (p) REVERT: A 947 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (mp) REVERT: F 16 LEU cc_start: 0.8285 (mm) cc_final: 0.8052 (mm) REVERT: F 85 GLU cc_start: 0.7438 (pm20) cc_final: 0.7209 (pm20) REVERT: F 193 GLU cc_start: 0.7425 (mp0) cc_final: 0.7091 (mp0) REVERT: F 214 PHE cc_start: 0.7444 (m-10) cc_final: 0.7097 (m-10) REVERT: G 40 MET cc_start: 0.7037 (mtt) cc_final: 0.6741 (ttt) REVERT: G 68 MET cc_start: 0.7111 (tpp) cc_final: 0.6887 (mpp) REVERT: G 112 SER cc_start: 0.7259 (m) cc_final: 0.6725 (p) REVERT: G 116 MET cc_start: 0.5730 (mmp) cc_final: 0.5070 (mmp) REVERT: G 124 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7418 (tm-30) REVERT: G 138 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7307 (tmtt) REVERT: G 151 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7982 (mt) REVERT: G 222 SER cc_start: 0.8049 (t) cc_final: 0.7721 (p) REVERT: G 229 MET cc_start: 0.5079 (mtm) cc_final: 0.4726 (mtm) REVERT: G 244 MET cc_start: 0.8216 (tmm) cc_final: 0.7912 (tmm) REVERT: H 25 GLU cc_start: 0.7933 (mp0) cc_final: 0.7441 (mp0) REVERT: H 80 LYS cc_start: 0.8294 (ttmt) cc_final: 0.8006 (ttmm) REVERT: H 130 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7288 (tm-30) outliers start: 36 outliers final: 28 residues processed: 323 average time/residue: 0.0934 time to fit residues: 43.0722 Evaluate side-chains 339 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 662 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 6 LEU Chi-restraints excluded: chain H residue 101 LEU 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: 0.9990 chunk 30 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** A 929 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.161452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133105 restraints weight = 18593.701| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.58 r_work: 0.3590 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12137 Z= 0.177 Angle : 0.656 8.320 16670 Z= 0.349 Chirality : 0.045 0.238 1923 Planarity : 0.004 0.066 1906 Dihedral : 19.011 65.932 2090 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 26.94 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1317 helix: 1.23 (0.23), residues: 506 sheet: 0.59 (0.29), residues: 347 loop : -0.41 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 146 TYR 0.036 0.002 TYR A 375 PHE 0.030 0.002 PHE F 215 TRP 0.010 0.002 TRP A 906 HIS 0.006 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (12136) covalent geometry : angle 0.65563 / 0.35 (16668) SS BOND : bond 0.00412 / 0.22 ( 1) SS BOND : angle 0.19743 / 0.10 ( 2) hydrogen bonds : bond 0.03858 / 2.59 ( 646) hydrogen bonds : angle 5.01020 / 3.54 ( 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 342 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8624 (tttt) cc_final: 0.8419 (ttpp) REVERT: A 459 GLU cc_start: 0.7318 (pm20) cc_final: 0.7064 (pm20) REVERT: A 752 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8029 (mtp180) REVERT: A 895 GLU cc_start: 0.7904 (pp20) cc_final: 0.7647 (tm-30) REVERT: A 910 GLU cc_start: 0.7800 (tp30) cc_final: 0.7439 (tp30) REVERT: A 913 VAL cc_start: 0.8942 (t) cc_final: 0.8673 (p) REVERT: A 932 VAL cc_start: 0.8486 (t) cc_final: 0.8245 (p) REVERT: A 947 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (mp) REVERT: F 16 LEU cc_start: 0.8279 (mm) cc_final: 0.8052 (mm) REVERT: F 85 GLU cc_start: 0.7447 (pm20) cc_final: 0.7243 (pm20) REVERT: F 193 GLU cc_start: 0.7448 (mp0) cc_final: 0.7067 (mp0) REVERT: F 214 PHE cc_start: 0.7457 (m-10) cc_final: 0.7187 (m-10) REVERT: G 13 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7715 (ttmt) REVERT: G 40 MET cc_start: 0.7059 (mtt) cc_final: 0.6763 (ttt) REVERT: G 68 MET cc_start: 0.7146 (tpp) cc_final: 0.6928 (mpp) REVERT: G 116 MET cc_start: 0.5641 (mmp) cc_final: 0.5080 (mmp) REVERT: G 124 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7436 (tm-30) REVERT: G 138 LYS cc_start: 0.7923 (tmtt) cc_final: 0.7623 (tmtt) REVERT: G 144 PHE cc_start: 0.8135 (t80) cc_final: 0.7868 (t80) REVERT: G 151 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7996 (mt) REVERT: G 222 SER cc_start: 0.8035 (t) cc_final: 0.7697 (p) REVERT: G 229 MET cc_start: 0.5108 (mtm) cc_final: 0.4790 (mtm) REVERT: G 244 MET cc_start: 0.8244 (tmm) cc_final: 0.7951 (tmm) REVERT: H 25 GLU cc_start: 0.7927 (mp0) cc_final: 0.7441 (mp0) REVERT: H 80 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8013 (ttmm) REVERT: H 119 MET cc_start: 0.3908 (OUTLIER) cc_final: 0.2450 (tmm) REVERT: H 130 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7319 (tm-30) REVERT: H 199 MET cc_start: 0.4269 (mtt) cc_final: 0.3689 (mmt) outliers start: 39 outliers final: 32 residues processed: 325 average time/residue: 0.0943 time to fit residues: 43.8580 Evaluate side-chains 339 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 662 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 23 ILE 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 167 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL 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 6 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: 0.0970 chunk 115 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** A 929 GLN ** 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 = 0.4090 r_free = 0.4090 target = 0.161432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133158 restraints weight = 18689.600| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.59 r_work: 0.3589 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2176 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= 0.171 Angle : 0.654 7.793 16670 Z= 0.346 Chirality : 0.044 0.233 1923 Planarity : 0.004 0.066 1906 Dihedral : 19.013 66.004 2090 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.32 % Allowed : 27.20 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1317 helix: 1.25 (0.23), residues: 506 sheet: 0.60 (0.29), residues: 348 loop : -0.39 (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 0.031 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/Z covalent geometry : bond 0.00378 / 0.17 (12136) covalent geometry : angle 0.65361 / 0.35 (16668) SS BOND : bond 0.00372 / 0.20 ( 1) SS BOND : angle 0.18895 / 0.10 ( 2) hydrogen bonds : bond 0.03789 / 2.55 ( 646) hydrogen bonds : angle 4.97803 / 3.52 ( 1778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.51 seconds wall clock time: 43 minutes 29.35 seconds (2609.35 seconds total)