Starting phenix.real_space_refine on Sun Aug 24 08:29:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_42446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_42446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_42446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_42446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8upf_42446/08_2025/8upf_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-2.0-5787/lib/python3.9/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: 3.15, 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: 0.95 Conformation dependent library (CDL) restraints added in 411.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.91 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: 2.49 Time building geometry restraints manager: 1.33 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=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.72e-02 3.38e+03 3.68e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C4' DG I 9 " pdb=" C3' DG I 9 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 20154 1.30 - 2.61: 1091 2.61 - 3.91: 82 3.91 - 5.21: 21 5.21 - 6.52: 10 Bond angle restraints: 21358 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 126.18 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C3' DT J 66 " pdb=" C2' DT J 66 " pdb=" C1' DT J 66 " ideal model delta sigma weight residual 101.60 97.80 3.80 1.50e+00 4.44e-01 6.43e+00 angle pdb=" C3' DT J -29 " pdb=" C2' DT J -29 " pdb=" C1' DT J -29 " ideal model delta sigma weight residual 101.60 97.87 3.73 1.50e+00 4.44e-01 6.19e+00 angle pdb=" N LYS E 37 " pdb=" CA LYS E 37 " pdb=" C LYS E 37 " ideal model delta sigma weight residual 111.00 117.52 -6.52 2.80e+00 1.28e-01 5.42e+00 angle pdb=" N LYS A 37 " pdb=" CA LYS A 37 " pdb=" C LYS A 37 " ideal model delta sigma weight residual 111.00 117.51 -6.51 2.80e+00 1.28e-01 5.41e+00 ... (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 - 0.033: 1533 0.033 - 0.067: 702 0.067 - 0.100: 133 0.100 - 0.133: 44 0.133 - 0.167: 8 Chirality restraints: 2420 Sorted by residual: 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 chirality pdb=" CA LYS A 37 " pdb=" N LYS A 37 " pdb=" C LYS A 37 " pdb=" CB LYS A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-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: 1.520 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.800 Find NCS groups from input model: 0.100 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: 19.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.008 0.283 14884 Z= 0.318 Angle : 0.735 27.209 21373 Z= 0.395 Chirality : 0.039 0.167 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 aren 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 covalent geometry : bond 0.00692 (14874) covalent geometry : angle 0.64995 (21358) hydrogen bonds : bond 0.10676 ( 828) hydrogen bonds : angle 5.05605 ( 2106) metal coordination : bond 0.15181 ( 8) metal coordination : angle 16.71906 ( 9) link_TRANS : bond 0.00050 ( 2) link_TRANS : angle 0.74427 ( 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 : 0.272 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: 0.8475 (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: 0.1699 time to fit residues: 38.4076 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 : 0.345 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: B 25 ASN 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 = 0.3927 r_free = 0.3927 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084501 restraints weight = 35757.654| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.99 r_work: 0.2876 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 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 = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14884 Z= 0.152 Angle : 0.571 8.039 21373 Z= 0.330 Chirality : 0.035 0.158 2420 Planarity : 0.004 0.034 1691 Dihedral : 29.596 156.520 4324 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.47 % Allowed : 10.35 % Favored : 89.19 % 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 aren not related in a simple way. whole: 0.09 (0.26), residues: 989 helix: 0.99 (0.20), residues: 655 sheet: -1.11 (1.07), residues: 23 loop : -1.87 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.021 0.001 TYR H 121 PHE 0.012 0.001 PHE L 62 TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00331 (14874) covalent geometry : angle 0.56458 (21358) hydrogen bonds : bond 0.03994 ( 828) hydrogen bonds : angle 3.23805 ( 2106) metal coordination : bond 0.01586 ( 8) metal coordination : angle 4.16128 ( 9) link_TRANS : bond 0.00180 ( 2) link_TRANS : angle 0.31718 ( 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 168 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9035 (m-80) cc_final: 0.8695 (m-80) REVERT: A 42 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7953 (mtp85) REVERT: A 59 GLU cc_start: 0.8381 (pm20) cc_final: 0.8081 (pm20) REVERT: D 68 ASP cc_start: 0.9121 (t70) cc_final: 0.8815 (t0) REVERT: D 83 TYR cc_start: 0.8679 (m-10) cc_final: 0.8159 (m-10) REVERT: D 108 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7350 (mtpp) REVERT: F 25 ASN cc_start: 0.8479 (m110) cc_final: 0.7936 (m-40) REVERT: F 91 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8736 (ttpp) REVERT: H 86 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8453 (ttm-80) REVERT: H 113 GLU cc_start: 0.8623 (tp30) cc_final: 0.8258 (tm-30) REVERT: K 20 MET cc_start: 0.7026 (mmp) cc_final: 0.6777 (mpp) REVERT: C 104 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8837 (tp40) REVERT: G 36 LYS cc_start: 0.8229 (pttt) cc_final: 0.7704 (mmtp) REVERT: G 92 GLU cc_start: 0.8374 (mp0) cc_final: 0.8006 (mp0) REVERT: G 104 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8779 (mm110) outliers start: 4 outliers final: 1 residues processed: 166 average time/residue: 0.1363 time to fit residues: 30.3860 Evaluate side-chains 140 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084356 restraints weight = 47398.344| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.30 r_work: 0.2859 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14884 Z= 0.154 Angle : 0.558 6.729 21373 Z= 0.321 Chirality : 0.034 0.146 2420 Planarity : 0.004 0.036 1691 Dihedral : 29.421 157.460 4324 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.40 % Allowed : 13.26 % Favored : 85.35 % 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 aren not related in a simple way. whole: 1.05 (0.27), residues: 989 helix: 1.75 (0.20), residues: 657 sheet: -0.28 (1.19), residues: 23 loop : -1.62 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.023 0.001 TYR H 121 PHE 0.007 0.001 PHE L 62 TRP 0.004 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00341 (14874) covalent geometry : angle 0.55459 (21358) hydrogen bonds : bond 0.03835 ( 828) hydrogen bonds : angle 3.02288 ( 2106) metal coordination : bond 0.01568 ( 8) metal coordination : angle 3.17681 ( 9) link_TRANS : bond 0.00158 ( 2) link_TRANS : angle 0.33052 ( 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 168 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8246 (pm20) cc_final: 0.7904 (pm20) REVERT: A 60 LEU cc_start: 0.9029 (mt) cc_final: 0.8766 (mt) REVERT: A 90 MET cc_start: 0.8383 (mmp) cc_final: 0.8176 (mmt) REVERT: B 84 MET cc_start: 0.8882 (mmm) cc_final: 0.8327 (mmm) REVERT: D 68 ASP cc_start: 0.9124 (t70) cc_final: 0.8804 (t0) REVERT: D 83 TYR cc_start: 0.8722 (m-10) cc_final: 0.8242 (m-80) REVERT: F 25 ASN cc_start: 0.8500 (m110) cc_final: 0.7959 (m-40) REVERT: F 91 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8728 (ttpp) REVERT: H 68 ASP cc_start: 0.9166 (t0) cc_final: 0.8930 (t0) REVERT: H 86 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.8352 (ttm-80) REVERT: H 113 GLU cc_start: 0.8627 (tp30) cc_final: 0.8210 (tm-30) REVERT: K 20 MET cc_start: 0.6949 (mmp) cc_final: 0.6680 (mpp) REVERT: L 30 MET cc_start: 0.6173 (mmm) cc_final: 0.5877 (ptt) REVERT: C 92 GLU cc_start: 0.8408 (mp0) cc_final: 0.8036 (mp0) REVERT: C 104 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8837 (tp40) REVERT: G 36 LYS cc_start: 0.8135 (pttt) cc_final: 0.7652 (mmtp) REVERT: G 92 GLU cc_start: 0.8534 (mp0) cc_final: 0.8045 (mp0) outliers start: 12 outliers final: 7 residues processed: 161 average time/residue: 0.1288 time to fit residues: 28.0607 Evaluate side-chains 144 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE 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: 40.0000 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078123 restraints weight = 44725.543| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.24 r_work: 0.2756 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14884 Z= 0.335 Angle : 0.667 7.464 21373 Z= 0.375 Chirality : 0.041 0.162 2420 Planarity : 