Starting phenix.real_space_refine on Tue Jul 29 23:35:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.map" model { file = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eoa_19850/07_2025/9eoa_19850.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.38, per 1000 atoms: 0.79 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: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 6.05 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: 6.36 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2640 1.33 - 1.45: 2692 1.45 - 1.57: 6570 1.57 - 1.69: 123 1.69 - 1.81: 111 Bond restraints: 12136 Sorted by residual: bond pdb=" N VAL F 233 " pdb=" CA VAL F 233 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.32e+01 bond pdb=" N MET H 139 " pdb=" CA MET H 139 " ideal model delta sigma weight residual 1.453 1.484 -0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" N THR H 219 " pdb=" CA THR H 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.04e-02 9.25e+03 1.07e+01 bond pdb=" N VAL H 48 " pdb=" CA VAL H 48 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N CYS G 135 " pdb=" CA CYS G 135 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.24e-02 6.50e+03 1.04e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15747 1.81 - 3.63: 781 3.63 - 5.44: 114 5.44 - 7.26: 21 7.26 - 9.07: 5 Bond angle restraints: 16668 Sorted by residual: angle pdb=" N PRO A 856 " pdb=" CA PRO A 856 " pdb=" C PRO A 856 " ideal model delta sigma weight residual 111.32 119.79 -8.47 1.71e+00 3.42e-01 2.45e+01 angle pdb=" C GLY A 854 " pdb=" N ILE A 855 " pdb=" CA ILE A 855 " ideal model delta sigma weight residual 123.04 118.60 4.44 9.20e-01 1.18e+00 2.33e+01 angle pdb=" N TYR A 683 " pdb=" CA TYR A 683 " pdb=" C TYR A 683 " ideal model delta sigma weight residual 114.64 107.45 7.19 1.52e+00 4.33e-01 2.23e+01 angle pdb=" N LEU A 462 " pdb=" CA LEU A 462 " pdb=" C LEU A 462 " ideal model delta sigma weight residual 109.54 103.08 6.46 1.37e+00 5.33e-01 2.22e+01 angle pdb=" C PRO A 770 " pdb=" N GLU A 771 " pdb=" CA GLU A 771 " ideal model delta sigma weight residual 122.77 116.57 6.20 1.33e+00 5.65e-01 2.17e+01 ... (remaining 16663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5932 17.92 - 35.85: 837 35.85 - 53.77: 338 53.77 - 71.70: 75 71.70 - 89.62: 10 Dihedral angle restraints: 7192 sinusoidal: 3289 harmonic: 3903 Sorted by residual: dihedral pdb=" CB CYS G 135 " pdb=" SG CYS G 135 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual -86.00 -133.08 47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA ARG A 739 " pdb=" C ARG A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C CYS G 135 " pdb=" N CYS G 135 " pdb=" CA CYS G 135 " pdb=" CB CYS G 135 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1489 0.055 - 0.110: 334 0.110 - 0.164: 65 0.164 - 0.219: 25 0.219 - 0.274: 10 Chirality restraints: 1923 Sorted by residual: chirality pdb=" CA CYS G 135 " pdb=" N CYS G 135 " pdb=" C CYS G 135 " pdb=" CB CYS G 135 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE H 147 " pdb=" CA ILE H 147 " pdb=" CG1 ILE H 147 " pdb=" CG2 ILE H 147 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1920 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 768 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLN A 768 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN A 768 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 769 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 46 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C SER H 46 " 0.050 2.00e-02 2.50e+03 pdb=" O SER H 46 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU H 47 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 42 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C SER H 42 " 0.048 2.00e-02 2.50e+03 pdb=" O SER H 42 " -0.019 2.00e-02 2.50e+03 pdb=" N SER H 43 " -0.016 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1203 2.74 - 3.28: 11914 3.28 - 3.82: 20843 3.82 - 4.36: 24428 4.36 - 4.90: 39583 Nonbonded interactions: 97971 Sorted by model distance: nonbonded pdb=" OH TYR A 822 " pdb=" OE2 GLU A1002 " model vdw 2.201 3.040 nonbonded pdb=" O THR G 73 " pdb=" OG SER G 76 " model vdw 2.221 3.040 nonbonded pdb=" O SER A 836 " pdb=" OG1 THR A 840 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 895 " pdb=" OG SER A 933 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR A 555 " pdb=" OD1 ASN A 861 " model vdw 2.287 3.040 ... (remaining 97966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 119 or resid 128 through 163 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'G' and (resid 1 through 119 or resid 128 through 163 or resid 167 throug \ h 185 or resid 193 through 253)) selection = (chain 'H' and resid 1 through 253) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 144.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 41.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12137 Z= 0.347 Angle : 0.857 9.073 16670 Z= 0.552 Chirality : 0.055 0.274 1923 Planarity : 0.005 0.061 1906 Dihedral : 19.327 89.622 4647 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.84 % Allowed : 23.27 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.023 0.003 TRP A 664 HIS 0.003 0.001 HIS A 485 PHE 0.019 0.002 PHE A 971 TYR 0.038 0.002 TYR A 375 ARG 0.007 0.001 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.17757 ( 646) hydrogen bonds : angle 7.24017 ( 1778) SS BOND : bond 0.02797 ( 1) SS BOND : angle 3.34981 ( 2) covalent geometry : bond 0.00558 (12136) covalent geometry : angle 0.85645 (16668) *********************** 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 : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8427 (tttt) cc_final: 0.8165 (ttpp) REVERT: A 522 VAL cc_start: 0.7714 (t) cc_final: 0.7499 (m) REVERT: A 632 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7436 (tp-100) REVERT: A 889 LEU cc_start: 0.8233 (tp) cc_final: 0.7965 (tp) REVERT: A 947 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 950 ASP cc_start: 0.7724 (p0) cc_final: 0.7368 (p0) REVERT: A 970 HIS cc_start: 0.7280 (m90) cc_final: 0.7052 (m90) REVERT: F 6 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7881 (tp) REVERT: F 16 LEU cc_start: 0.8241 (mm) cc_final: 0.8039 (mm) REVERT: F 80 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8270 (mtpt) REVERT: G 115 GLU cc_start: 0.7242 (pt0) cc_final: 0.6981 (pt0) REVERT: G 222 SER cc_start: 0.7608 (t) cc_final: 0.7134 (p) REVERT: G 229 MET cc_start: 0.5207 (mtm) cc_final: 0.4831 (mtm) REVERT: G 232 ASP cc_start: 0.7919 (m-30) cc_final: 0.7711 (m-30) outliers start: 45 outliers final: 33 residues processed: 353 average time/residue: 0.3473 time to fit residues: 170.3346 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 : 1.245 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 495 GLN A 506 GLN A 779 HIS A 929 GLN G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.161487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132406 restraints weight = 18269.929| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.63 r_work: 0.3578 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12137 Z= 0.206 Angle : 0.619 7.741 16670 Z= 0.334 Chirality : 0.044 0.298 1923 Planarity : 0.004 0.043 1906 Dihedral : 18.978 65.025 2148 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.58 % Allowed : 21.82 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1317 helix: 1.11 (0.23), residues: 505 sheet: 0.76 (0.28), residues: 350 loop : -0.34 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 664 HIS 0.006 0.001 HIS H 246 PHE 0.013 0.002 PHE A 673 TYR 0.017 0.002 TYR A 699 ARG 0.006 0.001 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 646) hydrogen bonds : angle 5.39319 ( 1778) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.22836 ( 2) covalent geometry : bond 0.00452 (12136) covalent geometry : angle 0.61952 (16668) *********************** 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 369 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 327 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8633 (tttt) cc_final: 0.8404 (ttpp) REVERT: A 628 LYS cc_start: 0.7384 (tmtt) cc_final: 0.7170 (tmtt) REVERT: A 778 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7633 (mmmt) REVERT: A 889 LEU cc_start: 0.8069 (tp) cc_final: 0.7856 (tp) REVERT: A 929 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7633 (mm-40) REVERT: A 932 VAL cc_start: 0.8445 (t) cc_final: 0.8244 (p) REVERT: A 950 ASP cc_start: 0.7278 (p0) cc_final: 0.6865 (p0) REVERT: A 1002 GLU cc_start: 0.8370 (pt0) cc_final: 0.8146 (pt0) REVERT: F 16 LEU cc_start: 0.8264 (mm) cc_final: 0.8018 (mm) REVERT: F 85 GLU cc_start: 0.7529 (pm20) cc_final: 0.7180 (pm20) REVERT: F 193 GLU cc_start: 0.7492 (mp0) cc_final: 0.7192 (mp0) REVERT: F 214 PHE cc_start: 0.7599 (m-10) cc_final: 0.7189 (m-10) REVERT: G 29 ASP cc_start: 0.7253 (t0) cc_final: 0.6882 (t0) REVERT: G 77 LYS cc_start: 0.8473 (mptt) cc_final: 0.8122 (mmtm) REVERT: G 138 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7198 (tmtt) REVERT: G 168 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7882 (mttt) REVERT: G 222 SER cc_start: 0.8005 (t) cc_final: 0.7668 (p) REVERT: G 229 MET cc_start: 0.5105 (mtm) cc_final: 0.4735 (mtm) REVERT: G 232 ASP cc_start: 0.7871 (m-30) cc_final: 0.7651 (m-30) REVERT: H 227 LEU cc_start: 0.7239 (mp) cc_final: 0.6959 (mp) REVERT: H 237 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.6100 (p) outliers start: 42 outliers final: 21 residues processed: 350 average time/residue: 0.2706 time to fit residues: 132.6085 Evaluate side-chains 349 