Starting phenix.real_space_refine on Sat Aug 8 08:16:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9u_64888/08_2026/9v9u_64888.cif" } resolution = 3.7 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= -0.000 sd= 0.003 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 14036 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 8 6.06 5 P 264 5.49 5 S 57 5.16 5 C 9181 2.51 5 N 2922 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 15920 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2688 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2724 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 909 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "P" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" 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} Chain: "N" 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} 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} Chain: "L" 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 11418 SG CYS M 18 69.259 25.876 73.137 1.00 69.49 S ATOM 11439 SG CYS M 21 67.869 22.468 72.898 1.00 75.69 S ATOM 11577 SG CYS M 39 68.539 24.647 69.713 1.00 71.48 S ATOM 11599 SG CYS M 42 65.525 25.165 72.027 1.00 63.87 S ATOM 11536 SG CYS M 34 72.408 39.228 73.126 1.00 62.32 S ATOM 11694 SG CYS M 53 70.186 37.509 75.756 1.00 57.81 S ATOM 11715 SG CYS M 56 72.370 40.519 76.730 1.00 59.42 S ATOM 12500 SG CYS N 51 87.226 39.402 54.890 1.00 83.72 S ATOM 12521 SG CYS N 54 90.840 39.534 54.691 1.00 90.14 S ATOM 12669 SG CYS N 72 89.219 41.302 57.751 1.00 77.28 S ATOM 12688 SG CYS N 75 88.938 42.790 54.313 1.00 70.00 S ATOM 12623 SG CYS N 67 73.875 41.191 55.392 1.00 53.71 S ATOM 12777 SG CYS N 87 76.118 42.353 52.490 1.00 76.05 S ATOM 12797 SG CYS N 90 72.371 41.778 51.944 1.00 78.81 S ATOM 13728 SG CYS K 18 58.014 124.698 54.216 1.00 60.77 S ATOM 13749 SG CYS K 21 58.832 127.949 52.448 1.00 65.75 S ATOM 13887 SG CYS K 39 57.890 124.848 50.457 1.00 52.43 S ATOM 13909 SG CYS K 42 61.280 125.050 52.224 1.00 45.24 S ATOM 13846 SG CYS K 34 54.583 112.921 58.955 1.00 43.81 S ATOM 14004 SG CYS K 53 57.192 115.355 60.457 1.00 50.92 S ATOM 14025 SG CYS K 56 54.984 113.135 62.725 1.00 58.82 S ATOM 14805 SG CYS L 51 38.046 105.952 43.578 1.00 75.00 S ATOM 14826 SG CYS L 54 34.367 105.832 43.930 1.00 81.64 S ATOM 14974 SG CYS L 72 36.664 105.613 47.114 1.00 63.48 S ATOM 14993 SG CYS L 75 36.114 102.745 45.094 1.00 63.10 S ATOM 14928 SG CYS L 67 51.858 103.951 43.712 1.00 59.92 S ATOM 15082 SG CYS L 87 49.460 101.835 41.549 1.00 68.09 S ATOM 15102 SG CYS L 90 52.934 102.809 40.163 1.00 70.56 S Time building chain proxies: 3.21, per 1000 atoms: 0.20 Number of scatterers: 15920 At special positions: 0 Unit cell: (124.3, 155.1, 119.9, 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 8 29.99 S 57 16.00 P 264 15.00 O 3488 8.00 N 2922 7.00 C 9181 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 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 527.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 42 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 34 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 53 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 42 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " Number of angles added : 36 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 7 sheets defined 48.6% alpha, 3.7% beta 127 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.222A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.749A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.624A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.090A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 114 removed outlier: 3.534A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.101A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 36 through 44 removed outlier: 3.879A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.508A pdb=" N THR H 119 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 16 Proline residue: M 14 - end of helix No H-bonds generated for 'chain 'M' and resid 10 through 16' Processing helix chain 'M' and resid 40 through 47 Processing helix chain 'M' and resid 65 through 68 Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'M' and resid 86 through 97 removed outlier: 3.879A pdb=" N MET M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 No H-bonds generated for 'chain 