0.005 0.037 1691 Dihedral : 30.061 157.373 4324 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.40 % Allowed : 16.28 % Favored : 82.33 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 989 helix: 1.56 (0.20), residues: 657 sheet: -0.18 (1.18), residues: 23 loop : -1.69 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 55 TYR 0.031 0.002 TYR H 121 PHE 0.015 0.002 PHE E 78 TRP 0.005 0.001 TRP L 33 HIS 0.006 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00789 (14874) covalent geometry : angle 0.66387 (21358) hydrogen bonds : bond 0.04884 ( 828) hydrogen bonds : angle 3.47503 ( 2106) metal coordination : bond 0.02075 ( 8) metal coordination : angle 3.36641 ( 9) link_TRANS : bond 0.00426 ( 2) link_TRANS : angle 0.40478 ( 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 146 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8194 (pm20) cc_final: 0.7796 (pm20) REVERT: D 68 ASP cc_start: 0.9116 (t70) cc_final: 0.8738 (t0) REVERT: F 25 ASN cc_start: 0.8534 (m110) cc_final: 0.7985 (m-40) REVERT: F 91 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8777 (ttpp) REVERT: H 68 ASP cc_start: 0.9323 (t0) cc_final: 0.9123 (t0) REVERT: H 113 GLU cc_start: 0.8672 (tp30) cc_final: 0.7674 (tm-30) REVERT: C 61 GLU cc_start: 0.8653 (tp30) cc_final: 0.8136 (tt0) REVERT: C 92 GLU cc_start: 0.8424 (mp0) cc_final: 0.8196 (mp0) REVERT: C 104 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8819 (tp40) REVERT: G 36 LYS cc_start: 0.8325 (pttt) cc_final: 0.7837 (mmtp) REVERT: G 92 GLU cc_start: 0.8666 (mp0) cc_final: 0.7772 (mp0) outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.1410 time to fit residues: 26.7919 Evaluate side-chains 134 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN L 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084404 restraints weight = 43907.495| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.19 r_work: 0.2853 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14884 Z= 0.152 Angle : 0.560 8.472 21373 Z= 0.324 Chirality : 0.034 0.144 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.353 159.393 4324 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 16.28 % Favored : 82.21 % 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 aren not related in a simple way. whole: 1.33 (0.27), residues: 989 helix: 1.93 (0.20), residues: 659 sheet: 0.15 (1.12), residues: 23 loop : -1.45 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.024 0.002 TYR H 121 PHE 0.014 0.001 PHE K 53 TRP 0.003 0.001 TRP L 33 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00336 (14874) covalent geometry : angle 0.55832 (21358) hydrogen bonds : bond 0.03784 ( 828) hydrogen bonds : angle 2.99353 ( 2106) metal coordination : bond 0.01191 ( 8) metal coordination : angle 2.27603 ( 9) link_TRANS : bond 0.00064 ( 2) link_TRANS : angle 0.23954 ( 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 156 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7993 (pm20) cc_final: 0.7723 (pm20) REVERT: B 84 MET cc_start: 0.8878 (mmm) cc_final: 0.8272 (mmm) REVERT: D 59 MET cc_start: 0.8666 (tpp) cc_final: 0.8278 (tpt) REVERT: D 68 ASP cc_start: 0.9095 (t70) cc_final: 0.8765 (t0) REVERT: F 25 ASN cc_start: 0.8502 (m110) cc_final: 0.7987 (m-40) REVERT: F 88 TYR cc_start: 0.8724 (m-80) cc_final: 0.8215 (m-80) REVERT: F 91 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8715 (ttpp) REVERT: H 68 ASP cc_start: 0.9248 (t0) cc_final: 0.9000 (t0) REVERT: K 20 MET cc_start: 0.7187 (mmm) cc_final: 0.6810 (mpp) REVERT: L 30 MET cc_start: 0.5949 (mmm) cc_final: 0.5071 (ptt) REVERT: C 61 GLU cc_start: 0.8610 (tp30) cc_final: 0.8279 (tt0) REVERT: C 92 GLU cc_start: 0.8364 (mp0) cc_final: 0.8094 (mp0) REVERT: C 104 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8829 (tp40) REVERT: C 110 ASN cc_start: 0.8818 (t0) cc_final: 0.8558 (t0) REVERT: G 36 LYS cc_start: 0.8198 (pttt) cc_final: 0.7743 (mmtp) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.1354 time to fit residues: 27.7939 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 : 0.361 ------------------------------------------------------------------------------- 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 112 ILE 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 L residue 99 ILE Chi-restraints excluded: chain G residue 11 SER 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: 5.9990 chunk 100 