Starting phenix.real_space_refine on Sat Jul 4 04:42:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.cif" model { file = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upf_42446/07_2026/8upf_42446.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 32 5.16 5 C 7901 2.51 5 N 2612 2.21 5 O 3172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14012 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1175 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10623 SG CYS K 31 73.925 71.146 46.276 1.00186.03 S ATOM 10773 SG CYS K 51 75.294 73.936 47.616 1.00186.41 S ATOM 10797 SG CYS K 54 74.227 74.593 43.507 1.00191.01 S ATOM 10514 SG CYS K 16 82.497 72.048 55.513 1.00233.53 S ATOM 10532 SG CYS K 19 84.522 73.207 59.045 1.00237.17 S ATOM 10662 SG CYS K 36 81.475 70.277 59.358 1.00213.12 S ATOM 10684 SG CYS K 39 81.052 73.736 58.594 1.00206.20 S Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 14012 At special positions: 0 Unit cell: (105.843, 127.422, 116.119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 293 15.00 O 3172 8.00 N 2612 7.00 C 7901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 485.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 64.8% alpha, 4.3% beta 135 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.575A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.872A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.519A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.679A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.828A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.575A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.916A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.802A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.544A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 46 Processing helix chain 'K' and resid 58 through 67 Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 93 removed outlier: 3.630A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid -1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.666A pdb=" N VAL L 102 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.544A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.568A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.708A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.456A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.237A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.629A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.411A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.590A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 481 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.65 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: 3005 1.33 - 1.45: 4434 1.45 - 1.57: 6805 1.57 - 1.69: 584 1.69 - 1.81: 46 Bond restraints: 14874 Sorted by residual: bond pdb=" C3' DA I 16 " pdb=" O3' DA I 16 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C3' DC I 7 " pdb=" O3' DC I 7 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N1 DC I 8 " pdb=" C6 DC I 8 " ideal model delta sigma weight residual 1.367 1.347 0.020 6.00e-03 2.78e+04 1.12e+01 bond pdb=" C3' DA I -14 " pdb=" O3' DA I -14 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C3' DG J 62 " pdb=" C2' DG J 62 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 19232 1.30 - 2.61: 1909 2.61 - 3.91: 179 3.91 - 5.21: 28 5.21 - 6.52: 10 Bond angle restraints: 21358 Sorted by residual: angle pdb=" O4' DG I 9 " pdb=" C4' DG I 9 " pdb=" C3' DG I 9 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DC J -26 " pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" O4' DA I -54 " pdb=" C4' DA I -54 " pdb=" C3' DA I -54 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.43e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4' DC J 52 " pdb=" C4' DC J 52 " pdb=" C3' DC J 52 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 ... (remaining 21353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 6572 31.32 - 62.63: 1618 62.63 - 93.95: 47 93.95 - 125.27: 0 125.27 - 156.58: 2 Dihedral angle restraints: 8239 sinusoidal: 5301 harmonic: 2938 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.42 156.58 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 65.18 154.82 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 8236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1513 0.038 - 0.077: 615 0.077 - 0.115: 227 0.115 - 0.154: 61 0.154 - 0.192: 4 Chirality restraints: 2420 Sorted by residual: chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" C3' DC J -20 " pdb=" C4' DC J -20 " pdb=" O3' DC J -20 " pdb=" C2' DC J -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA LYS E 37 " pdb=" N LYS E 37 " pdb=" C LYS E 37 " pdb=" CB LYS E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 2417 not shown) Planarity restraints: 1693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.029 2.00e-02 2.50e+03 1.19e-02 4.28e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -5 " -0.028 2.00e-02 2.50e+03 1.24e-02 4.22e+00 pdb=" N9 DA I -5 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -5 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -5 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -5 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -5 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -5 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -5 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -5 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -5 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -5 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 32 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1690 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 195 2.63 - 3.20: 12339 3.20 - 3.77: 25525 3.77 - 4.33: 33601 4.33 - 4.90: 48902 Nonbonded interactions: 120562 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.065 2.496 nonbonded pdb=" OG SER D 78 " pdb=" O TYR C 39 " model vdw 2.141 3.040 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.216 3.040 ... (remaining 120557 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.009 0.283 14884 Z= 0.614 Angle : 0.856 27.209 21373 Z= 0.658 Chirality : 0.048 0.192 2420 Planarity : 0.004 0.046 1691 Dihedral : 26.919 156.584 6337 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.47 % Allowed : 5.00 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.24), residues: 989 helix: -0.85 (0.18), residues: 647 sheet: -1.85 (0.94), residues: 23 loop : -2.60 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 136 TYR 0.013 0.002 TYR C 50 PHE 0.011 0.001 PHE E 78 TRP 0.003 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.61 (14874) covalent geometry : angle 0.78421 / 0.65 (21358) hydrogen bonds : bond 0.10676 / 6.82 ( 828) hydrogen bonds : angle 5.05605 / 3.68 ( 2106) metal coordination : bond 0.15181 / 7.15 ( 8) metal coordination : angle 16.71906 / 8.20 ( 9) link_TRANS : bond 0.00050 / 0.02 ( 2) link_TRANS : angle 0.74427 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9188 (m-80) cc_final: 0.8895 (m-80) REVERT: A 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.8160 (pm20) REVERT: A 60 LEU cc_start: 0.9166 (mt) cc_final: 0.8852 (mt) REVERT: A 80 THR cc_start: 0.8601 (t) cc_final: 0.8045 (t) REVERT: B 92 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8347 (ttp80) REVERT: D 59 MET cc_start: 0.8950 (tpp) cc_final: 0.7857 (tpt) REVERT: D 83 TYR cc_start: 0.8630 (m-10) cc_final: 0.8335 (m-10) REVERT: D 108 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7484 (mtpp) REVERT: E 50 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7417 (mt-10) REVERT: F 25 ASN cc_start: 0.8460 (m110) cc_final: 0.7918 (m-40) REVERT: F 91 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8768 (ttpp) REVERT: H 86 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8579 (ttm-80) REVERT: H 113 GLU cc_start: 0.8517 (tp30) cc_final: 0.8249 (tm-30) REVERT: H 120 LYS cc_start: 0.8474 (tttm) cc_final: 0.8222 (tttt) REVERT: K 20 MET cc_start: 0.7240 (mmp) cc_final: 0.6847 (mpp) REVERT: L 30 MET cc_start: 0.6403 (ptt) cc_final: 0.6106 (mmm) REVERT: C 104 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8731 (tp40) REVERT: G 36 LYS cc_start: 0.8543 (pttt) cc_final: 0.8029 (mmmm) REVERT: G 104 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8464 (mm-40) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.1771 time to fit residues: 40.3863 Evaluate side-chains 156 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS K 41 GLN K 81 GLN K 83 HIS L 77 ASN C 112 GLN G 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082897 restraints weight = 35682.236| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.92 r_work: 0.2856 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 14884 Z= 0.152 Angle : 0.650 8.053 21373 Z= 0.372 Chirality : 0.044 0.230 2420 Planarity : 0.005 0.038 1691 Dihedral : 30.239 158.412 4324 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.58 % Allowed : 10.47 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 989 helix: 0.82 (0.20), residues: 654 sheet: -0.85 (1.13), residues: 23 loop : -1.95 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.021 0.002 TYR H 121 PHE 0.018 0.001 PHE L 62 TRP 0.007 0.001 TRP K 61 HIS 0.006 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (14874) covalent geometry : angle 0.64525 / 0.37 (21358) hydrogen bonds : bond 0.04948 / 3.23 ( 828) hydrogen bonds : angle 3.51067 / 2.57 ( 2106) metal coordination : bond 0.04709 / 2.34 ( 8) metal coordination : angle 4.00866 / 1.88 ( 9) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.30294 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8969 (m-80) cc_final: 0.8696 (m-80) REVERT: A 53 ARG cc_start: 0.8754 (ttt-90) cc_final: 0.8350 (ttt-90) REVERT: A 59 GLU cc_start: 0.8501 (pm20) cc_final: 0.8145 (pm20) REVERT: A 60 LEU cc_start: 0.8991 (mt) cc_final: 0.8640 (mt) REVERT: B 84 MET cc_start: 0.8883 (mmm) cc_final: 0.8250 (mmm) REVERT: D 47 GLN cc_start: 0.8745 (mt0) cc_final: 0.8525 (tt0) REVERT: D 68 ASP cc_start: 0.9098 (t70) cc_final: 0.8710 (t0) REVERT: D 83 TYR cc_start: 0.8653 (m-10) cc_final: 0.8351 (m-80) REVERT: D 108 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7347 (mtpp) REVERT: F 25 ASN cc_start: 0.8383 (m110) cc_final: 0.7774 (m-40) REVERT: F 84 MET cc_start: 0.8706 (mmm) cc_final: 0.7935 (mmm) REVERT: F 91 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8709 (ttpp) REVERT: H 86 ARG cc_start: 0.8770 (mmt-90) cc_final: 0.8510 (ttm-80) REVERT: H 113 GLU cc_start: 0.8619 (tp30) cc_final: 0.8274 (tm-30) REVERT: L 10 LEU cc_start: 0.8462 (pp) cc_final: 0.8165 (mm) REVERT: L 30 MET cc_start: 0.6380 (ptt) cc_final: 0.6163 (mmm) REVERT: C 104 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8837 (tp40) REVERT: G 36 LYS cc_start: 0.8183 (pttt) cc_final: 0.7644 (mmtp) REVERT: G 104 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8656 (mm110) outliers start: 5 outliers final: 2 residues processed: 175 average time/residue: 0.1420 time to fit residues: 33.7564 Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain C residue 118 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081209 restraints weight = 43482.336| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.17 r_work: 0.2810 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14884 Z= 0.179 Angle : 0.644 11.337 21373 Z= 0.363 Chirality : 0.043 0.265 2420 Planarity : 0.005 0.041 1691 Dihedral : 30.218 159.831 4324 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.28 % Allowed : 12.79 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.27), residues: 989 helix: 1.39 (0.21), residues: 655 sheet: -0.57 (1.10), residues: 23 loop : -1.84 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.023 0.002 TYR H 121 PHE 0.016 0.002 PHE L 51 TRP 0.005 0.001 TRP K 61 HIS 0.007 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (14874) covalent geometry : angle 0.63918 / 0.36 (21358) hydrogen bonds : bond 0.04827 / 3.17 ( 828) hydrogen bonds : angle 3.34830 / 2.45 ( 2106) metal coordination : bond 0.02042 / 1.01 ( 8) metal coordination : angle 3.92132 / 1.71 ( 9) link_TRANS : bond 0.00170 / 0.09 ( 2) link_TRANS : angle 0.30988 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9033 (m-80) cc_final: 0.8714 (m-80) REVERT: A 53 ARG cc_start: 0.8645 (ttt-90) cc_final: 0.8255 (ttt-90) REVERT: A 59 GLU cc_start: 0.8416 (pm20) cc_final: 0.8018 (pm20) REVERT: D 47 GLN cc_start: 0.8789 (mt0) cc_final: 0.8571 (tt0) REVERT: D 68 ASP cc_start: 0.9127 (t70) cc_final: 0.8763 (t0) REVERT: D 83 TYR cc_start: 0.8697 (m-10) cc_final: 0.8173 (m-10) REVERT: F 25 ASN cc_start: 0.8443 (m110) cc_final: 0.7924 (m-40) REVERT: F 91 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8725 (ttpp) REVERT: H 68 ASP cc_start: 0.9154 (t0) cc_final: 0.8917 (t0) REVERT: H 86 ARG cc_start: 0.8729 (mmt-90) cc_final: 0.8451 (ttm-80) REVERT: H 113 GLU cc_start: 0.8646 (tp30) cc_final: 0.8270 (tm-30) REVERT: H 119 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8675 (t) REVERT: C 92 GLU cc_start: 0.8326 (mp0) cc_final: 0.8048 (mp0) REVERT: C 104 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8829 (tp40) REVERT: G 36 LYS cc_start: 0.8190 (pttt) cc_final: 0.7614 (mmtp) outliers start: 11 outliers final: 7 residues processed: 150 average time/residue: 0.1396 time to fit residues: 28.4674 Evaluate side-chains 148 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 90 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081372 restraints weight = 44352.345| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.27 r_work: 0.2792 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14884 Z= 0.209 Angle : 0.659 7.939 21373 Z= 0.366 Chirality : 0.044 0.290 2420 Planarity : 0.004 0.036 1691 Dihedral : 30.283 161.330 4324 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.51 % Allowed : 14.30 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 989 helix: 1.51 (0.20), residues: 656 sheet: -0.54 (1.16), residues: 23 loop : -1.74 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 63 TYR 0.027 0.002 TYR H 121 PHE 0.015 0.002 PHE L 69 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (14874) covalent geometry : angle 0.65576 / 0.37 (21358) hydrogen bonds : bond 0.04876 / 3.18 ( 828) hydrogen bonds : angle 3.37923 / 2.48 ( 2106) metal coordination : bond 0.02147 / 1.07 ( 8) metal coordination : angle 3.15983 / 1.36 ( 9) link_TRANS : bond 0.00248 / 0.13 ( 2) link_TRANS : angle 0.30984 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9007 (m-80) cc_final: 0.8668 (m-80) REVERT: A 59 GLU cc_start: 0.8290 (pm20) cc_final: 0.7899 (pm20) REVERT: A 60 LEU cc_start: 0.9003 (mt) cc_final: 0.8743 (mt) REVERT: D 68 ASP cc_start: 0.9091 (t70) cc_final: 0.8727 (t0) REVERT: D 83 TYR cc_start: 0.8717 (m-10) cc_final: 0.8364 (m-80) REVERT: D 101 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8547 (mp) REVERT: F 25 ASN cc_start: 0.8414 (m110) cc_final: 0.7864 (m-40) REVERT: F 91 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8722 (ttpp) REVERT: H 68 ASP cc_start: 0.9198 (t0) cc_final: 0.8971 (t0) REVERT: H 113 GLU cc_start: 0.8610 (tp30) cc_final: 0.8206 (tm-30) REVERT: H 119 THR cc_start: 0.8807 (t) cc_final: 0.8586 (t) REVERT: L 30 MET cc_start: 0.6147 (mmm) cc_final: 0.5528 (ptt) REVERT: C 61 GLU cc_start: 0.8594 (tp30) cc_final: 0.8159 (tt0) REVERT: C 92 GLU cc_start: 0.8352 (mp0) cc_final: 0.8116 (mp0) REVERT: C 104 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8765 (tp40) REVERT: G 36 LYS cc_start: 0.8138 (pttt) cc_final: 0.7618 (mmtp) outliers start: 13 outliers final: 7 residues processed: 149 average time/residue: 0.1418 time to fit residues: 28.5449 Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082782 restraints weight = 43795.547| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.19 r_work: 0.2836 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14884 Z= 0.140 Angle : 0.599 10.137 21373 Z= 0.343 Chirality : 0.042 0.276 2420 Planarity : 0.004 0.037 1691 Dihedral : 30.053 162.918 4324 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.16 % Allowed : 15.23 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 989 helix: 1.76 (0.21), residues: 656 sheet: -0.37 (1.08), residues: 23 loop : -1.51 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.025 0.001 TYR H 121 PHE 0.016 0.001 PHE K 53 TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (14874) covalent geometry : angle 0.59576 / 0.34 (21358) hydrogen bonds : bond 0.04342 / 2.81 ( 828) hydrogen bonds : angle 3.12836 / 2.29 ( 2106) metal coordination : bond 0.01857 / 0.92 ( 8) metal coordination : angle 2.97509 / 1.30 ( 9) link_TRANS : bond 0.00087 / 0.04 ( 2) link_TRANS : angle 0.31356 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9067 (m-80) cc_final: 0.8719 (m-80) REVERT: A 58 THR cc_start: 0.8830 (p) cc_final: 0.8629 (t) REVERT: A 59 GLU cc_start: 0.8279 (pm20) cc_final: 0.7922 (pm20) REVERT: A 60 LEU cc_start: 0.9060 (mt) cc_final: 0.8809 (mt) REVERT: B 84 MET cc_start: 0.8876 (mmm) cc_final: 0.8295 (mmm) REVERT: D 47 GLN cc_start: 0.8694 (tt0) cc_final: 0.8491 (tt0) REVERT: D 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8751 (t0) REVERT: D 83 TYR cc_start: 0.8703 (m-10) cc_final: 0.8293 (m-80) REVERT: F 25 ASN cc_start: 0.8442 (m110) cc_final: 0.7894 (m-40) REVERT: F 84 MET cc_start: 0.8552 (mmm) cc_final: 0.8344 (mmm) REVERT: F 88 TYR cc_start: 0.8633 (m-80) cc_final: 0.8413 (m-80) REVERT: F 91 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8698 (ttpp) REVERT: H 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8978 (t0) REVERT: H 113 GLU cc_start: 0.8634 (tp30) cc_final: 0.8227 (tm-30) REVERT: H 119 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8614 (t) REVERT: C 61 GLU cc_start: 0.8580 (tp30) cc_final: 0.8227 (tt0) REVERT: C 92 GLU cc_start: 0.8331 (mp0) cc_final: 0.8113 (mp0) REVERT: C 104 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8829 (tp40) REVERT: G 36 LYS cc_start: 0.8218 (pttt) cc_final: 0.7622 (mmtp) outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 0.1441 time to fit residues: 28.8206 Evaluate side-chains 143 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080644 restraints weight = 42139.804| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.17 r_work: 0.2806 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14884 Z= 0.215 Angle : 0.649 8.162 21373 Z= 0.360 Chirality : 0.044 0.309 2420 Planarity : 0.004 0.035 1691 Dihedral : 30.194 163.329 4324 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.86 % Allowed : 15.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 989 helix: 1.67 (0.20), residues: 658 sheet: -0.24 (1.07), residues: 23 loop : -1.50 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.027 0.002 TYR H 121 PHE 0.017 0.002 PHE K 53 TRP 0.006 0.001 TRP K 61 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (14874) covalent geometry : angle 0.64540 / 0.36 (21358) hydrogen bonds : bond 0.04737 / 3.09 ( 828) hydrogen bonds : angle 3.27922 / 2.39 ( 2106) metal coordination : bond 0.01708 / 0.85 ( 8) metal coordination : angle 3.26571 / 1.40 ( 9) link_TRANS : bond 0.00296 / 0.15 ( 2) link_TRANS : angle 0.28669 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9117 (m-80) cc_final: 0.8794 (m-80) REVERT: A 58 THR cc_start: 0.8832 (p) cc_final: 0.8602 (t) REVERT: A 59 GLU cc_start: 0.8275 (pm20) cc_final: 0.7873 (pm20) REVERT: A 60 LEU cc_start: 0.9072 (mt) cc_final: 0.8797 (mt) REVERT: D 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8796 (t0) REVERT: D 101 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8654 (mp) REVERT: F 25 ASN cc_start: 0.8483 (m110) cc_final: 0.7951 (m-40) REVERT: F 91 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8743 (ttpp) REVERT: H 68 ASP cc_start: 0.9281 (t0) cc_final: 0.9052 (t0) REVERT: H 113 GLU cc_start: 0.8649 (tp30) cc_final: 0.8247 (tm-30) REVERT: C 61 GLU cc_start: 0.8677 (tp30) cc_final: 0.8262 (tt0) REVERT: C 92 GLU cc_start: 0.8393 (mp0) cc_final: 0.8193 (mp0) REVERT: C 104 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8837 (tp40) REVERT: G 11 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8228 (m) REVERT: G 36 LYS cc_start: 0.8276 (pttt) cc_final: 0.7766 (mmtp) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 0.1585 time to fit residues: 31.3845 Evaluate side-chains 145 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082317 restraints weight = 38899.636| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.03 r_work: 0.2832 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14884 Z= 0.162 Angle : 0.618 10.546 21373 Z= 0.349 Chirality : 0.042 0.301 2420 Planarity : 0.004 0.037 1691 Dihedral : 30.104 164.441 4324 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.81 % Allowed : 17.33 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 989 helix: 1.75 (0.20), residues: 658 sheet: -0.01 (1.08), residues: 23 loop : -1.43 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.028 0.002 TYR H 121 PHE 0.017 0.001 PHE K 53 TRP 0.003 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14874) covalent geometry : angle 0.61513 / 0.35 (21358) hydrogen bonds : bond 0.04455 / 2.89 ( 828) hydrogen bonds : angle 3.14659 / 2.30 ( 2106) metal coordination : bond 0.01349 / 0.67 ( 8) metal coordination : angle 3.05817 / 1.27 ( 9) link_TRANS : bond 0.00166 / 0.09 ( 2) link_TRANS : angle 0.25163 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8242 (pm20) cc_final: 0.7843 (pm20) REVERT: A 60 LEU cc_start: 0.9054 (mt) cc_final: 0.8794 (mt) REVERT: B 84 MET cc_start: 0.8896 (mmm) cc_final: 0.8264 (mmm) REVERT: D 68 ASP cc_start: 0.9122 (t70) cc_final: 0.8760 (t0) REVERT: D 101 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8637 (mp) REVERT: F 25 ASN cc_start: 0.8480 (m110) cc_final: 0.7939 (m-40) REVERT: F 84 MET cc_start: 0.8583 (mmm) cc_final: 0.7797 (mmm) REVERT: F 91 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8716 (ttpp) REVERT: H 68 ASP cc_start: 0.9265 (t0) cc_final: 0.9025 (t0) REVERT: H 113 GLU cc_start: 0.8639 (tp30) cc_final: 0.8234 (tm-30) REVERT: C 61 GLU cc_start: 0.8639 (tp30) cc_final: 0.8248 (tt0) REVERT: C 104 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8821 (tp40) REVERT: G 36 LYS cc_start: 0.8160 (pttt) cc_final: 0.7664 (mmtp) outliers start: 7 outliers final: 3 residues processed: 143 average time/residue: 0.1503 time to fit residues: 29.1676 Evaluate side-chains 140 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.082186 restraints weight = 36420.246| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.93 r_work: 0.2830 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14884 Z= 0.176 Angle : 0.634 9.610 21373 Z= 0.355 Chirality : 0.043 0.313 2420 Planarity : 0.004 0.037 1691 Dihedral : 30.119 165.134 4324 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.51 % Allowed : 17.21 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 989 helix: 1.76 (0.20), residues: 658 sheet: 0.13 (1.09), residues: 23 loop : -1.44 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.026 0.002 TYR H 121 PHE 0.020 0.002 PHE K 53 TRP 0.007 0.001 TRP K 61 HIS 0.006 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (14874) covalent geometry : angle 0.63144 / 0.36 (21358) hydrogen bonds : bond 0.04526 / 2.95 ( 828) hydrogen bonds : angle 3.22107 / 2.36 ( 2106) metal coordination : bond 0.01422 / 0.70 ( 8) metal coordination : angle 3.09829 / 1.28 ( 9) link_TRANS : bond 0.00198 / 0.10 ( 2) link_TRANS : angle 0.25020 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9058 (m-80) cc_final: 0.8673 (m-80) REVERT: A 59 GLU cc_start: 0.8222 (pm20) cc_final: 0.7785 (pm20) REVERT: A 60 LEU cc_start: 0.9060 (mt) cc_final: 0.8772 (mt) REVERT: B 84 MET cc_start: 0.8908 (mmm) cc_final: 0.8208 (mmm) REVERT: D 68 ASP cc_start: 0.9122 (t70) cc_final: 0.8764 (t0) REVERT: D 83 TYR cc_start: 0.8696 (m-10) cc_final: 0.8427 (m-80) REVERT: D 101 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8631 (mp) REVERT: F 25 ASN cc_start: 0.8471 (m110) cc_final: 0.7942 (m-40) REVERT: F 84 MET cc_start: 0.8572 (mmm) cc_final: 0.8317 (mmm) REVERT: F 88 TYR cc_start: 0.8725 (m-80) cc_final: 0.8398 (m-80) REVERT: F 91 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8715 (ttpp) REVERT: H 68 ASP cc_start: 0.9282 (t0) cc_final: 0.9060 (t0) REVERT: H 93 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: C 61 GLU cc_start: 0.8662 (tp30) cc_final: 0.8244 (tt0) REVERT: C 104 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8817 (tp40) REVERT: G 11 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8201 (m) REVERT: G 36 LYS cc_start: 0.8244 (pttt) cc_final: 0.7764 (mmtp) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 0.1469 time to fit residues: 28.8833 Evaluate side-chains 145 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 0.0770 chunk 76 optimal weight: 10.0000 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082772 restraints weight = 41680.572| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.13 r_work: 0.2838 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14884 Z= 0.150 Angle : 0.626 10.712 21373 Z= 0.354 Chirality : 0.042 0.309 2420 Planarity : 0.004 0.038 1691 Dihedral : 30.041 165.922 4324 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.05 % Allowed : 17.79 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 989 helix: 1.85 (0.20), residues: 657 sheet: 0.33 (1.10), residues: 23 loop : -1.41 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.028 0.002 TYR H 121 PHE 0.020 0.001 PHE K 53 TRP 0.005 0.001 TRP K 61 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (14874) covalent geometry : angle 0.62303 / 0.35 (21358) hydrogen bonds : bond 0.04339 / 2.81 ( 828) hydrogen bonds : angle 3.14307 / 2.30 ( 2106) metal coordination : bond 0.01271 / 0.63 ( 8) metal coordination : angle 3.14121 / 1.33 ( 9) link_TRANS : bond 0.00183 / 0.10 ( 2) link_TRANS : angle 0.37422 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9068 (m-80) cc_final: 0.8648 (m-80) REVERT: A 59 GLU cc_start: 0.8139 (pm20) cc_final: 0.7688 (pm20) REVERT: A 60 LEU cc_start: 0.9010 (mt) cc_final: 0.8755 (mt) REVERT: B 84 MET cc_start: 0.8869 (mmm) cc_final: 0.8295 (mmm) REVERT: D 68 ASP cc_start: 0.9103 (t70) cc_final: 0.8743 (t0) REVERT: D 83 TYR cc_start: 0.8681 (m-10) cc_final: 0.8408 (m-80) REVERT: D 101 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8605 (mp) REVERT: F 25 ASN cc_start: 0.8453 (m110) cc_final: 0.7942 (m-40) REVERT: F 84 MET cc_start: 0.8559 (mmm) cc_final: 0.8321 (mmm) REVERT: F 88 TYR cc_start: 0.8697 (m-80) cc_final: 0.8354 (m-80) REVERT: F 91 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8707 (ttpp) REVERT: H 68 ASP cc_start: 0.9263 (t0) cc_final: 0.9026 (t0) REVERT: H 93 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: L 30 MET cc_start: 0.6173 (mmm) cc_final: 0.5129 (ptt) REVERT: C 61 GLU cc_start: 0.8623 (tp30) cc_final: 0.8232 (tt0) REVERT: C 104 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8804 (tp40) REVERT: G 11 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8200 (m) REVERT: G 36 LYS cc_start: 0.8200 (pttt) cc_final: 0.7729 (mmtp) outliers start: 9 outliers final: 6 residues processed: 142 average time/residue: 0.1464 time to fit residues: 28.2074 Evaluate side-chains 150 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 35 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.084078 restraints weight = 47177.056| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.30 r_work: 0.2853 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14884 Z= 0.136 Angle : 0.615 11.843 21373 Z= 0.351 Chirality : 0.041 0.306 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.915 167.114 4324 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.16 % Allowed : 18.02 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.27), residues: 989 helix: 1.95 (0.20), residues: 659 sheet: 0.53 (1.10), residues: 23 loop : -1.40 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 79 TYR 0.025 0.001 TYR H 121 PHE 0.022 0.001 PHE K 53 TRP 0.003 0.001 TRP K 77 HIS 0.008 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (14874) covalent geometry : angle 0.61186 / 0.35 (21358) hydrogen bonds : bond 0.04168 / 2.69 ( 828) hydrogen bonds : angle 3.05371 / 2.24 ( 2106) metal coordination : bond 0.01018 / 0.50 ( 8) metal coordination : angle 3.27485 / 1.34 ( 9) link_TRANS : bond 0.00111 / 0.06 ( 2) link_TRANS : angle 0.38109 / 0.20 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8979 (mt) cc_final: 0.8702 (mt) REVERT: B 84 MET cc_start: 0.8863 (mmm) cc_final: 0.8270 (mmm) REVERT: D 68 ASP cc_start: 0.9107 (t70) cc_final: 0.8757 (t0) REVERT: D 83 TYR cc_start: 0.8721 (m-10) cc_final: 0.8430 (m-80) REVERT: D 101 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8606 (mp) REVERT: F 25 ASN cc_start: 0.8459 (m110) cc_final: 0.7947 (m-40) REVERT: F 91 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8702 (ttpp) REVERT: H 68 ASP cc_start: 0.9263 (t0) cc_final: 0.9036 (t0) REVERT: H 93 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: L 30 MET cc_start: 0.6149 (mmm) cc_final: 0.5646 (ptt) REVERT: L 110 LEU cc_start: 0.6174 (mt) cc_final: 0.5499 (tp) REVERT: C 61 GLU cc_start: 0.8639 (tp30) cc_final: 0.8288 (tt0) REVERT: C 104 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8976 (mm-40) REVERT: G 11 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8192 (m) REVERT: G 36 LYS cc_start: 0.8183 (pttt) cc_final: 0.7633 (mmtp) REVERT: G 92 GLU cc_start: 0.8623 (mp0) cc_final: 0.8256 (mp0) outliers start: 10 outliers final: 7 residues processed: 155 average time/residue: 0.1374 time to fit residues: 29.3565 Evaluate side-chains 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 110 optimal weight: 0.0270 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084608 restraints weight = 36073.138| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.95 r_work: 0.2875 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14884 Z= 0.144 Angle : 0.626 10.150 21373 Z= 0.352 Chirality : 0.041 0.315 2420 Planarity : 0.004 0.042 1691 Dihedral : 29.933 167.489 4324 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.16 % Allowed : 18.37 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.27), residues: 989 helix: 1.97 (0.20), residues: 658 sheet: 0.57 (1.11), residues: 23 loop : -1.33 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 79 TYR 0.053 0.002 TYR H 83 PHE 0.022 0.001 PHE K 53 TRP 0.008 0.001 TRP L 33 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (14874) covalent geometry : angle 0.62282 / 0.35 (21358) hydrogen bonds : bond 0.04206 / 2.72 ( 828) hydrogen bonds : angle 3.09815 / 2.28 ( 2106) metal coordination : bond 0.00987 / 0.49 ( 8) metal coordination : angle 3.19471 / 1.31 ( 9) link_TRANS : bond 0.00134 / 0.07 ( 2) link_TRANS : angle 0.37578 / 0.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3887.67 seconds wall clock time: 66 minutes 59.73 seconds (4019.73 seconds total)