Starting phenix.real_space_refine on Fri Aug 7 00:59:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upf_42446/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.cif" model { file = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2026/8upf_42446.map" } 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-2.2rc3-6140/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: 3.56, per 1000 atoms: 0.25 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: 1.25 Conformation dependent library (CDL) restraints added in 510.4 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: 1.95 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: 2.71 Time building geometry restraints manager: 1.69 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: 19200 1.30 - 2.61: 1940 2.61 - 3.91: 180 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 16.940 Find NCS groups from input model: 0.110 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- 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= 0.615 Angle : 0.861 27.209 21373 Z= 0.663 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 0.78995 / 0.66 (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 : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9188 (m-80) cc_final: 0.8898 (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: 0.7855 (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: 0.7419 (mt-10) REVERT: F 25 ASN cc_start: 0.8460 (m110) cc_final: 0.7917 (m-40) REVERT: F 91 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8766 (ttpp) 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: 0.8221 (tttt) REVERT: K 20 MET cc_start: 0.7240 (mmp) cc_final: 0.6846 (mpp) REVERT: L 30 MET cc_start: 0.6403 (ptt) cc_final: 0.6107 (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: 0.8463 (mm-40) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.1995 time to fit residues: 45.5828 Evaluate side-chains 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.9990 chunk 97 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.140353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083368 restraints weight = 35735.741| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.93 r_work: 0.2860 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 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 = 0.2861 r_free = 0.2861 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: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 14884 Z= 0.149 Angle : 0.657 8.134 21373 Z= 0.375 Chirality : 0.045 0.245 2420 Planarity : 0.005 0.038 1691 Dihedral : 30.140 157.468 4324 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.47 % Allowed : 10.58 % 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: -0.09 (0.26), residues: 989 helix: 0.85 (0.20), residues: 654 sheet: -0.82 (1.13), residues: 23 loop : -1.93 (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 0.008 0.001 TRP K 61 HIS 0.007 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (14874) covalent geometry : angle 0.65292 / 0.37 (21358) hydrogen bonds : bond 0.04889 / 3.18 ( 828) hydrogen bonds : angle 3.47322 / 2.54 ( 2106) metal coordination : bond 0.04664 / 2.33 ( 8) metal coordination : angle 3.73737 / 1.76 ( 9) link_TRANS : bond 0.00039 / 0.02 ( 2) link_TRANS : angle 0.30947 / 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 177 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8974 (m-80) cc_final: 0.8687 (m-80) REVERT: A 53 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8430 (ttt-90) REVERT: A 59 GLU cc_start: 0.8523 (pm20) cc_final: 0.8160 (pm20) REVERT: A 60 LEU cc_start: 0.9001 (mt) cc_final: 0.8654 (mt) REVERT: B 84 MET cc_start: 0.8894 (mmm) cc_final: 0.8259 (mmm) REVERT: D 47 GLN cc_start: 0.8751 (mt0) cc_final: 0.8538 (tt0) REVERT: D 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8723 (t0) REVERT: D 83 TYR cc_start: 0.8667 (m-10) cc_final: 0.8345 (m-80) REVERT: D 108 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7363 (mtpp) REVERT: F 25 ASN cc_start: 0.8393 (m110) cc_final: 0.7783 (m-40) REVERT: F 84 MET cc_start: 0.8707 (mmm) cc_final: 0.7961 (mmm) REVERT: F 91 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8712 (ttpp) REVERT: H 113 GLU cc_start: 0.8630 (tp30) cc_final: 0.8289 (tm-30) REVERT: K 20 MET cc_start: 0.6996 (mmp) cc_final: 0.6771 (mpp) REVERT: L 10 LEU cc_start: 0.8464 (pp) cc_final: 0.8163 (mm) REVERT: L 30 MET cc_start: 0.6372 (ptt) cc_final: 0.6152 (mmm) REVERT: C 104 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8840 (tp40) REVERT: G 36 LYS cc_start: 0.8180 (pttt) cc_final: 0.7644 (mmtp) REVERT: G 104 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8663 (mm110) outliers start: 4 outliers final: 1 residues processed: 174 average time/residue: 0.1472 time to fit residues: 35.1646 Evaluate side-chains 144 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 64 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 20.0000 chunk 12 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082359 restraints weight = 43755.026| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.19 r_work: 0.2825 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 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 = 0.2822 r_free = 0.2822 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: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14884 Z= 0.159 Angle : 0.640 10.836 21373 Z= 0.361 Chirality : 0.043 0.277 2420 Planarity : 0.004 0.037 1691 Dihedral : 30.064 158.944 4324 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.40 % Allowed : 12.67 % 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: 0.61 (0.27), residues: 989 helix: 1.44 (0.20), residues: 655 sheet: -0.49 (1.13), residues: 23 loop : -1.82 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.022 0.001 TYR H 121 PHE 0.015 0.002 PHE L 51 TRP 0.005 0.001 TRP K 61 HIS 0.006 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (14874) covalent geometry : angle 0.63541 / 0.36 (21358) hydrogen bonds : bond 0.04665 / 3.05 ( 828) hydrogen bonds : angle 3.27824 / 2.40 ( 2106) metal coordination : bond 0.02129 / 1.06 ( 8) metal coordination : angle 3.90094 / 1.80 ( 9) link_TRANS : bond 0.00129 / 0.07 ( 2) link_TRANS : angle 0.30066 / 0.14 ( 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: 12 poor density : 143 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9014 (m-80) cc_final: 0.8693 (m-80) REVERT: A 53 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.8219 (ttt-90) REVERT: A 59 GLU cc_start: 0.8421 (pm20) cc_final: 0.7975 (pm20) REVERT: D 68 ASP cc_start: 0.9125 (t70) cc_final: 0.8757 (t0) REVERT: D 83 TYR cc_start: 0.8685 (m-10) cc_final: 0.8229 (m-80) REVERT: D 108 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7313 (mtpp) REVERT: F 25 ASN cc_start: 0.8440 (m110) cc_final: 0.7909 (m-40) REVERT: F 91 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8718 (ttpp) REVERT: H 113 GLU cc_start: 0.8648 (tp30) cc_final: 0.8275 (tm-30) REVERT: H 119 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8642 (t) REVERT: K 20 MET cc_start: 0.6985 (mmp) cc_final: 0.6759 (mpp) REVERT: C 104 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8830 (tp40) REVERT: G 36 LYS cc_start: 0.8167 (pttt) cc_final: 0.7589 (mmmm) outliers start: 12 outliers final: 6 residues processed: 147 average time/residue: 0.1467 time to fit residues: 29.4464 Evaluate side-chains 145 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 66 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.138798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080738 restraints weight = 44511.530| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.19 r_work: 0.2798 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 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 = 0.2797 r_free = 0.2797 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: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14884 Z= 0.194 Angle : 0.657 7.788 21373 Z= 0.363 Chirality : 0.044 0.305 2420 Planarity : 0.004 0.036 1691 Dihedral : 30.140 160.267 4324 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.63 % Allowed : 14.19 % 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: 0.82 (0.27), residues: 989 helix: 1.56 (0.20), residues: 657 sheet: -0.54 (1.15), residues: 23 loop : -1.65 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.026 0.002 TYR H 121 PHE 0.012 0.002 PHE E 78 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 0.00408 / 0.19 (14874) covalent geometry : angle 0.65344 / 0.36 (21358) hydrogen bonds : bond 0.04768 / 3.11 ( 828) hydrogen bonds : angle 3.27957 / 2.40 ( 2106) metal coordination : bond 0.01867 / 0.93 ( 8) metal coordination : angle 3.29513 / 1.56 ( 9) link_TRANS : bond 0.00257 / 0.13 ( 2) link_TRANS : angle 0.28646 / 0.13 ( 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 158 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9066 (m-80) cc_final: 0.8841 (m-80) REVERT: A 59 GLU cc_start: 0.8319 (pm20) cc_final: 0.7928 (pm20) REVERT: A 60 LEU cc_start: 0.9035 (mt) cc_final: 0.8799 (mt) REVERT: D 68 ASP cc_start: 0.9134 (t70) cc_final: 0.8772 (t0) REVERT: D 83 TYR cc_start: 0.8737 (m-10) cc_final: 0.8380 (m-80) REVERT: D 101 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8618 (mp) REVERT: D 108 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7307 (mtpp) REVERT: F 25 ASN cc_start: 0.8446 (m110) cc_final: 0.7901 (m-40) REVERT: F 91 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8749 (ttpp) REVERT: H 68 ASP cc_start: 0.9229 (t0) cc_final: 0.8998 (t0) REVERT: H 113 GLU cc_start: 0.8649 (tp30) cc_final: 0.8247 (tm-30) REVERT: H 119 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8654 (t) REVERT: K 20 MET cc_start: 0.7035 (mmp) cc_final: 0.6790 (mpp) REVERT: L 30 MET cc_start: 0.6173 (mmm) cc_final: 0.5539 (ptt) REVERT: C 61 GLU cc_start: 0.8617 (tp30) cc_final: 0.8227 (tt0) REVERT: C 92 GLU cc_start: 0.8336 (mp0) cc_final: 0.8095 (mp0) REVERT: C 104 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8779 (tp40) REVERT: G 36 LYS cc_start: 0.8185 (pttt) cc_final: 0.7633 (mmtp) outliers start: 14 outliers final: 8 residues processed: 151 average time/residue: 0.1381 time to fit residues: 28.2422 Evaluate side-chains 149 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 H residue 119 THR Chi-restraints excluded: chain L residue 99 ILE 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: 0.0470 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 84 ASN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.083586 restraints weight = 43696.711| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.20 r_work: 0.2849 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 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: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14884 Z= 0.134 Angle : 0.604 10.218 21373 Z= 0.345 Chirality : 0.042 0.292 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.899 161.984 4324 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 1.18 (0.27), residues: 989 helix: 1.82 (0.20), residues: 657 sheet: -0.37 (1.12), residues: 23 loop : -1.45 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.024 0.001 TYR H 121 PHE 0.009 0.001 PHE L 69 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 0.00234 / 0.13 (14874) covalent geometry : angle 0.60196 / 0.34 (21358) hydrogen bonds : bond 0.04244 / 2.73 ( 828) hydrogen bonds : angle 3.04731 / 2.24 ( 2106) metal coordination : bond 0.01404 / 0.70 ( 8) metal coordination : angle 2.29127 / 1.13 ( 9) link_TRANS : bond 0.00064 / 0.03 ( 2) link_TRANS : angle 0.28683 / 0.11 ( 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 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9073 (m-80) cc_final: 0.8751 (m-80) REVERT: A 59 GLU cc_start: 0.8295 (pm20) cc_final: 0.7939 (pm20) REVERT: A 60 LEU cc_start: 0.9080 (mt) cc_final: 0.8844 (mt) REVERT: B 84 MET cc_start: 0.8857 (mmm) cc_final: 0.8294 (mmm) REVERT: D 68 ASP cc_start: 0.9108 (t70) cc_final: 0.8748 (t0) REVERT: D 83 TYR cc_start: 0.8670 (m-10) cc_final: 0.8252 (m-80) REVERT: D 108 LYS cc_start: 0.7485 (ttpt) cc_final: 0.7270 (mtpp) REVERT: F 25 ASN cc_start: 0.8440 (m110) cc_final: 0.7900 (m-40) REVERT: F 91 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8695 (ttpp) REVERT: H 68 ASP cc_start: 0.9192 (t0) cc_final: 0.8944 (t0) REVERT: H 113 GLU cc_start: 0.8623 (tp30) cc_final: 0.8214 (tm-30) REVERT: K 20 MET cc_start: 0.7019 (mmp) cc_final: 0.6751 (mpp) REVERT: C 61 GLU cc_start: 0.8556 (tp30) cc_final: 0.8237 (tt0) REVERT: C 92 GLU cc_start: 0.8325 (mp0) cc_final: 0.8105 (mp0) REVERT: C 104 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8828 (tp40) REVERT: G 36 LYS cc_start: 0.8197 (pttt) cc_final: 0.7621 (mmtp) outliers start: 10 outliers final: 6 residues processed: 148 average time/residue: 0.1383 time to fit residues: 27.7538 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 : 0.290 ------------------------------------------------------------------------------- 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 L residue 99 ILE 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: 0.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082731 restraints weight = 42246.875| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.14 r_work: 0.2832 rms_B_bonded: 4.56 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: 0.8214 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14884 Z= 0.163 Angle : 0.624 8.268 21373 Z= 0.351 Chirality : 0.042 0.313 2420 Planarity : 0.004 0.040 1691 Dihedral : 29.952 162.373 4324 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.51 % Allowed : 15.93 % Favored : 82.56 % 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: 1.24 (0.27), residues: 989 helix: 1.84 (0.20), residues: 657 sheet: -0.22 (1.14), residues: 23 loop : -1.38 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.026 0.001 TYR H 121 PHE 0.009 0.001 PHE E 78 TRP 0.003 0.001 TRP K 61 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (14874) covalent geometry : angle 0.62182 / 0.35 (21358) hydrogen bonds : bond 0.04422 / 2.87 ( 828) hydrogen bonds : angle 3.12899 / 2.29 ( 2106) metal coordination : bond 0.01607 / 0.80 ( 8) metal coordination : angle 2.46465 / 1.18 ( 9) link_TRANS : bond 0.00180 / 0.09 ( 2) link_TRANS : angle 0.23648 / 0.11 ( 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 147 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9093 (m-80) cc_final: 0.8751 (m-80) REVERT: A 59 GLU cc_start: 0.8254 (pm20) cc_final: 0.7836 (pm20) REVERT: A 60 LEU cc_start: 0.9060 (mt) cc_final: 0.8792 (mt) REVERT: D 68 ASP cc_start: 0.9126 (t70) cc_final: 0.8772 (t0) REVERT: D 83 TYR cc_start: 0.8733 (m-10) cc_final: 0.8263 (m-80) REVERT: D 101 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (mp) REVERT: D 108 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7336 (mtpp) REVERT: F 25 ASN cc_start: 0.8477 (m110) cc_final: 0.7927 (m-40) REVERT: F 88 TYR cc_start: 0.8630 (m-80) cc_final: 0.8351 (m-80) REVERT: F 91 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8701 (ttpp) REVERT: H 68 ASP cc_start: 0.9223 (t0) cc_final: 0.8988 (t0) REVERT: H 113 GLU cc_start: 0.8626 (tp30) cc_final: 0.8218 (tm-30) REVERT: K 20 MET cc_start: 0.7023 (mmp) cc_final: 0.6743 (mpp) REVERT: L 30 MET cc_start: 0.5993 (mmm) cc_final: 0.5166 (ptt) REVERT: C 61 GLU cc_start: 0.8573 (tp30) cc_final: 0.8241 (tt0) REVERT: C 92 GLU cc_start: 0.8349 (mp0) cc_final: 0.8133 (mp0) REVERT: C 104 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8821 (tp40) REVERT: G 11 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8234 (m) REVERT: G 36 LYS cc_start: 0.8102 (pttt) cc_final: 0.7624 (mmtp) outliers start: 13 outliers final: 7 residues processed: 139 average time/residue: 0.1417 time to fit residues: 26.6509 Evaluate side-chains 143 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN 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 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 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 91 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 chunk 104 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.140708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083309 restraints weight = 38827.632| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.02 r_work: 0.2853 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 