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 929 GLN Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 77 optimal weight: 0.0170 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN F 71 ASN G 38 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.163667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134465 restraints weight = 18537.259| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.68 r_work: 0.3605 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12137 Z= 0.136 Angle : 0.573 7.474 16670 Z= 0.305 Chirality : 0.042 0.266 1923 Planarity : 0.004 0.040 1906 Dihedral : 18.649 65.874 2096 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.67 % Allowed : 22.59 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1317 helix: 1.36 (0.23), residues: 506 sheet: 0.64 (0.28), residues: 345 loop : -0.28 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 664 HIS 0.006 0.001 HIS H 246 PHE 0.014 0.001 PHE F 215 TYR 0.027 0.002 TYR A 375 ARG 0.008 0.000 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 646) hydrogen bonds : angle 5.04955 ( 1778) SS BOND : bond 0.00373 ( 1) SS BOND : angle 0.20168 ( 2) covalent geometry : bond 0.00301 (12136) covalent geometry : angle 0.57340 (16668) *********************** 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 353 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 310 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.6725 (tp30) cc_final: 0.6501 (mm-30) REVERT: A 422 PHE cc_start: 0.7886 (t80) cc_final: 0.7622 (t80) REVERT: A 425 LYS cc_start: 0.8575 (tttt) cc_final: 0.8344 (ttpp) REVERT: A 605 TYR cc_start: 0.8578 (t80) cc_final: 0.8304 (t80) REVERT: A 611 MET cc_start: 0.8442 (tpp) cc_final: 0.7943 (ttm) REVERT: A 632 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7546 (tp-100) REVERT: A 778 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7596 (mmmt) REVERT: A 910 GLU cc_start: 0.7810 (tp30) cc_final: 0.7479 (tp30) REVERT: A 932 VAL cc_start: 0.8492 (t) cc_final: 0.8282 (p) REVERT: A 950 ASP cc_start: 0.7208 (p0) cc_final: 0.6796 (p0) REVERT: F 16 LEU cc_start: 0.8249 (mm) cc_final: 0.8031 (mm) REVERT: F 167 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7143 (m) REVERT: F 193 GLU cc_start: 0.7390 (mp0) cc_final: 0.7039 (mp0) REVERT: F 214 PHE cc_start: 0.7583 (m-10) cc_final: 0.7121 (m-10) REVERT: G 47 LEU cc_start: 0.7997 (tp) cc_final: 0.7788 (tp) REVERT: G 116 MET cc_start: 0.5681 (mmp) cc_final: 0.5079 (mmp) REVERT: G 119 MET cc_start: 0.5675 (mmt) cc_final: 0.5472 (mmp) REVERT: G 124 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7501 (tm-30) REVERT: G 138 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7143 (tmtt) REVERT: G 168 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7869 (mttt) REVERT: G 175 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7696 (pt) REVERT: G 222 SER cc_start: 0.7990 (t) cc_final: 0.7640 (p) REVERT: G 229 MET cc_start: 0.5200 (mtm) cc_final: 0.4847 (mtm) REVERT: H 130 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7296 (tm-30) REVERT: H 237 VAL cc_start: 0.6328 (OUTLIER) cc_final: 0.6128 (p) outliers start: 43 outliers final: 20 residues processed: 334 average time/residue: 0.3565 time to fit residues: 171.6177 Evaluate side-chains 335 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 78 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 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 = 0.4081 r_free = 0.4081 target = 0.160682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132198 restraints weight = 18435.540| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.56 r_work: 0.3582 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12137 Z= 0.198 Angle : 0.594 7.210 16670 Z= 0.318 Chirality : 0.043 0.261 1923 Planarity : 0.004 0.043 1906 Dihedral : 18.675 66.079 2090 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.35 % Allowed : 22.93 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1317 helix: 1.31 (0.23), residues: 504 sheet: 0.70 (0.29), residues: 336 loop : -0.28 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 638 HIS 0.006 0.001 HIS H 246 PHE 0.047 0.002 PHE F 215 TYR 0.030 0.003 TYR A 375 ARG 0.007 0.001 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 646) hydrogen bonds : angle 5.03029 ( 1778) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.22400 ( 2) covalent geometry : bond 0.00439 (12136) covalent geometry : angle 0.59430 (16668) *********************** 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 364 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8636 (tttt) cc_final: 0.8424 (ttpp) REVERT: A 447 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6943 (mt) REVERT: A 605 TYR cc_start: 0.8577 (t80) cc_final: 0.8333 (t80) REVERT: A 632 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7729 (tp-100) REVERT: A 722 LEU cc_start: 0.8088 (mp) cc_final: 0.7880 (mt) REVERT: A 778 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7593 (mmmt) REVERT: A 834 GLU cc_start: 0.7172 (tp30) cc_final: 0.6937 (tp30) REVERT: A 888 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7166 (mm-40) REVERT: A 889 LEU cc_start: 0.8158 (tp) cc_final: 0.7892 (tp) REVERT: A 932 VAL cc_start: 0.8477 (t) cc_final: 0.8272 (p) REVERT: A 947 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 950 ASP cc_start: 0.7257 (p0) cc_final: 0.6818 (p0) REVERT: F 16 LEU cc_start: 0.8265 (mm) cc_final: 0.8035 (mm) REVERT: F 167 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7159 (m) REVERT: F 193 GLU cc_start: 0.7460 (mp0) cc_final: 0.7094 (mp0) REVERT: F 214 PHE cc_start: 0.7592 (m-10) cc_final: 0.7211 (m-10) REVERT: G 47 LEU cc_start: 0.7959 (tp) cc_final: 0.7702 (tp) REVERT: G 116 MET cc_start: 0.5788 (mmp) cc_final: 0.5276 (mmp) REVERT: G 124 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7319 (tm-30) REVERT: G 138 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7202 (tmtt) REVERT: G 168 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7905 (mttt) REVERT: G 175 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7630 (pt) REVERT: G 222 SER cc_start: 0.8093 (t) cc_final: 0.7751 (p) REVERT: G 229 MET cc_start: 0.5221 (mtm) cc_final: 0.4855 (mtm) REVERT: G 232 ASP cc_start: 0.7815 (m-30) cc_final: 0.7615 (m-30) REVERT: H 80 LYS cc_start: 0.8280 (tttt) cc_final: 0.7954 (ttmm) REVERT: H 130 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7337 (tm-30) outliers start: 51 outliers final: 31 residues processed: 341 average time/residue: 0.3410 time to fit residues: 163.7371 Evaluate side-chains 340 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 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 241 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 970 HIS ** 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 = 0.4099 r_free = 0.4099 target = 0.162104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133705 restraints weight = 18401.603| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.55 r_work: 0.3597 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12137 Z= 0.159 Angle : 0.580 7.410 16670 Z= 0.309 Chirality : 0.042 0.250 1923 Planarity : 0.004 0.045 1906 Dihedral : 18.701 66.706 2090 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.84 % Allowed : 24.38 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1317 helix: 1.35 (0.23), residues: 506 sheet: 0.65 (0.29), residues: 348 loop : -0.33 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 708 HIS 0.006 0.001 HIS H 246 PHE 0.075 0.002 PHE F 215 TYR 0.033 0.002 TYR A 375 ARG 0.007 0.001 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 646) hydrogen bonds : angle 4.91537 ( 1778) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.12995 ( 2) covalent geometry : bond 0.00357 (12136) covalent geometry : angle 0.57984 (16668) *********************** 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 363 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8618 (tttt) cc_final: 0.8401 (ttpp) REVERT: A 447 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6845 (mt) REVERT: A 591 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7775 (ttp-110) REVERT: A 632 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7725 (tp-100) REVERT: A 722 LEU cc_start: 0.8063 (mp) cc_final: 0.7808 (mt) REVERT: A 723 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: A 778 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7549 (mmmt) REVERT: A 869 ASP cc_start: 0.7360 (m-30) cc_final: 0.7111 (m-30) REVERT: A 889 LEU cc_start: 0.8133 (tp) cc_final: 0.7899 (tp) REVERT: A 895 GLU cc_start: 0.7730 (pp20) cc_final: 0.7475 (tm-30) REVERT: A 910 GLU cc_start: 0.7808 (tp30) cc_final: 0.7583 (tp30) REVERT: A 932 VAL cc_start: 0.8445 (t) cc_final: 0.8241 (p) REVERT: A 947 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (mp) REVERT: F 16 LEU cc_start: 0.8277 (mm) cc_final: 0.8050 (mm) REVERT: F 85 GLU cc_start: 0.7466 (pm20) cc_final: 0.7174 (pm20) REVERT: F 167 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (m) REVERT: F 193 GLU cc_start: 0.7408 (mp0) cc_final: 0.7047 (mp0) REVERT: F 214 PHE cc_start: 0.7484 (m-10) cc_final: 0.7231 (m-10) REVERT: G 40 MET cc_start: 0.7082 (mtt) cc_final: 0.6782 (ttt) REVERT: G 47 LEU cc_start: 0.7979 (tp) cc_final: 0.7763 (tp) REVERT: G 68 MET cc_start: 0.7189 (tpp) cc_final: 0.6974 (mpp) REVERT: G 77 LYS cc_start: 0.8600 (mptt) cc_final: 0.8209 (mmtm) REVERT: G 112 SER cc_start: 0.7293 (m) cc_final: 0.6737 (p) REVERT: G 116 MET cc_start: 0.5697 (mmp) cc_final: 0.5170 (mmp) REVERT: G 124 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7235 (tm-30) REVERT: G 139 MET cc_start: 0.7721 (ptp) cc_final: 0.7468 (ptt) REVERT: G 168 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7869 (mttt) REVERT: G 175 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7576 (pt) REVERT: G 222 SER cc_start: 0.8097 (t) cc_final: 0.7738 (p) REVERT: G 229 MET cc_start: 0.5148 (mtm) cc_final: 0.4836 (mtm) REVERT: H 25 GLU cc_start: 0.7928 (mp0) cc_final: 0.7462 (mp0) REVERT: H 80 LYS cc_start: 0.8253 (tttt) cc_final: 0.7935 (ttmm) REVERT: H 130 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 45 outliers final: 27 residues processed: 344 average time/residue: 0.2522 time to fit residues: 122.1492 Evaluate side-chains 340 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 54 SER 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 201 GLU 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 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 26 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 115 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 490 ASN A 632 GLN A 861 ASN A 965 ASN A 970 HIS G 184 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 = 0.4094 r_free = 0.4094 target = 0.161667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133209 restraints weight = 18582.461| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.58 r_work: 0.3588 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12137 Z= 0.177 Angle : 0.600 9.563 16670 Z= 0.317 Chirality : 0.043 0.219 1923 Planarity : 0.004 0.045 1906 Dihedral : 18.705 66.968 2090 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.09 % Allowed : 24.30 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1317 helix: 1.32 (0.23), residues: 504 sheet: 0.64 (0.29), residues: 348 loop : -0.37 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 708 HIS 0.006 0.001 HIS F 246 PHE 0.087 0.002 PHE F 215 TYR 0.035 0.002 TYR A 375 ARG 0.008 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 646) hydrogen bonds : angle 4.89802 ( 1778) SS BOND : bond 0.00335 ( 1) SS BOND : angle 0.16356 ( 2) covalent geometry : bond 0.00398 (12136) covalent geometry : angle 0.59971 (16668) *********************** 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 359 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8645 (tttt) cc_final: 0.8425 (ttpp) REVERT: A 447 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6884 (mt) REVERT: A 632 GLN cc_start: 0.8001 (tp40) cc_final: 0.7749 (tp-100) REVERT: A 778 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7562 (mmmt) REVERT: A 869 ASP cc_start: 0.7363 (m-30) cc_final: 0.7105 (m-30) REVERT: A 889 LEU cc_start: 0.8156 (tp) cc_final: 0.7927 (tp) REVERT: A 895 GLU cc_start: 0.7742 (pp20) cc_final: 0.7405 (tm-30) REVERT: A 947 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 961 LEU cc_start: 0.7976 (mt) cc_final: 0.7769 (mt) REVERT: F 16 LEU cc_start: 0.8311 (mm) cc_final: 0.8087 (mm) REVERT: F 193 GLU cc_start: 0.7392 (mp0) cc_final: 0.7013 (mp0) REVERT: G 40 MET cc_start: 0.7033 (mtt) cc_final: 0.6739 (ttt) REVERT: G 68 MET cc_start: 0.7294 (tpp) cc_final: 0.7064 (mpp) REVERT: G 77 LYS cc_start: 0.8524 (mptt) cc_final: 0.8209 (mttp) REVERT: G 116 MET cc_start: 0.5478 (mmp) cc_final: 0.4994 (mmp) REVERT: G 124 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7490 (tm-30) REVERT: G 168 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7884 (mttt) REVERT: G 175 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7564 (pt) REVERT: G 199 MET cc_start: 0.7196 (tmm) cc_final: 0.6819 (ttp) REVERT: G 222 SER cc_start: 0.8152 (t) cc_final: 0.7768 (p) REVERT: G 229 MET cc_start: 0.5127 (mtm) cc_final: 0.4790 (mtm) REVERT: H 25 GLU cc_start: 0.7938 (mp0) cc_final: 0.7471 (mp0) REVERT: H 80 LYS cc_start: 0.8268 (tttt) cc_final: 0.7936 (ttmm) REVERT: H 119 MET cc_start: 0.4154 (OUTLIER) cc_final: 0.2353 (tmm) REVERT: H 130 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7330 (tm-30) REVERT: H 169 PHE cc_start: 0.7516 (m-80) cc_final: 0.7307 (m-80) outliers start: 48 outliers final: 29 residues processed: 337 average time/residue: 0.2475 time to fit residues: 117.1748 Evaluate side-chains 339 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 447 ILE 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 769 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 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.160458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131917 restraints weight = 18614.903| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.59 r_work: 0.3578 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12137 Z= 0.197 Angle : 0.627 7.860 16670 Z= 0.331 Chirality : 0.043 0.223 1923 Planarity : 0.004 0.049 1906 Dihedral : 18.773 68.256 2090 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.75 % Allowed : 25.40 