Starting phenix.real_space_refine on Sat Jul 4 22:01:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9y_64892/07_2026/9v9y_64892.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 12543 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 5 6.06 5 P 263 5.49 5 S 37 5.16 5 C 7829 2.51 5 N 2555 2.21 5 O 3074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 13763 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" 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: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} 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: "K" 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: "L" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11383 SG CYS M 18 68.934 25.472 72.531 1.00 37.58 S ATOM 11404 SG CYS M 21 67.133 22.287 72.918 1.00 39.51 S ATOM 11542 SG CYS M 39 67.376 23.795 69.526 1.00 40.13 S ATOM 11564 SG CYS M 42 65.155 25.472 72.629 1.00 39.68 S ATOM 11501 SG CYS M 34 71.422 37.429 72.014 1.00 36.64 S ATOM 11659 SG CYS M 53 69.896 35.658 75.038 1.00 33.24 S ATOM 11680 SG CYS M 56 72.176 38.725 75.579 1.00 34.81 S ATOM 12357 SG CYS N 51 86.764 38.472 53.917 1.00 43.33 S ATOM 12378 SG CYS N 54 90.525 37.980 53.890 1.00 45.02 S ATOM 12526 SG CYS N 72 88.610 38.376 57.167 1.00 38.79 S ATOM 12545 SG CYS N 75 89.207 41.365 54.816 1.00 31.59 S ATOM 12480 SG CYS N 67 74.200 40.393 55.126 1.00 35.95 S ATOM 12634 SG CYS N 87 76.342 41.310 52.101 1.00 41.98 S ATOM 12654 SG CYS N 90 72.942 39.679 51.587 1.00 44.84 S ATOM 13503 SG CYS L 27 41.861 99.249 43.672 1.00 45.79 S ATOM 13522 SG CYS L 30 43.401 99.493 40.190 1.00 44.64 S ATOM 13610 SG CYS L 41 39.986 97.776 40.723 1.00 53.03 S ATOM 13630 SG CYS L 44 43.148 96.124 41.862 1.00 51.06 S Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 13763 At special positions: 0 Unit cell: (126.5, 132, 118.8, 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 5 29.99 S 37 16.00 P 263 15.00 O 3074 8.00 N 2555 7.00 C 7829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 407.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " