Starting phenix.real_space_refine on Sun Jul 5 09:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9u_64888/07_2026/9v9u_64888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9u_64888/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9v9u_64888/07_2026/9v9u_64888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9u_64888/07_2026/9v9u_64888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9u_64888/07_2026/9v9u_64888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9u_64888/07_2026/9v9u_64888.map" } 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-dev-6108/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: 3.15, 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: 0.90 Conformation dependent library (CDL) restraints added in 489.7 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: 10.85 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: 2.37 Time building geometry restraints manager: 1.19 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: 23167 2.15 - 4.30: 526 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.790 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- 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 : 0.674 10.754 23753 Z= 0.561 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 0.65667 / 0.56 (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 : 0.557 Fit side-chains REVERT: D 48 ASP cc_start: 0.7050 (p0) cc_final: 0.6694 (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: 0.1338 time to fit residues: 42.1903 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 : 0.433 ------------------------------------------------------------------------------- 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 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4026 r_free = 0.4026 target = 0.136923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108106 restraints weight = 35577.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107060 restraints weight = 58352.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107618 restraints weight = 50018.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107684 restraints weight = 39266.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.107864 restraints weight = 42727.746| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 16754 Z= 0.255 Angle : 0.756 10.891 23753 Z= 0.412 Chirality : 0.049 0.253 2730 Planarity : 0.006 0.062 2089 Dihedral : 28.716 171.701 4341 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.52 % Allowed : 11.19 % Favored : 86.30 % 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: 0.23 (0.23), residues: 1295 helix: 1.52 (0.20), residues: 669 sheet: -0.87 (0.70), residues: 54 loop : -1.46 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 45 TYR 0.018 0.002 TYR L 22 PHE 0.017 0.002 PHE C 25 TRP 0.007 0.002 TRP N 17 HIS 0.008 0.001 HIS P 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (16722) covalent geometry : angle 0.74054 / 0.41 (23717) hydrogen bonds : bond 0.07358 / 4.98 ( 754) hydrogen bonds : angle 3.10065 / 2.28 ( 1831) metal coordination : bond 0.02096 / 1.62 ( 32) metal coordination : angle 3.98299 / 3.25 ( 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 224 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.537 Fit side-chains REVERT: A 60 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7806 (tp) REVERT: D 48 ASP cc_start: 0.7140 (p0) cc_final: 0.6655 (p0) REVERT: D 81 ASN cc_start: 0.8466 (t0) cc_final: 0.8042 (t0) REVERT: K 8 LYS cc_start: 0.5990 (tppt) cc_final: 0.5428 (tppt) REVERT: K 25 PHE cc_start: 0.7815 (m-10) cc_final: 0.7591 (m-80) outliers start: 29 outliers final: 20 residues processed: 209 average time/residue: 0.1282 time to fit residues: 40.2750 Evaluate side-chains 193 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 L residue 95 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.137880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110215 restraints weight = 35985.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109069 restraints weight = 60538.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109607 restraints weight = 59092.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109743 restraints weight = 42842.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.109944 restraints weight = 42354.022| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16754 Z= 0.162 Angle : 0.608 8.034 23753 Z= 0.343 Chirality : 0.042 0.201 2730 Planarity : 0.005 0.060 2089 Dihedral : 28.700 172.479 4341 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.43 % Allowed : 14.22 % Favored : 83.35 % 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: 0.46 (0.24), residues: 1295 helix: 1.73 (0.21), residues: 665 sheet: -0.73 (0.71), residues: 54 loop : -1.37 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 70 TYR 0.022 0.001 TYR D 39 PHE 0.012 0.001 PHE B 100 TRP 0.003 0.001 TRP N 17 HIS 0.004 0.001 HIS L 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (16722) covalent geometry : angle 0.59433 / 0.34 (23717) hydrogen bonds : bond 0.05565 / 3.73 ( 754) hydrogen bonds : angle 2.72241 / 1.99 ( 1831) metal coordination : bond 0.01019 / 0.77 ( 32) metal coordination : angle 3.39312 / 2.49 ( 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 207 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.512 Fit side-chains REVERT: D 44 GLN cc_start: 0.7633 (tt0) cc_final: 0.7380 (tm-30) REVERT: D 48 ASP cc_start: 0.7103 (p0) cc_final: 0.6665 (p0) REVERT: O 1 MET cc_start: 0.3957 (tpp) cc_final: 0.2851 (ttt) REVERT: K 8 LYS cc_start: 0.6030 (tppt) cc_final: 0.5442 (tppt) REVERT: L 63 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7327 (p) outliers start: 28 outliers final: 19 residues processed: 192 average time/residue: 0.1248 time to fit residues: 36.4751 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 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 C residue 72 ASP 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 N residue 27 THR 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 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 L residue 63 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: 6.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4022 r_free = 0.4022 target = 0.136631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108105 restraints weight = 35733.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106735 restraints weight = 56908.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107298 restraints weight = 54996.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107376 restraints weight = 40587.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107614 restraints weight = 40217.867| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16754 Z= 0.169 Angle : 0.618 9.140 23753 Z= 0.344 Chirality : 0.043 0.209 2730 Planarity : 0.005 0.058 2089 Dihedral : 28.776 172.673 4341 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.52 % Allowed : 16.91 % Favored : 80.57 % 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: 0.44 (0.24), residues: 1295 helix: 1.70 (0.21), residues: 671 sheet: -0.86 (0.69), residues: 54 loop : -1.37 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 70 TYR 0.023 0.001 TYR L 22 PHE 0.026 0.002 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 0.00353 / 0.17 (16722) covalent geometry : angle 0.60321 / 0.34 (23717) hydrogen bonds : bond 0.05513 / 3.70 ( 754) hydrogen bonds : angle 2.69186 / 1.98 ( 1831) metal coordination : bond 0.01091 / 0.82 ( 32) metal coordination : angle 3.53802 / 2.48 ( 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 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.492 Fit side-chains REVERT: D 44 GLN cc_start: 0.7625 (tt0) cc_final: 0.7377 (tm-30) REVERT: D 48 ASP cc_start: 0.7102 (p0) cc_final: 0.6644 (p0) REVERT: O 1 MET cc_start: 0.3982 (tpp) cc_final: 0.2969 (ttt) REVERT: K 8 LYS cc_start: 0.6090 (tppt) cc_final: 0.5546 (tppt) REVERT: K 25 PHE cc_start: 0.7745 (m-10) cc_final: 0.7434 (m-80) REVERT: L 63 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7344 (p) outliers start: 29 outliers final: 22 residues processed: 196 average time/residue: 0.1195 time to fit residues: 35.6644 Evaluate side-chains 197 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 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 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 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 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 63 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 3 optimal weight: 0.0980 chunk 107 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 83 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 84 optimal weight: 50.0000 chunk 109 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 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 = 0.4022 r_free = 0.4022 target = 0.136615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108347 restraints weight = 35613.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106918 restraints weight = 60194.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107526 restraints weight = 55617.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107614 restraints weight = 41182.