'M' and resid 111 through 114' Processing helix chain 'N' and resid 22 through 25 Processing helix chain 'N' and resid 73 through 82 Processing helix chain 'N' and resid 97 through 99 No H-bonds generated for 'chain 'N' and resid 97 through 99' Processing helix chain 'N' and resid 104 through 113 Processing helix chain 'O' and resid 23 through 33 Processing helix chain 'O' and resid 56 through 58 No H-bonds generated for 'chain 'O' and resid 56 through 58' Processing helix chain 'K' and resid 40 through 47 Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 73 through 82 Processing helix chain 'K' and resid 86 through 98 removed outlier: 3.906A pdb=" N MET K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'L' and resid 21 through 24 No H-bonds generated for 'chain 'L' and resid 21 through 24' Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 97 through 99 No H-bonds generated for 'chain 'L' and resid 97 through 99' Processing helix chain 'L' and resid 104 through 113 Processing helix chain 'P' and resid 23 through 33 Processing helix chain 'P' and resid 56 through 58 No H-bonds generated for 'chain 'P' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'M' and resid 36 through 38 removed outlier: 4.205A pdb=" N HIS M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE M 31 " --> pdb=" O HIS M 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 62 through 64 Processing sheet with id= C, first strand: chain 'O' and resid 12 through 14 removed outlier: 3.572A pdb=" N ILE O 13 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER O 65 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS O 68 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE O 44 " --> pdb=" O HIS O 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 36 through 39 removed outlier: 3.771A pdb=" N HIS K 36 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 70 " --> pdb=" O THR K 30 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 70 through 72 removed outlier: 3.615A pdb=" N PHE L 71 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'P' and resid 42 through 44 removed outlier: 3.560A pdb=" N ARG P 42 " --> pdb=" O VAL P 70 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL P 70 " --> pdb=" O ARG P 42 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE P 44 " --> pdb=" O HIS P 68 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS P 68 " --> pdb=" O ILE P 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 431 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 323 hydrogen bonds 646 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4153 1.34 - 1.46: 4127 1.46 - 1.58: 7837 1.58 - 1.70: 526 1.70 - 1.82: 79 Bond restraints: 16722 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT J 57 " pdb=" C2' DT J 57 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 74 " pdb=" C2' DC I 74 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 ... (remaining 16717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 23163 2.15 - 4.30: 530 4.30 - 6.45: 21 6.45 - 8.60: 2 8.60 - 10.75: 1 Bond angle restraints: 23717 Sorted by residual: angle pdb=" N ILE M 32 " pdb=" CA ILE M 32 " pdb=" C ILE M 32 " ideal model delta sigma weight residual 106.21 111.13 -4.92 1.07e+00 8.73e-01 2.12e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 77 " pdb=" C4 DT I 77 " pdb=" O4 DT I 77 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 87 " pdb=" C4 DT J 87 " pdb=" O4 DT J 87 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 ... (remaining 23712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8279 35.34 - 70.68: 1184 70.68 - 106.02: 29 106.02 - 141.36: 2 141.36 - 176.71: 2 Dihedral angle restraints: 9496 sinusoidal: 5635 harmonic: 3861 Sorted by residual: dihedral pdb=" CA ILE K 32 " pdb=" C ILE K 32 " pdb=" N GLU K 33 " pdb=" CA GLU K 33 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE M 32 " pdb=" C ILE M 32 " pdb=" N GLU M 33 " pdb=" CA GLU M 33 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 36.71 -176.71 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 9493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1743 0.034 - 0.069: 713 0.069 - 0.103: 233 0.103 - 0.138: 39 0.138 - 0.172: 2 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA ASP L 103 " pdb=" N ASP L 103 " pdb=" C ASP L 103 " pdb=" CB ASP L 103 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" C3' DG J 131 " pdb=" C4' DG J 131 " pdb=" O3' DG J 131 " pdb=" C2' DG J 131 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.17e-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 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2727 not shown) Planarity restraints: 2089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO A 38 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 36 " 0.031 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO P 37 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO P 37 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 37 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO G 80 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.026 5.00e-02 4.00e+02 ... (remaining 2086 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2129 2.76 - 3.30: 14584 3.30 - 3.83: 28620 3.83 - 4.37: 32015 4.37 - 4.90: 49577 Nonbonded interactions: 126925 Sorted by model distance: nonbonded pdb=" OG1 THR L 61 " pdb=" OD1 ASP L 103 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG K 94 " pdb=" OH TYR K 98 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU C 92 " pdb=" OG SER N 96 " model vdw 2.265 3.040 nonbonded pdb=" NE2 GLN O 31 " pdb=" O ILE O 36 " model vdw 2.268 3.120 nonbonded pdb=" O SER N 41 " pdb=" OG SER N 44 " model vdw 2.292 3.040 ... (remaining 126920 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' and resid 40 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 120) } ncs_group { reference = chain 'K' selection = (chain 'M' and (resid 4 through 117 or resid 201 through 202)) } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.720 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.005 0.036 16754 Z= 0.417 Angle : 0.679 10.754 23753 Z= 0.566 Chirality : 0.041 0.172 2730 Planarity : 0.004 0.062 2089 Dihedral : 24.565 176.706 6990 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1295 helix: 2.70 (0.21), residues: 668 sheet: -0.74 (0.70), residues: 54 loop : -1.13 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 95 TYR 0.011 0.001 TYR H 80 PHE 0.018 0.001 PHE K 38 TRP 0.002 0.001 TRP L 17 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.42 (16722) covalent geometry : angle 0.66163 / 0.57 (23717) hydrogen bonds : bond 0.12321 / 8.32 ( 754) hydrogen bonds : angle 3.34761 / 2.48 ( 1831) metal coordination : bond 0.00518 / 0.44 ( 32) metal coordination : angle 3.92348 / 2.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.354 Fit side-chains REVERT: D 48 ASP cc_start: 0.7050 (p0) cc_final: 0.6696 (p0) REVERT: D 65 ASP cc_start: 0.7356 (t70) cc_final: 0.7142 (t0) REVERT: H 73 GLU cc_start: 0.8357 (tp30) cc_final: 0.8137 (tp30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1178 time to fit residues: 37.1873 Evaluate side-chains 184 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 64 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108225 restraints weight = 35578.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107157 restraints weight = 60104.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107744 restraints weight = 50634.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107777 restraints weight = 39643.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.107995 restraints weight = 40095.457| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 16754 Z= 0.254 Angle : 0.769 10.703 23753 Z= 0.413 Chirality : 0.049 0.248 2730 Planarity : 0.006 0.064 2089 Dihedral : 28.641 171.912 4341 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.43 % Allowed : 11.19 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1295 helix: 1.44 (0.20), residues: 669 sheet: -0.89 (0.69), residues: 54 loop : -1.49 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 45 TYR 0.023 0.002 TYR D 39 PHE 0.016 0.003 PHE C 25 TRP 0.008 0.004 TRP N 17 HIS 0.008 0.001 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 (16722) covalent geometry : angle 0.75407 / 0.41 (23717) hydrogen bonds : bond 0.07314 / 4.97 ( 754) hydrogen bonds : angle 3.12814 / 2.31 ( 1831) metal coordination : bond 0.01974 / 1.52 ( 32) metal coordination : angle 3.98253 / 3.