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1317 helix: 1.27 (0.23), residues: 504 sheet: 0.59 (0.29), residues: 347 loop : -0.37 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 708 HIS 0.005 0.001 HIS H 246 PHE 0.027 0.002 PHE F 215 TYR 0.037 0.003 TYR A 375 ARG 0.007 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 646) hydrogen bonds : angle 4.95345 ( 1778) SS BOND : bond 0.00340 ( 1) SS BOND : angle 0.19277 ( 2) covalent geometry : bond 0.00443 (12136) covalent geometry : angle 0.62698 (16668) *********************** 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: 44 poor density : 313 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 PHE cc_start: 0.7870 (t80) cc_final: 0.7669 (t80) REVERT: A 425 LYS cc_start: 0.8651 (tttt) cc_final: 0.8436 (ttpp) REVERT: A 447 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6915 (mt) REVERT: A 632 GLN cc_start: 0.7977 (tp40) cc_final: 0.7748 (mm-40) REVERT: A 869 ASP cc_start: 0.7486 (m-30) cc_final: 0.7202 (m-30) REVERT: A 884 GLU cc_start: 0.7945 (tp30) cc_final: 0.7733 (tp30) REVERT: A 888 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7368 (mm-40) REVERT: A 889 LEU cc_start: 0.8174 (tp) cc_final: 0.7925 (tp) REVERT: A 895 GLU cc_start: 0.7786 (pp20) cc_final: 0.7430 (tm-30) REVERT: A 947 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 961 LEU cc_start: 0.7980 (mt) cc_final: 0.7779 (mt) REVERT: F 16 LEU cc_start: 0.8294 (mm) cc_final: 0.8073 (mm) REVERT: F 85 GLU cc_start: 0.7405 (pm20) cc_final: 0.7159 (pm20) REVERT: F 159 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8157 (m) REVERT: F 193 GLU cc_start: 0.7404 (mp0) cc_final: 0.6983 (mp0) REVERT: F 214 PHE cc_start: 0.7423 (m-10) cc_final: 0.7123 (m-10) REVERT: G 29 ASP cc_start: 0.7233 (t0) cc_final: 0.6842 (t0) REVERT: G 68 MET cc_start: 0.7432 (tpp) cc_final: 0.7147 (mpp) REVERT: G 116 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.5055 (mmp) REVERT: G 122 ASP cc_start: 0.6723 (t0) cc_final: 0.6346 (t0) REVERT: G 124 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 151 LEU cc_start: 0.8549 (mp) cc_final: 0.8184 (mt) REVERT: G 168 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7894 (mttt) REVERT: G 199 MET cc_start: 0.7248 (tmm) cc_final: 0.6836 (ttp) REVERT: G 222 SER cc_start: 0.8189 (t) cc_final: 0.7818 (p) REVERT: G 229 MET cc_start: 0.5228 (mtm) cc_final: 0.4858 (mtm) REVERT: H 25 GLU cc_start: 0.7970 (mp0) cc_final: 0.7453 (mp0) REVERT: H 80 LYS cc_start: 0.8292 (tttt) cc_final: 0.7966 (ttmm) REVERT: H 119 MET cc_start: 0.4437 (OUTLIER) cc_final: 0.2743 (tmm) REVERT: H 130 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7331 (tm-30) REVERT: H 148 CYS cc_start: 0.8117 (m) cc_final: 0.7645 (m) outliers start: 44 outliers final: 29 residues processed: 336 average time/residue: 0.2527 time to fit residues: 118.9208 Evaluate side-chains 340 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 56 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 832 HIS ** 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 = 0.4138 r_free = 0.4138 target = 0.167448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139571 restraints weight = 18701.030| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.64 r_work: 0.3613 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12137 Z= 0.134 Angle : 0.600 8.345 16670 Z= 0.313 Chirality : 0.042 0.224 1923 Planarity : 0.004 0.039 1906 Dihedral : 18.706 68.244 2090 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.07 % Allowed : 25.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1317 helix: 1.40 (0.23), residues: 507 sheet: 0.64 (0.29), residues: 346 loop : -0.42 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 664 HIS 0.006 0.001 HIS F 246 PHE 0.026 0.001 PHE F 215 TYR 0.036 0.002 TYR A 375 ARG 0.010 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 646) hydrogen bonds : angle 4.77358 ( 1778) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.22218 ( 2) covalent geometry : bond 0.00305 (12136) covalent geometry : angle 0.59961 (16668) *********************** 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 351 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8637 (tttt) cc_final: 0.8423 (ttpp) REVERT: A 591 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7764 (ttp-110) REVERT: A 752 ARG cc_start: 0.8234 (mtp85) cc_final: 0.8033 (mtp180) REVERT: A 778 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7567 (mmmt) REVERT: A 869 ASP cc_start: 0.7398 (m-30) cc_final: 0.7146 (m-30) REVERT: A 889 LEU cc_start: 0.8097 (tp) cc_final: 0.7889 (tp) REVERT: A 895 GLU cc_start: 0.7738 (pp20) cc_final: 0.7360 (tm-30) REVERT: A 913 VAL cc_start: 0.8883 (t) cc_final: 0.8652 (p) REVERT: A 947 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7942 (mp) REVERT: F 16 