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107870 restraints weight = 40688.802| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16754 Z= 0.155 Angle : 0.602 8.739 23753 Z= 0.336 Chirality : 0.042 0.205 2730 Planarity : 0.005 0.073 2089 Dihedral : 28.829 173.023 4341 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.69 % Allowed : 17.95 % Favored : 79.36 % 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: 1.72 (0.21), residues: 672 sheet: -0.90 (0.68), residues: 54 loop : -1.33 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 70 TYR 0.013 0.001 TYR C 57 PHE 0.033 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 0.00315 / 0.15 (16722) covalent geometry : angle 0.58838 / 0.34 (23717) hydrogen bonds : bond 0.05277 / 3.54 ( 754) hydrogen bonds : angle 2.61277 / 1.91 ( 1831) metal coordination : bond 0.01031 / 0.78 ( 32) metal coordination : angle 3.27948 / 2.31 ( 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 221 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.514 Fit side-chains REVERT: D 44 GLN cc_start: 0.7679 (tt0) cc_final: 0.7339 (tm-30) REVERT: D 48 ASP cc_start: 0.7239 (p0) cc_final: 0.6887 (p0) REVERT: O 1 MET cc_start: 0.3992 (tpp) cc_final: 0.3030 (ttt) REVERT: K 25 PHE cc_start: 0.7815 (m-10) cc_final: 0.7530 (m-80) REVERT: L 63 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7419 (p) outliers start: 31 outliers final: 25 residues processed: 206 average time/residue: 0.1151 time to fit residues: 36.3089 Evaluate side-chains 205 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 45 VAL 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 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 61 THR Chi-restraints excluded: chain L residue 63 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: 5.9990 chunk 117 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.134946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.106373 restraints weight = 35594.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105285 restraints weight = 58725.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.105866 restraints weight = 53411.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.105839 restraints weight = 41472.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106089 restraints weight = 42666.321| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2909 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= 0.193 Angle : 0.649 9.455 23753 Z= 0.358 Chirality : 0.044 0.203 2730 Planarity : 0.005 0.073 2089 Dihedral : 28.981 172.630 4341 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.82 % Allowed : 18.04 % Favored : 78.14 % 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: 0.28 (0.24), residues: 1295 helix: 1.57 (0.21), residues: 670 sheet: -1.06 (0.68), residues: 54 loop : -1.43 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 70 TYR 0.016 0.002 TYR C 57 PHE 0.034 0.002 PHE L 106 TRP 0.003 0.001 TRP L 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (16722) covalent geometry : angle 0.63582 / 0.36 (23717) hydrogen bonds : bond 0.05851 / 3.92 ( 754) hydrogen bonds : angle 2.75563 / 2.02 ( 1831) metal coordination : bond 0.01378 / 1.03 ( 32) metal coordination : angle 3.34563 / 2.37 ( 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 232 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.477 Fit side-chains REVERT: D 44 GLN cc_start: 0.7651 (tt0) cc_final: 0.7316 (tm-30) REVERT: D 48 ASP cc_start: 0.7198 (p0) cc_final: 0.6846 (p0) REVERT: M 17 MET cc_start: 0.4611 (tpt) cc_final: 0.4225 (tpt) REVERT: O 1 MET cc_start: 0.4138 (tpp) cc_final: 0.3177 (ttt) REVERT: K 25 PHE cc_start: 0.7783 (m-10) cc_final: 0.7419 (m-80) REVERT: L 63 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7318 (p) outliers start: 44 outliers final: 33 residues processed: 212 average time/residue: 0.1187 time to fit residues: 38.5707 Evaluate side-chains 216 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 65 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 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 46 VAL 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 31 ILE 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 27 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105973 restraints weight = 35438.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104585 restraints weight = 56588.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105127 restraints weight = 55191.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105169 restraints weight = 41190.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105427 restraints weight = 40547.789| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2999 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= 0.165 Angle : 0.628 8.372 23753 Z= 0.348 Chirality : 0.043 0.201 2730 Planarity : 0.005 0.071 2089 Dihedral : 28.986 172.859 4341 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.21 % Allowed : 18.82 % Favored : 77.97 % 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: 0.33 (0.24), residues: 1295 helix: 1.61 (0.21), residues: 667 sheet: -1.08 (0.67), residues: 54 loop : -1.38 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 94 TYR 0.014 0.001 TYR C 57 PHE 0.029 0.002 PHE L 106 TRP 0.003 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (16722) covalent geometry : angle 0.61634 / 0.35 (23717) hydrogen bonds : bond 0.05466 / 3.66 ( 754) hydrogen bonds : angle 2.68295 / 1.97 ( 1831) metal coordination : bond 0.01063 / 