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081696 restraints weight = 42438.233| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.11 r_work: 0.2812 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 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 = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14884 Z= 0.221 Angle : 0.594 8.176 21373 Z= 0.338 Chirality : 0.036 0.142 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.657 158.887 4324 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.51 % Allowed : 16.51 % 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 aren not related in a simple way. whole: 1.30 (0.27), residues: 989 helix: 1.88 (0.20), residues: 659 sheet: 0.29 (1.08), residues: 23 loop : -1.41 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.030 0.002 TYR H 121 PHE 0.015 0.001 PHE K 53 TRP 0.026 0.002 TRP K 61 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00511 (14874) covalent geometry : angle 0.59163 (21358) hydrogen bonds : bond 0.04225 ( 828) hydrogen bonds : angle 3.16486 ( 2106) metal coordination : bond 0.01474 ( 8) metal coordination : angle 2.43911 ( 9) link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.29257 ( 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 148 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8878 (mmm) cc_final: 0.8300 (mmm) REVERT: D 68 ASP cc_start: 0.9096 (t70) cc_final: 0.8734 (t0) REVERT: D 83 TYR cc_start: 0.8977 (m-10) cc_final: 0.8684 (m-80) REVERT: F 25 ASN cc_start: 0.8481 (m110) cc_final: 0.7996 (m-40) REVERT: H 68 ASP cc_start: 0.9297 (t0) cc_final: 0.9076 (t0) REVERT: K 20 MET cc_start: 0.7246 (mmm) cc_final: 0.6919 (mpp) REVERT: L 30 MET cc_start: 0.6033 (mmm) cc_final: 0.5179 (ptt) REVERT: C 61 GLU cc_start: 0.8612 (tp30) cc_final: 0.8236 (tt0) REVERT: C 92 GLU cc_start: 0.8399 (mp0) cc_final: 0.8165 (mp0) REVERT: C 104 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8823 (tp40) REVERT: G 36 LYS cc_start: 0.8241 (pttt) cc_final: 0.7726 (mmtp) outliers start: 13 outliers final: 9 residues processed: 141 average time/residue: 0.1390 time to fit residues: 26.6735 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 : 0.308 ------------------------------------------------------------------------------- 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 F residue 50 ILE Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN K 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080036 restraints weight = 39173.062| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.01 r_work: 0.2792 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14884 Z= 0.264 Angle : 0.622 8.870 21373 Z= 0.353 Chirality : 0.038 0.171 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.877 158.675 4324 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 16.74 % Favored : 81.63 % 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 aren not related in a simple way. whole: 1.13 (0.27), residues: 989 helix: 1.76 (0.20), residues: 657 sheet: 0.32 (1.08), residues: 23 loop : -1.49 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.031 0.002 TYR H 121 PHE 0.016 0.002 PHE K 53 TRP 0.041 0.002 TRP K 61 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00617 (14874) covalent geometry : angle 0.61958 (21358) hydrogen bonds : bond 0.04489 ( 828) hydrogen bonds : angle 3.28007 ( 2106) metal coordination : bond 0.01663 ( 8) metal coordination : angle 2.88343 ( 9) link_TRANS : bond 0.00300 ( 2) link_TRANS : angle 0.40119 ( 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 156 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8047 (pm20) cc_final: 0.7636 (pm20) REVERT: B 84 MET cc_start: 0.8943 (mmm) cc_final: 0.8350 (mmm) REVERT: D 68 ASP cc_start: 0.9084 (t70) cc_final: 0.8698 (t0) REVERT: D 83 TYR cc_start: 0.8991 (m-10) cc_final: 0.8689 (m-80) REVERT: D 101 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8555 (mp) REVERT: F 25 ASN cc_start: 0.8477 (m110) cc_final: 0.7967 (m-40) REVERT: F 88 TYR cc_start: 0.8695 (m-80) cc_final: 0.8402 (m-80) REVERT: H 68 ASP cc_start: 0.9298 (t0) cc_final: 0.9085 (t0) REVERT: K 20 MET cc_start: 0.7188 (mmm) cc_final: 0.6878 (mpp) REVERT: K 68 ARG cc_start: 0.8203 (ptp-170) cc_final: 0.7913 (ptp-170) REVERT: L 65 PRO cc_start: 0.6581 (Cg_endo) cc_final: 0.6189 (Cg_exo) REVERT: C 61 GLU cc_start: 0.8663 (tp30) cc_final: 0.8106 (tt0) REVERT: C 92 GLU cc_start: 0.8391 (mp0) cc_final: 