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 = 0.2850 r_free = 0.2850 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: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14884 Z= 0.147 Angle : 0.608 8.037 21373 Z= 0.345 Chirality : 0.042 0.316 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.914 163.054 4324 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.40 % Allowed : 15.93 % Favored : 82.67 % 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: 1.35 (0.27), residues: 989 helix: 1.91 (0.20), residues: 657 sheet: -0.09 (1.15), residues: 23 loop : -1.32 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.027 0.001 TYR H 121 PHE 0.008 0.001 PHE L 62 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 0.00281 / 0.15 (14874) covalent geometry : angle 0.60664 / 0.34 (21358) hydrogen bonds : bond 0.04319 / 2.80 ( 828) hydrogen bonds : angle 3.07389 / 2.25 ( 2106) metal coordination : bond 0.01310 / 0.65 ( 8) metal coordination : angle 2.18472 / 1.05 ( 9) link_TRANS : bond 0.00131 / 0.07 ( 2) link_TRANS : angle 0.23143 / 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 158 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8212 (pm20) cc_final: 0.7791 (pm20) REVERT: A 60 LEU cc_start: 0.9040 (mt) cc_final: 0.8800 (mt) REVERT: B 84 MET cc_start: 0.8908 (mmm) cc_final: 0.8324 (mmm) REVERT: D 68 ASP cc_start: 0.9123 (t70) cc_final: 0.8768 (t0) REVERT: D 101 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8635 (mp) REVERT: D 108 LYS cc_start: 0.7566 (ttpt) cc_final: 0.7331 (mtpp) REVERT: F 25 ASN cc_start: 0.8474 (m110) cc_final: 0.7969 (m-40) REVERT: F 88 TYR cc_start: 0.8668 (m-80) cc_final: 0.8141 (m-80) REVERT: F 91 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8714 (ttpp) REVERT: H 68 ASP cc_start: 0.9230 (t0) cc_final: 0.9002 (t0) REVERT: H 113 GLU cc_start: 0.8609 (tp30) cc_final: 0.8197 (tm-30) REVERT: K 20 MET cc_start: 0.7051 (mmp) cc_final: 0.6760 (mpp) REVERT: L 29 ASP cc_start: 0.4937 (p0) cc_final: 0.4684 (p0) REVERT: L 30 MET cc_start: 0.5928 (mmm) cc_final: 0.5072 (ptt) REVERT: C 61 GLU cc_start: 0.8583 (tp30) cc_final: 0.8266 (tt0) REVERT: C 104 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8816 (tp40) REVERT: G 11 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8212 (m) REVERT: G 36 LYS cc_start: 0.8211 (pttt) cc_final: 0.7638 (mmtp) outliers start: 12 outliers final: 6 residues processed: 150 average time/residue: 0.1573 time to fit residues: 32.2515 Evaluate side-chains 145 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 11 SER 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: 4.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083649 restraints weight = 36392.449| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.93 r_work: 0.2860 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 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 = 0.2858 r_free = 0.2858 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: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14884 Z= 0.155 Angle : 0.612 7.532 21373 Z= 0.346 Chirality : 0.042 0.327 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.915 163.992 4324 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.40 % Allowed : 16.74 % 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: 1.36 (0.27), residues: 989 helix: 1.93 (0.20), residues: 657 sheet: 0.00 (1.12), residues: 23 loop : -1.36 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.028 0.002 TYR H 121 PHE 0.007 0.001 PHE A 78 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 0.00303 / 0.15 (14874) covalent geometry : angle 0.61064 / 0.35 (21358) hydrogen bonds : bond 0.04353 / 2.82 ( 828) hydrogen bonds : angle 3.08537 / 2.26 ( 2106) metal coordination : bond 0.01206 / 0.60 ( 8) metal coordination : angle 2.33722 / 1.10 ( 9) link_TRANS : bond 0.00105 / 0.05 ( 2) link_TRANS : angle 0.22158 / 0.10 ( 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 149 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9034 (m-80) cc_final: 0.8669 (m-80) REVERT: A 59 GLU cc_start: 0.8204 (pm20) cc_final: 0.7781 (pm20) REVERT: A 60 LEU cc_start: 0.9042 (mt) cc_final: 0.8783 (mt) REVERT: B 84 MET cc_start: 0.8898 (mmm) cc_final: 0.8274 (mmm) REVERT: D 68 ASP cc_start: 0.9120 (t70) cc_final: 0.8762 (t0) REVERT: D 101 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8639 (mp) REVERT: D 108 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7331 (mtpp) REVERT: F 25 ASN cc_start: 0.8468 (m110) cc_final: 0.7946 (m-40) REVERT: F 91 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8749 (ttpp) REVERT: H 68 ASP cc_start: 0.9230 (t0) cc_final: 0.8992 (t0) REVERT: C 61 GLU cc_start: 0.8580 (tp30) cc_final: 0.8260 (tt0) REVERT: C 104 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8814 (tp40) REVERT: G 11 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8205 (m) REVERT: G 36 LYS cc_start: 0.8102 (pttt) cc_final: 0.7635 (mmtp) outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.1386 time to fit residues: 27.1929 Evaluate side-chains 143 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE 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: 5.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082462 restraints weight = 41735.204| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.13 r_work: 0.2837 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 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 = 0.2824 r_free = 0.2824 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: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14884 Z= 0.176 Angle : 0.646 11.312 21373 Z= 0.358 Chirality : 0.043 0.339 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.972 164.711 4324 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.93 % Allowed : 17.09 % Favored : 81.98 % 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: 1.32 (0.27), residues: 989 helix: 1.89 (0.20), residues: 658 sheet: 0.14 (1.13), residues: 23 loop : -1.37 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.038 0.002 TYR F 88 PHE 0.010 0.001 PHE E 78 TRP 0.002 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 0.64446 / 0.36 (21358) hydrogen bonds : bond 0.04466 / 2.91 ( 828) hydrogen bonds : angle 3.14970 / 2.30 ( 2106) metal coordination : bond 0.01279 / 0.64 ( 8) metal coordination : angle 2.29379 / 1.05 ( 9) link_TRANS : bond 0.00239 / 0.12 ( 2) link_TRANS : angle 0.29316 / 0.15 ( 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 148 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8176 (pm20) cc_final: 0.7700 (pm20) REVERT: A 60 LEU cc_start: 0.9038 (mt) cc_final: 0.8745 (mt) REVERT: B 84 MET cc_start: 0.8901 (mmm) cc_final: 0.8285 (mmm) REVERT: D 68 ASP cc_start: 0.9136 (t70) cc_final: 0.8768 (t0) REVERT: D 101 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8662 (mp) REVERT: D 108 LYS cc_start: 0.7612 (ttpt) cc_final: 0.7347 (mtpp) REVERT: F 25 ASN cc_start: 0.8458 (m110) cc_final: 0.7961 (m-40) REVERT: F 91 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8756 (ttpp) REVERT: H 68 ASP cc_start: 0.9294 (t0) cc_final: 0.9072 (t0) REVERT: K 20 MET cc_start: 0.7356 (mmm) cc_final: 0.7068 (mpp) REVERT: L 30 MET cc_start: 0.6099 (mmm) cc_final: 0.5128 (ptt) REVERT: C 61 GLU cc_start: 0.8615 (tp30) cc_final: 0.8274 (tt0) REVERT: C 104 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8824 (tp40) REVERT: G 11 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8218 (m) REVERT: G 36 LYS cc_start: 0.8122 (pttt) cc_final: 0.7647 (mmtp) outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 0.1453 time to fit residues: 28.5547 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 : 0.366 ------------------------------------------------------------------------------- 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 H residue 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 11 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: 0.7980 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.142296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084807 restraints weight = 47245.555| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.29 r_work: 0.2866 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 