0.78 ( 32) metal coordination : angle 3.21211 / 2.20 ( 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 225 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.499 Fit side-chains REVERT: D 44 GLN cc_start: 0.7593 (tt0) cc_final: 0.7231 (tm-30) REVERT: D 48 ASP cc_start: 0.7246 (p0) cc_final: 0.6858 (p0) REVERT: O 1 MET cc_start: 0.4076 (tpp) cc_final: 0.3165 (ttt) REVERT: K 25 PHE cc_start: 0.7793 (m-10) cc_final: 0.7471 (m-80) REVERT: L 63 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7442 (p) outliers start: 37 outliers final: 29 residues processed: 209 average time/residue: 0.1185 time to fit residues: 37.8822 Evaluate side-chains 215 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL 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 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 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 31 ILE 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 27 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 84 optimal weight: 50.0000 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.135069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105401 restraints weight = 35514.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104008 restraints weight = 57160.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104598 restraints weight = 53195.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104560 restraints weight = 41989.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104594 restraints weight = 45148.884| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3085 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= 0.159 Angle : 0.627 8.884 23753 Z= 0.347 Chirality : 0.043 0.202 2730 Planarity : 0.005 0.074 2089 Dihedral : 29.000 173.048 4341 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.95 % Allowed : 19.51 % Favored : 77.54 % 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: 0.35 (0.24), residues: 1295 helix: 1.66 (0.21), residues: 661 sheet: -1.08 (0.68), residues: 54 loop : -1.37 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 94 TYR 0.015 0.001 TYR D 39 PHE 0.027 0.001 PHE L 106 TRP 0.003 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16722) covalent geometry : angle 0.61475 / 0.35 (23717) hydrogen bonds : bond 0.05370 / 3.58 ( 754) hydrogen bonds : angle 2.65542 / 1.95 ( 1831) metal coordination : bond 0.01006 / 0.72 ( 32) metal coordination : angle 3.24266 / 2.18 ( 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 220 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.513 Fit side-chains REVERT: D 44 GLN cc_start: 0.7662 (tt0) cc_final: 0.7287 (tm-30) REVERT: D 48 ASP cc_start: 0.7232 (p0) cc_final: 0.6855 (p0) REVERT: M 17 MET cc_start: 0.4791 (tpt) cc_final: 0.4461 (tpt) REVERT: O 1 MET cc_start: 0.4153 (tpp) cc_final: 0.3263 (ttt) REVERT: K 25 PHE cc_start: 0.7777 (m-10) cc_final: 0.7459 (m-80) REVERT: L 63 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7452 (p) outliers start: 34 outliers final: 28 residues processed: 207 average time/residue: 0.1241 time to fit residues: 39.2944 Evaluate side-chains 213 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 31 ILE 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 27 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 63 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN E 113 HIS F 25 ASN O 41 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.107009 restraints weight = 35513.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105621 restraints weight = 58111.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106222 restraints weight = 55240.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106298 restraints weight = 41086.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.106551 restraints weight = 40279.642| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16754 Z= 0.137 Angle : 0.609 9.173 23753 Z= 0.338 Chirality : 0.041 0.201 2730 Planarity : 0.005 0.075 2089 Dihedral : 28.947 173.678 4341 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.25 % Allowed : 20.99 % Favored : 76.76 % 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: 1.76 (0.21), residues: 663 sheet: -1.00 (0.69), residues: 54 loop : -1.33 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.013 0.001 TYR D 39 PHE 0.024 0.001 PHE L 106 TRP 0.003 0.001 TRP L 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (16722) covalent geometry : angle 0.59648 / 0.34 (23717) hydrogen bonds : bond 0.04905 / 3.26 ( 754) hydrogen bonds : angle 2.54890 / 1.87 ( 1831) metal coordination : bond 0.00833 / 0.59 ( 32) metal coordination : angle 3.22893 / 2.12 ( 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 216 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.514 Fit side-chains REVERT: D 44 GLN cc_start: 0.7506 (tt0) cc_final: 0.7231 (tm-30) REVERT: D 48 ASP cc_start: 0.7214 (p0) cc_final: 0.6853 (p0) REVERT: D 81 ASN