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.495 Fit side-chains REVERT: A 60 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7794 (tp) REVERT: D 48 ASP cc_start: 0.7161 (p0) cc_final: 0.6675 (p0) REVERT: D 81 ASN cc_start: 0.8510 (t0) cc_final: 0.8084 (t0) REVERT: K 25 PHE cc_start: 0.7825 (m-10) cc_final: 0.7611 (m-80) outliers start: 28 outliers final: 19 residues processed: 208 average time/residue: 0.1309 time to fit residues: 40.8415 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 139 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 chunk 68 optimal weight: 0.3980 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.139269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111020 restraints weight = 36051.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109840 restraints weight = 56290.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110412 restraints weight = 53224.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110451 restraints weight = 40160.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110691 restraints weight = 40272.857| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 16754 Z= 0.136 Angle : 0.596 7.986 23753 Z= 0.338 Chirality : 0.042 0.211 2730 Planarity : 0.005 0.060 2089 Dihedral : 28.563 173.143 4341 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.82 % Allowed : 14.40 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.24), residues: 1295 helix: 1.83 (0.21), residues: 665 sheet: -0.64 (0.71), residues: 54 loop : -1.31 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 70 TYR 0.019 0.001 TYR D 39 PHE 0.012 0.001 PHE L 106 TRP 0.002 0.001 TRP N 17 HIS 0.005 0.001 HIS L 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (16722) covalent geometry : angle 0.58271 / 0.34 (23717) hydrogen bonds : bond 0.05219 / 3.50 ( 754) hydrogen bonds : angle 2.61867 / 1.92 ( 1831) metal coordination : bond 0.00720 / 0.55 ( 32) metal coordination : angle 3.28747 / 2.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.443 Fit side-chains REVERT: D 44 GLN cc_start: 0.7654 (tt0) cc_final: 0.7395 (tm-30) REVERT: D 48 ASP cc_start: 0.7131 (p0) cc_final: 0.6708 (p0) REVERT: O 1 MET cc_start: 0.3977 (tpp) cc_final: 0.2789 (ttt) REVERT: P 72 ARG cc_start: 0.5575 (mtp85) cc_final: 0.5199 (mtp-110) outliers start: 21 outliers final: 16 residues processed: 192 average time/residue: 0.1172 time to fit residues: 34.1840 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 148 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 137 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109035 restraints weight = 35764.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.107862 restraints weight = 54549.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108397 restraints weight = 52129.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108388 restraints weight = 39635.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108612 restraints weight = 39934.459| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16754 Z= 0.171 Angle : 0.618 9.284 23753 Z= 0.344 Chirality : 0.043 0.217 2730 Planarity : 0.005 0.058 2089 Dihedral : 28.669 173.232 4341 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.52 % Allowed : 15.78 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1295 helix: 1.71 (0.21), residues: 672 sheet: -0.78 (0.71), residues: 54 loop : -1.33 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.016 0.001 TYR L 22 PHE 0.023 0.002 PHE L 106 TRP 0.004 0.002 TRP N 17 HIS 0.004 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (16722) covalent geometry : angle 0.60381 / 0.34 (23717) hydrogen bonds : bond 0.05488 / 3.68 ( 754) hydrogen bonds : angle 2.67475 / 1.96 ( 1831) metal coordination : bond 0.01330 / 1.04 ( 32) metal coordination : angle 3.46929 / 2.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.521 Fit side-chains REVERT: D 44 GLN cc_start: 0.7639 (tt0) cc_final: 0.7397 (tm-30) REVERT: D 48 ASP cc_start: 0.7144 (p0) cc_final: 0.6671 (p0) REVERT: H 110 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7212 (mt-10) REVERT: O 1 MET cc_start: 0.3965 (tpp) cc_final: 0.2896 (ttt) REVERT: K 8 LYS cc_start: 0.6083 (tppt) cc_final: 0.5560 (tppt) REVERT: K 25 PHE cc_start: 0.7719 (m-10) cc_final: 0.7385 (m-80) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.1238 time to fit residues: 36.5791 Evaluate side-chains 196 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 3 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 chunk 109 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110629 restraints weight = 35825.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.109575 restraints weight = 56605.