0.8159 (mp0) REVERT: C 104 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8736 (tp40) REVERT: G 36 LYS cc_start: 0.8267 (pttt) cc_final: 0.7720 (mmtp) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.1330 time to fit residues: 27.2459 Evaluate side-chains 142 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.142100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085177 restraints weight = 36722.968| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.97 r_work: 0.2886 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14884 Z= 0.153 Angle : 0.569 10.312 21373 Z= 0.327 Chirality : 0.034 0.139 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.262 160.350 4324 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.40 % Allowed : 17.67 % Favored : 80.93 % 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 aren not related in a simple way. whole: 1.50 (0.27), residues: 989 helix: 2.03 (0.20), residues: 658 sheet: 0.50 (1.11), residues: 23 loop : -1.33 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.024 0.002 TYR H 121 PHE 0.017 0.001 PHE K 53 TRP 0.031 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00340 (14874) covalent geometry : angle 0.56776 (21358) hydrogen bonds : bond 0.03738 ( 828) hydrogen bonds : angle 2.93629 ( 2106) metal coordination : bond 0.01008 ( 8) metal coordination : angle 2.11749 ( 9) link_TRANS : bond 0.00070 ( 2) link_TRANS : angle 0.27212 ( 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 151 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9013 (m-80) cc_final: 0.8608 (m-80) REVERT: B 84 MET cc_start: 0.8816 (mmm) cc_final: 0.8287 (mmm) REVERT: D 68 ASP cc_start: 0.8984 (t70) cc_final: 0.8644 (t0) REVERT: F 25 ASN cc_start: 0.8453 (m110) cc_final: 0.7966 (m-40) REVERT: H 68 ASP cc_start: 0.9219 (t0) cc_final: 0.8997 (t0) REVERT: K 20 MET cc_start: 0.7159 (mmm) cc_final: 0.6862 (mpp) REVERT: K 68 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.8085 (ptp-170) REVERT: L 65 PRO cc_start: 0.6558 (Cg_endo) cc_final: 0.6166 (Cg_exo) REVERT: C 23 LEU cc_start: 0.8733 (mt) cc_final: 0.8514 (mt) REVERT: C 61 GLU cc_start: 0.8548 (tp30) cc_final: 0.8200 (tt0) REVERT: C 92 GLU cc_start: 0.8347 (mp0) cc_final: 0.8122 (mp0) REVERT: C 104 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8655 (tp40) REVERT: C 110 ASN cc_start: 0.8819 (t0) cc_final: 0.8596 (t0) REVERT: G 36 LYS cc_start: 0.8146 (pttt) cc_final: 0.7698 (mmtp) outliers start: 12 outliers final: 9 residues processed: 146 average time/residue: 0.1350 time to fit residues: 27.0515 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 : 0.313 ------------------------------------------------------------------------------- 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 112 ILE 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 L residue 99 ILE Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 0.0270 chunk 76 optimal weight: 5.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085014 restraints weight = 42098.754| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.15 r_work: 0.2874 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 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 = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14884 Z= 0.154 Angle : 0.575 10.118 21373 Z= 0.328 Chirality : 0.034 0.138 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.310 160.111 4324 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 18.60 % Favored : 80.35 % 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 aren not related in a simple way. whole: 1.58 (0.27), residues: 989 helix: 2.09 (0.20), residues: 660 sheet: 0.53 (1.11), residues: 23 loop : -1.30 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 79 TYR 0.025 0.002 TYR H 121 PHE 0.019 0.001 PHE K 53 TRP 0.035 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00341 (14874) covalent geometry : angle 0.57369 (21358) hydrogen bonds : bond 0.03756 ( 828) hydrogen bonds : angle 2.92775 ( 2106) metal coordination : bond 0.00604 ( 8) metal coordination : angle 2.07710 ( 9) link_TRANS : bond 0.00075 ( 2) link_TRANS : angle 0.26342 ( 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 : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8813 (mmm) cc_final: 0.8318 (mmm) REVERT: D 68 ASP cc_start: 0.8998 (t70) cc_final: 0.8670 (t0) REVERT: D 101 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8556 (mp) REVERT: F 25 ASN cc_start: 0.8414 (m110) cc_final: 0.7898 (m-40) REVERT: H 37 TYR cc_start: 0.9095 (m-80) cc_final: 0.8865 (m-80) REVERT: H 68 ASP cc_start: 0.9249 (t0) cc_final: 0.8996 (t0) REVERT: K 20 MET cc_start: 0.7096 (mmm) cc_final: 0.6894 (mpp) REVERT: L 65 PRO cc_start: 0.6553 (Cg_endo) cc_final: 0.6160 (Cg_exo) REVERT: C 61 GLU cc_start: 0.8547 (tp30) cc_final: 0.8214 (tt0) REVERT: C 92 GLU cc_start: 0.8368 (mp0) cc_final: 0.8144 (mp0) REVERT: C 104 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8668 (tp40) REVERT: G 36 LYS cc_start: 0.8159 (pttt) cc_final: 0.7697 (mmtp) outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.1587 time to fit residues: 30.2890 Evaluate side-chains 142 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 C residue 118 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.3980 chunk 44 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086884 restraints weight = 47639.493| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.32 r_work: 0.2903 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14884 Z= 0.140 Angle : 0.564 9.999 21373 Z= 0.322 Chirality : 0.034 0.138 2420 Planarity : 0.004 0.040 1691 Dihedral : 29.119 160.171 4324 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.93 % Allowed : 18.49 % Favored : 80.58 % 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 aren not related in a simple way. whole: 1.79 (0.27), residues: 989 helix: 2.22 (0.20), residues: 659 sheet: 0.73 (1.13), residues: 23 loop : -1.15 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.023 0.001 TYR H 121 PHE 0.019 0.001 PHE K 53 TRP 0.033 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00301 (14874) covalent geometry : angle 0.56244 (21358) hydrogen bonds : bond 0.03592 ( 828) hydrogen bonds : angle 2.83286 ( 2106) metal coordination : bond 0.00200 ( 8) metal coordination : angle 2.17780 ( 9) link_TRANS : bond 0.00032 ( 2) link_TRANS : angle 0.24112 ( 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 144 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.383 Fit side-chains REVERT: A 41 TYR cc_start: 0.9023 (m-80) cc_final: 0.8604 (m-80) REVERT: B 84 MET cc_start: 0.8780 (mmm) cc_final: 0.8271 (mmm) REVERT: D 68 ASP cc_start: 0.9006 (t70) cc_final: 0.8716 (t0) REVERT: D 101 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8610 (mp) REVERT: F 25 ASN cc_start: 0.8435 (m110) cc_final: 0.7923 (m-40) REVERT: H 68 ASP cc_start: 0.9248 (t0) cc_final: 0.9026 (t0) REVERT: L 65 PRO cc_start: 0.6443 (Cg_endo) cc_final: 0.6040 (Cg_exo) REVERT: C 61 GLU cc_start: 0.8566 (tp30) cc_final: 0.8285 (tt0) REVERT: C 92 GLU cc_start: 0.8383 (mp0) cc_final: 0.8152 (mp0) REVERT: G 36 LYS cc_start: 0.8252 (pttt) cc_final: 0.7712 (mmtp) REVERT: G 72 ASP cc_start: 0.8869 (m-30) cc_final: 0.8553 (m-30) outliers start: 8 outliers final: 5 residues processed: 139 average time/residue: 0.1387 time to fit residues: 26.4652 Evaluate side-chains 138 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 112 ILE 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 C residue 118 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.086613 restraints weight = 36438.636| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.98 r_work: 0.2910 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 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 = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14884 Z= 0.154 Angle : 0.575 10.741 21373 Z= 0.326 Chirality : 0.034 0.137 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.182 159.494 4324 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.70 % Allowed : 19.30 % Favored : 80.00 % 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 aren not related in a simple way. whole: 1.77 (0.27), residues: 989 helix: 2.20 (0.20), residues: 662 sheet: 0.70 (1.14), residues: 23 loop : -1.19 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.024 0.002 TYR H 121 PHE 0.022 0.001 PHE K 53 TRP 0.034 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00342 (14874) covalent geometry : angle 0.57389 (21358) hydrogen bonds : bond 0.03716 ( 828) hydrogen bonds : angle 2.87092 ( 2106) metal coordination : bond 0.00258 ( 8) metal coordination : angle 1.98874 ( 9) link_TRANS : bond 0.00088 ( 2) link_TRANS : angle 0.24891 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.22 seconds wall clock time: 63 minutes 43.81 seconds (3823.81 seconds total)