cc_start: 0.8178 (t0) cc_final: 0.7897 (t0) REVERT: H 39 TYR cc_start: 0.8292 (t80) cc_final: 0.7997 (t80) REVERT: M 17 MET cc_start: 0.4706 (tpt) cc_final: 0.4372 (tpt) REVERT: N 110 ILE cc_start: 0.4339 (mm) cc_final: 0.4052 (tt) REVERT: O 1 MET cc_start: 0.4191 (tpp) cc_final: 0.3255 (ttt) REVERT: L 63 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7384 (p) outliers start: 26 outliers final: 21 residues processed: 206 average time/residue: 0.1163 time to fit residues: 37.0300 Evaluate side-chains 206 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 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 61 THR Chi-restraints excluded: chain L residue 63 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: 2.9990 chunk 33 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 96 optimal weight: 40.0000 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 25 ASN O 41 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105971 restraints weight = 35486.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104498 restraints weight = 58768.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105100 restraints weight = 55364.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105128 restraints weight = 41528.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105379 restraints weight = 41809.544| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16754 Z= 0.165 Angle : 0.638 12.217 23753 Z= 0.350 Chirality : 0.043 0.206 2730 Planarity : 0.005 0.078 2089 Dihedral : 29.004 173.498 4341 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.43 % Allowed : 21.08 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.24), residues: 1295 helix: 1.67 (0.21), residues: 664 sheet: -1.03 (0.69), residues: 54 loop : -1.38 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 94 TYR 0.012 0.001 TYR C 57 PHE 0.027 0.002 PHE L 106 TRP 0.004 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (16722) covalent geometry : angle 0.62544 / 0.35 (23717) hydrogen bonds : bond 0.05260 / 3.50 ( 754) hydrogen bonds : angle 2.63727 / 1.95 ( 1831) metal coordination : bond 0.00962 / 0.70 ( 32) metal coordination : angle 3.26156 / 2.12 ( 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 212 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.522 Fit side-chains REVERT: D 44 GLN cc_start: 0.7572 (tt0) cc_final: 0.7204 (tm-30) REVERT: D 48 ASP cc_start: 0.7268 (p0) cc_final: 0.6883 (p0) REVERT: D 81 ASN cc_start: 0.8294 (t0) cc_final: 0.7975 (t0) REVERT: M 17 MET cc_start: 0.4775 (tpt) cc_final: 0.4334 (tpt) REVERT: N 110 ILE cc_start: 0.4611 (mm) cc_final: 0.4254 (tt) REVERT: O 1 MET cc_start: 0.4129 (tpp) cc_final: 0.3249 (ttt) REVERT: L 63 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7382 (p) outliers start: 28 outliers final: 24 residues processed: 203 average time/residue: 0.1164 time to fit residues: 36.5106 Evaluate side-chains 208 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 46 VAL 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 M residue 66 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain O residue 7 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 63 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 111 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 chunk 74 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 73 ASN F 25 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.135861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106841 restraints weight = 35474.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105471 restraints weight = 58219.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106044 restraints weight = 55473.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106098 restraints weight = 41042.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106325 restraints weight = 41152.434| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3206 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= 0.134 Angle : 0.617 10.659 23753 Z= 0.341 Chirality : 0.042 0.207 2730 Planarity : 0.005 0.075 2089 Dihedral : 28.970 173.657 4341 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.08 % Allowed : 21.25 % Favored : 76.67 % 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: 0.46 (0.24), residues: 1295 helix: 1.71 (0.21), residues: 666 sheet: -0.99 (0.70), residues: 54 loop : -1.31 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 94 TYR 0.012 0.001 TYR D 39 PHE 0.024 0.001 PHE L 106 TRP 0.003 0.001 TRP L 17 HIS 0.002 0.000 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (16722) covalent geometry : angle 0.60538 / 0.34 (23717) hydrogen bonds : bond 0.04896 / 3.25 ( 754) hydrogen bonds : angle 2.54141 / 1.88 ( 1831) metal coordination : bond 0.00715 / 0.52 ( 32) metal coordination : angle 3.13811 / 2.05 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.28 seconds wall clock time: 55 minutes 35.01 seconds (3335.01 seconds total)