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110019 restraints weight = 59394.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110118 restraints weight = 42966.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.110329 restraints weight = 41505.138| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16754 Z= 0.129 Angle : 0.575 8.554 23753 Z= 0.325 Chirality : 0.041 0.208 2730 Planarity : 0.005 0.071 2089 Dihedral : 28.649 173.950 4341 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.08 % Allowed : 17.87 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.24), residues: 1295 helix: 1.84 (0.21), residues: 673 sheet: -0.66 (0.73), residues: 54 loop : -1.24 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 101 TYR 0.014 0.001 TYR C 57 PHE 0.035 0.001 PHE L 106 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.000 HIS L 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (16722) covalent geometry : angle 0.56650 / 0.33 (23717) hydrogen bonds : bond 0.04799 / 3.20 ( 754) hydrogen bonds : angle 2.47841 / 1.82 ( 1831) metal coordination : bond 0.00775 / 0.59 ( 32) metal coordination : angle 2.63939 / 1.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.571 Fit side-chains REVERT: D 44 GLN cc_start: 0.7575 (tt0) cc_final: 0.7369 (tm-30) REVERT: D 48 ASP cc_start: 0.7115 (p0) cc_final: 0.6646 (p0) REVERT: O 1 MET cc_start: 0.3880 (tpp) cc_final: 0.2807 (ttt) REVERT: K 8 LYS cc_start: 0.6037 (tppt) cc_final: 0.5527 (tppt) REVERT: K 25 PHE cc_start: 0.7640 (m-10) cc_final: 0.7330 (m-80) outliers start: 24 outliers final: 18 residues processed: 196 average time/residue: 0.1229 time to fit residues: 36.8184 Evaluate side-chains 194 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 122 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.137378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.109728 restraints weight = 35736.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108347 restraints weight = 61030.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108936 restraints weight = 57112.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108955 restraints weight = 42313.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109212 restraints weight = 42972.825| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16754 Z= 0.149 Angle : 0.599 8.752 23753 Z= 0.335 Chirality : 0.042 0.210 2730 Planarity : 0.005 0.071 2089 Dihedral : 28.741 173.832 4341 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.99 % Allowed : 18.47 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1295 helix: 1.82 (0.21), residues: 673 sheet: -0.73 (0.72), residues: 54 loop : -1.26 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 70 TYR 0.012 0.001 TYR D 39 PHE 0.032 0.001 PHE L 106 TRP 0.002 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (16722) covalent geometry : angle 0.58726 / 0.33 (23717) hydrogen bonds : bond 0.05071 / 3.38 ( 754) hydrogen bonds : angle 2.52650 / 1.86 ( 1831) metal coordination : bond 0.01253 / 1.01 ( 32) metal coordination : angle 3.04266 / 2.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.501 Fit side-chains REVERT: D 44 GLN cc_start: 0.7640 (tt0) cc_final: 0.7323 (tm-30) REVERT: D 48 ASP cc_start: 0.7236 (p0) cc_final: 0.6784 (p0) REVERT: N 110 ILE cc_start: 0.4704 (mm) cc_final: 0.4330 (tt) REVERT: O 1 MET cc_start: 0.3864 (tpp) cc_final: 0.2826 (ttt) REVERT: L 74 ASP cc_start: 0.6712 (p0) cc_final: 0.6476 (p0) outliers start: 23 outliers final: 20 residues processed: 201 average time/residue: 0.1263 time to fit residues: 38.4394 Evaluate side-chains 198 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.137180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.109605 restraints weight = 35516.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108290 restraints weight = 60834.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.108864 restraints weight = 56574.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108895 restraints weight = 41866.