LEU cc_start: 0.8258 (mm) cc_final: 0.8056 (mm) REVERT: F 85 GLU cc_start: 0.7458 (pm20) cc_final: 0.7148 (pm20) REVERT: F 193 GLU cc_start: 0.7335 (mp0) cc_final: 0.6946 (mp0) REVERT: F 214 PHE cc_start: 0.7299 (m-10) cc_final: 0.6997 (m-10) REVERT: F 217 LYS cc_start: 0.8863 (mttm) cc_final: 0.8488 (mttt) REVERT: G 40 MET cc_start: 0.7045 (mtt) cc_final: 0.6741 (ttt) REVERT: G 68 MET cc_start: 0.7275 (tpp) cc_final: 0.6980 (mpp) REVERT: G 78 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7098 (mm) REVERT: G 116 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5127 (mmp) REVERT: G 122 ASP cc_start: 0.6721 (t0) cc_final: 0.6364 (t0) REVERT: G 124 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7508 (tm-30) REVERT: G 138 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7434 (tmtt) REVERT: G 151 LEU cc_start: 0.8460 (mp) cc_final: 0.8056 (mt) REVERT: G 164 LYS cc_start: 0.8575 (mttt) cc_final: 0.8360 (mttt) REVERT: G 168 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: G 199 MET cc_start: 0.7261 (tmm) cc_final: 0.6901 (ttp) REVERT: G 222 SER cc_start: 0.8149 (t) cc_final: 0.7768 (p) REVERT: G 229 MET cc_start: 0.5286 (mtm) cc_final: 0.4928 (mtm) REVERT: H 25 GLU cc_start: 0.7909 (mp0) cc_final: 0.7379 (mp0) REVERT: H 80 LYS cc_start: 0.8232 (tttt) cc_final: 0.7896 (ttmm) REVERT: H 119 MET cc_start: 0.4377 (OUTLIER) cc_final: 0.2645 (tmm) REVERT: H 130 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7377 (tm-30) REVERT: H 148 CYS cc_start: 0.8143 (m) cc_final: 0.7682 (m) outliers start: 36 outliers final: 20 residues processed: 336 average time/residue: 0.2502 time to fit residues: 118.0776 Evaluate side-chains 326 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134316 restraints weight = 18643.152| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.61 r_work: 0.3590 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12137 Z= 0.158 Angle : 0.629 10.439 16670 Z= 0.328 Chirality : 0.043 0.228 1923 Planarity : 0.004 0.060 1906 Dihedral : 18.717 68.133 2089 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.15 % Allowed : 26.34 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1317 helix: 1.38 (0.23), residues: 508 sheet: 0.65 (0.29), residues: 346 loop : -0.43 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 708 HIS 0.006 0.001 HIS F 246 PHE 0.029 0.001 PHE F 215 TYR 0.034 0.002 TYR A 375 ARG 0.008 0.000 ARG A 752 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 646) hydrogen bonds : angle 4.78217 ( 1778) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.11767 ( 2) covalent geometry : bond 0.00361 (12136) covalent geometry : angle 0.62924 (16668) *********************** 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 334 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 778 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7582 (mmmt) REVERT: A 869 ASP cc_start: 0.7447 (m-30) cc_final: 0.7168 (m-30) REVERT: A 884 GLU cc_start: 0.7942 (tp30) cc_final: 0.7718 (tp30) REVERT: A 889 LEU cc_start: 0.8147 (tp) cc_final: 0.7928 (tp) REVERT: A 895 GLU cc_start: 0.7797 (pp20) cc_final: 0.7431 (tm-30) REVERT: A 913 VAL cc_start: 0.8911 (t) cc_final: 0.8694 (p) REVERT: A 947 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 961 LEU cc_start: 0.7978 (mt) cc_final: 0.7774 (mt) REVERT: F 16 LEU cc_start: 0.8279 (mm) cc_final: 0.8071 (mm) REVERT: F 85 GLU cc_start: 0.7553 (pm20) cc_final: 0.7172 (pm20) REVERT: F 193 GLU cc_start: 0.7344 (mp0) cc_final: 0.6934 (mp0) REVERT: F 214 PHE cc_start: 0.7347 (m-10) cc_final: 0.7047 (m-10) REVERT: G 40 MET cc_start: 0.7086 (mtt) cc_final: 0.6766 (ttt) REVERT: G 68 MET cc_start: 0.7377 (tpp) cc_final: 0.7066 (mpp) REVERT: G 78 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7070 (mm) REVERT: G 116 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5136 (mmp) REVERT: G 124 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7502 (tm-30) REVERT: G 138 LYS cc_start: 0.7822 (tmtt) cc_final: 0.7475 (tmtt) REVERT: G 151 LEU cc_start: 0.8525 (mp) cc_final: 0.8112 (mt) REVERT: G 164 LYS cc_start: 0.8573 (mttt) cc_final: 0.8347 (mttt) REVERT: G 168 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7915 (mttt) REVERT: G 199 MET cc_start: 0.7262 (tmm) cc_final: 0.6906 (ttp) REVERT: G 222 SER cc_start: 0.8188 (t) cc_final: 0.7806 (p) REVERT: G 229 MET cc_start: 0.5350 (mtm) cc_final: 0.4976 (mtm) REVERT: H 25 GLU cc_start: 0.7901 (mp0) cc_final: 0.7376 (mp0) REVERT: H 80 LYS cc_start: 0.8229 (tttt) cc_final: 0.7908 (ttmm) REVERT: H 119 MET cc_start: 0.4422 (OUTLIER) cc_final: 0.2539 (tmm) REVERT: H 130 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7364 (tm-30) REVERT: H 148 CYS cc_start: 0.8104 (m) cc_final: 0.7639 (m) REVERT: H 199 MET cc_start: 0.3680 (mtt) cc_final: 0.3373 (mmm) outliers start: 