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: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14884 Z= 0.133 Angle : 0.618 11.422 21373 Z= 0.349 Chirality : 0.041 0.324 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.797 165.844 4324 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.70 % Allowed : 17.56 % Favored : 81.74 % 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: 1.48 (0.27), residues: 989 helix: 2.01 (0.20), residues: 658 sheet: 0.42 (1.17), residues: 23 loop : -1.31 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.038 0.002 TYR D 83 PHE 0.007 0.001 PHE L 62 TRP 0.007 0.001 TRP K 61 HIS 0.009 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (14874) covalent geometry : angle 0.61702 / 0.35 (21358) hydrogen bonds : bond 0.04150 / 2.67 ( 828) hydrogen bonds : angle 3.02073 / 2.21 ( 2106) metal coordination : bond 0.01049 / 0.52 ( 8) metal coordination : angle 1.91959 / 0.86 ( 9) link_TRANS : bond 0.00103 / 0.05 ( 2) link_TRANS : angle 0.38194 / 0.19 ( 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: 6 poor density : 155 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9028 (m-80) cc_final: 0.8633 (m-80) REVERT: A 59 GLU cc_start: 0.8094 (pm20) cc_final: 0.7614 (pm20) REVERT: A 60 LEU cc_start: 0.8977 (mt) cc_final: 0.8752 (mt) REVERT: D 68 ASP cc_start: 0.9111 (t70) cc_final: 0.8746 (t0) REVERT: D 83 TYR cc_start: 0.8648 (m-80) cc_final: 0.8252 (m-80) REVERT: D 101 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8623 (mp) REVERT: D 108 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7381 (mtpp) REVERT: F 25 ASN cc_start: 0.8466 (m110) cc_final: 0.7959 (m-40) REVERT: F 84 MET cc_start: 0.8043 (mmm) cc_final: 0.7801 (mmm) REVERT: F 91 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8722 (ttpp) REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.9027 (t0) REVERT: K 20 MET cc_start: 0.7333 (mmm) cc_final: 0.7034 (mpp) REVERT: L 30 MET cc_start: 0.6018 (mmm) cc_final: 0.5471 (ptt) REVERT: L 110 LEU cc_start: 0.6246 (mt) cc_final: 0.5543 (tp) REVERT: C 61 GLU cc_start: 0.8594 (tp30) cc_final: 0.8285 (tt0) REVERT: C 104 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8958 (mm-40) REVERT: G 11 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8198 (m) REVERT: G 36 LYS cc_start: 0.8164 (pttt) cc_final: 0.7637 (mmtp) outliers start: 6 outliers final: 4 residues processed: 157 average time/residue: 0.1570 time to fit residues: 33.7448 Evaluate side-chains 155 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 11 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: 0.9980 chunk 110 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 10 optimal weight: 0.0170 chunk 120 optimal weight: 0.0050 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.4432 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.143186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086448 restraints weight = 36100.568| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.96 r_work: 0.2903 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14884 Z= 0.130 Angle : 0.611 9.820 21373 Z= 0.347 Chirality : 0.041 0.330 2420 Planarity : 0.004 0.048 1691 Dihedral : 29.734 166.576 4324 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.58 % Allowed : 18.37 % Favored : 81.05 % 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: 1.60 (0.27), residues: 989 helix: 2.11 (0.20), residues: 657 sheet: 0.59 (1.19), residues: 23 loop : -1.27 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 79 TYR 0.035 0.002 TYR D 83 PHE 0.007 0.001 PHE H 70 TRP 0.036 0.002 TRP K 61 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (14874) covalent geometry : angle 0.61040 / 0.35 (21358) hydrogen bonds : bond 0.04068 / 2.62 ( 828) hydrogen bonds : angle 2.99900 / 2.19 ( 2106) metal coordination : bond 0.00781 / 0.39 ( 8) metal coordination : angle 1.87796 / 0.86 ( 9) link_TRANS : bond 0.00102 / 0.05 ( 2) link_TRANS : angle 0.36722 / 0.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.12 seconds wall clock time: 69 minutes 54.40 seconds (4194.40 seconds total)