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109150 restraints weight = 42075.899| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16754 Z= 0.146 Angle : 0.604 9.204 23753 Z= 0.336 Chirality : 0.042 0.211 2730 Planarity : 0.005 0.072 2089 Dihedral : 28.782 173.758 4341 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.25 % Allowed : 19.34 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1295 helix: 1.79 (0.21), residues: 673 sheet: -0.78 (0.71), residues: 54 loop : -1.25 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 70 TYR 0.012 0.001 TYR C 57 PHE 0.027 0.001 PHE L 106 TRP 0.005 0.002 TRP N 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (16722) covalent geometry : angle 0.59523 / 0.34 (23717) hydrogen bonds : bond 0.05011 / 3.34 ( 754) hydrogen bonds : angle 2.53805 / 1.86 ( 1831) metal coordination : bond 0.00946 / 0.72 ( 32) metal coordination : angle 2.74818 / 1.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.524 Fit side-chains REVERT: D 44 GLN cc_start: 0.7586 (tt0) cc_final: 0.7258 (tm-30) REVERT: D 48 ASP cc_start: 0.7253 (p0) cc_final: 0.6884 (p0) REVERT: N 110 ILE cc_start: 0.4692 (mm) cc_final: 0.4333 (tt) REVERT: O 1 MET cc_start: 0.3867 (tpp) cc_final: 0.2836 (ttt) outliers start: 26 outliers final: 21 residues processed: 199 average time/residue: 0.1224 time to fit residues: 37.4053 Evaluate side-chains 199 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 37 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 148 optimal weight: 0.0970 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.134276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105719 restraints weight = 35412.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104483 restraints weight = 59861.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105036 restraints weight = 53841.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105020 restraints weight = 41932.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105258 restraints weight = 42568.998| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16754 Z= 0.208 Angle : 0.692 11.826 23753 Z= 0.375 Chirality : 0.046 0.218 2730 Planarity : 0.006 0.075 2089 Dihedral : 29.029 172.510 4341 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.86 % Allowed : 18.91 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1295 helix: 1.53 (0.21), residues: 670 sheet: -1.03 (0.69), residues: 54 loop : -1.47 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 70 TYR 0.016 0.002 TYR C 57 PHE 0.029 0.002 PHE L 106 TRP 0.007 0.002 TRP L 17 HIS 0.004 0.001 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (16722) covalent geometry : angle 0.67897 / 0.37 (23717) hydrogen bonds : bond 0.06254 / 4.18 ( 754) hydrogen bonds : angle 2.80652 / 2.06 ( 1831) metal coordination : bond 0.01552 / 1.19 ( 32) metal coordination : angle 3.50032 / 2.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.509 Fit side-chains REVERT: D 44 GLN cc_start: 0.7632 (tt0) cc_final: 0.7211 (tm-30) REVERT: D 48 ASP cc_start: 0.7355 (p0) cc_final: 0.6952 (p0) REVERT: D 81 ASN cc_start: 0.8414 (t0) cc_final: 0.8054 (t0) REVERT: N 110 ILE cc_start: 0.4597 (mm) cc_final: 0.4268 (tt) REVERT: O 1 MET cc_start: 0.4140 (tpp) cc_final: 0.3219 (ttt) REVERT: K 25 PHE cc_start: 0.7764 (m-10) cc_final: 0.7439 (m-80) outliers start: 33 outliers final: 28 residues processed: 209 average time/residue: 0.1101 time to fit residues: 35.0477 Evaluate side-chains 212 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 72 CYS Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 50.0000 chunk 12 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 46 HIS ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.135489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105861 restraints weight = 35498.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104492 restraints weight = 56553.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105123 restraints weight = 54058.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105093 restraints weight = 40946.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105333 restraints weight = 41964.796| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16754 Z= 0.145 Angle : 0.631 9.139 23753 Z= 0.348 Chirality : 0.043 0.214 2730 Planarity : 0.005 0.075 2089 Dihedral : 28.944 173.192 4341 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.73 % Allowed : 20.03 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1295 helix: 1.65 (0.21), residues: 670 sheet: -0.96 (0.70), residues: 54 loop : -1.38 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 72 TYR 0.016 0.001 TYR C 57 PHE 0.023 0.001 PHE L 106 TRP 0.002 0.001 TRP L 17 HIS 0.002 0.001 HIS M 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (16722) covalent geometry : angle 0.61848 / 0.35 (23717) hydrogen bonds : bond 0.05167 / 3.45 ( 754) hydrogen bonds : angle 2.62150 / 1.91 ( 1831) metal coordination : bond 0.01034 / 0.79 ( 32) metal coordination : angle 3.23935 / 2.