37 outliers final: 26 residues processed: 319 average time/residue: 0.2846 time to fit residues: 127.8642 Evaluate side-chains 322 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 490 ASN G 108 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 = 0.4074 r_free = 0.4074 target = 0.159987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131519 restraints weight = 18440.442| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.57 r_work: 0.3570 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12137 Z= 0.217 Angle : 0.670 10.591 16670 Z= 0.350 Chirality : 0.045 0.229 1923 Planarity : 0.004 0.063 1906 Dihedral : 18.844 68.960 2089 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 26.43 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1317 helix: 1.18 (0.23), residues: 507 sheet: 0.57 (0.29), residues: 346 loop : -0.47 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 638 HIS 0.007 0.001 HIS F 246 PHE 0.034 0.002 PHE F 215 TYR 0.035 0.003 TYR A 375 ARG 0.008 0.001 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 646) hydrogen bonds : angle 4.90239 ( 1778) SS BOND : bond 0.00356 ( 1) SS BOND : angle 0.23330 ( 2) covalent geometry : bond 0.00493 (12136) covalent geometry : angle 0.67043 (16668) ********************** 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 357 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 318 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7798 (tpt90) REVERT: A 752 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7846 (mtp85) REVERT: A 778 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7531 (mmmt) REVERT: A 869 ASP cc_start: 0.7560 (m-30) cc_final: 0.7257 (m-30) REVERT: A 889 LEU cc_start: 0.8191 (tp) cc_final: 0.7957 (tp) REVERT: A 895 GLU cc_start: 0.7835 (pp20) cc_final: 0.7461 (tm-30) REVERT: A 947 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7968 (mp) REVERT: F 16 LEU cc_start: 0.8245 (mm) cc_final: 0.8000 (mm) REVERT: F 85 GLU cc_start: 0.7648 (pm20) cc_final: 0.7143 (pm20) REVERT: F 193 GLU cc_start: 0.7373 (mp0) cc_final: 0.6939 (mp0) REVERT: F 214 PHE cc_start: 0.7421 (m-10) cc_final: 0.7091 (m-10) REVERT: G 40 MET cc_start: 0.7050 (mtt) cc_final: 0.6740 (ttt) REVERT: G 68 MET cc_start: 0.7568 (tpp) cc_final: 0.7210 (mpp) REVERT: G 78 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7121 (mm) REVERT: G 116 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.5219 (mmp) REVERT: G 122 ASP cc_start: 0.6845 (t0) cc_final: 0.6520 (t0) REVERT: G 124 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7452 (tm-30) REVERT: G 138 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7545 (tmtt) REVERT: G 151 LEU cc_start: 0.8505 (mp) cc_final: 0.8096 (mt) REVERT: G 164 LYS cc_start: 0.8573 (mttt) cc_final: 0.8334 (mttt) REVERT: G 168 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7857 (mttt) REVERT: G 199 MET cc_start: 0.7232 (tmm) cc_final: 0.6859 (ttp) REVERT: G 222 SER cc_start: 0.8243 (t) cc_final: 0.7874 (p) REVERT: H 25 GLU cc_start: 0.7961 (mp0) cc_final: 0.7423 (mp0) REVERT: H 80 LYS cc_start: 0.8332 (tttt) cc_final: 0.7999 (ttmm) REVERT: H 119 MET cc_start: 0.4490 (OUTLIER) cc_final: 0.2796 (tmm) REVERT: H 130 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7373 (tm-30) REVERT: H 148 CYS cc_start: 0.8090 (m) cc_final: 0.7619 (m) outliers start: 39 outliers final: 27 residues processed: 335 average time/residue: 0.2493 time to fit residues: 117.2694 Evaluate side-chains 337 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 537 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 127 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 490 ASN A 965 ASN A 970 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138350 restraints weight = 18469.854| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.63 r_work: 0.3590 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2848 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= 0.167 Angle : 0.653 11.111 16670 Z= 0.339 Chirality : 0.044 0.231 1923 Planarity : 0.004 0.059 1906 Dihedral : 18.827 69.578 2089 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.81 % Allowed : 27.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1317 helix: 1.28 (0.23), residues: 507 sheet: 0.56 (0.29), residues: 347 loop : -0.49 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 919 HIS 0.007 0.001 HIS F 246 PHE 0.032 0.002 PHE G 144 TYR 0.035 0.002 TYR A 375 ARG 0.008 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 646) hydrogen bonds : angle 4.84180 ( 1778) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.10836 ( 2) covalent geometry : bond 0.00384 (12136) covalent geometry : angle 0.65324 (16668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7291.43 seconds wall clock time: 131 minutes 45.70 seconds (7905.70 seconds total)