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.492 Fit side-chains REVERT: D 44 GLN cc_start: 0.7558 (tt0) cc_final: 0.7225 (tm-30) REVERT: D 48 ASP cc_start: 0.7231 (p0) cc_final: 0.6848 (p0) REVERT: D 81 ASN cc_start: 0.8267 (t0) cc_final: 0.7843 (t0) REVERT: H 39 TYR cc_start: 0.8287 (t80) cc_final: 0.7966 (t80) REVERT: N 110 ILE cc_start: 0.4760 (mm) cc_final: 0.4444 (tt) REVERT: O 1 MET cc_start: 0.4126 (tpp) cc_final: 0.3170 (ttt) outliers start: 20 outliers final: 19 residues processed: 200 average time/residue: 0.1172 time to fit residues: 35.9213 Evaluate side-chains 194 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 138 optimal weight: 40.0000 chunk 49 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104900 restraints weight = 35426.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103542 restraints weight = 55967.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104077 restraints weight = 55126.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104154 restraints weight = 41617.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104321 restraints weight = 42761.148| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16754 Z= 0.176 Angle : 0.660 9.477 23753 Z= 0.360 Chirality : 0.044 0.216 2730 Planarity : 0.005 0.077 2089 Dihedral : 29.010 173.089 4341 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.17 % Allowed : 19.77 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1295 helix: 1.60 (0.21), residues: 670 sheet: -1.03 (0.69), residues: 54 loop : -1.43 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 94 TYR 0.016 0.001 TYR C 57 PHE 0.010 0.001 PHE L 106 TRP 0.007 0.002 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (16722) covalent geometry : angle 0.64603 / 0.36 (23717) hydrogen bonds : bond 0.05576 / 3.72 ( 754) hydrogen bonds : angle 2.70291 / 1.98 ( 1831) metal coordination : bond 0.01199 / 0.91 ( 32) metal coordination : angle 3.47187 / 2.39 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.611 Fit side-chains REVERT: D 44 GLN cc_start: 0.7600 (tt0) cc_final: 0.7216 (tm-30) REVERT: D 48 ASP cc_start: 0.7315 (p0) cc_final: 0.6913 (p0) REVERT: D 81 ASN cc_start: 0.8355 (t0) cc_final: 0.7948 (t0) REVERT: H 39 TYR cc_start: 0.8369 (t80) cc_final: 0.8033 (t80) REVERT: N 110 ILE cc_start: 0.4538 (mm) cc_final: 0.4185 (tt) REVERT: O 1 MET cc_start: 0.4148 (tpp) cc_final: 0.3248 (ttt) outliers start: 25 outliers final: 22 residues processed: 201 average time/residue: 0.1183 time to fit residues: 36.8561 Evaluate side-chains 203 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain K residue 24 TYR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 50.0000 chunk 74 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.135741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.106633 restraints weight = 35493.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105161 restraints weight = 58370.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105838 restraints weight = 54504.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105831 restraints weight = 40694.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106079 restraints weight = 41126.032| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.046 16754 Z= 0.133 Angle : 0.632 9.660 23753 Z= 0.347 Chirality : 0.042 0.219 2730 Planarity : 0.005 0.075 2089 Dihedral : 28.927 173.783 4341 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.65 % Allowed : 21.16 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1295 helix: 1.70 (0.21), residues: 672 sheet: -0.92 (0.70), residues: 54 loop : -1.32 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 94 TYR 0.013 0.001 TYR C 57 PHE 0.008 0.001 PHE N 106 TRP 0.006 0.001 TRP N 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (16722) covalent geometry : angle 0.61865 / 0.35 (23717) hydrogen bonds : bond 0.04884 / 3.26 ( 754) hydrogen bonds : angle 2.55957 / 1.87 ( 1831) metal coordination : bond 0.00876 / 0.67 ( 32) metal coordination : angle 3.33025 / 2.24 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.21 seconds wall clock time: 38 minutes 12.05 seconds (2292.05 seconds total)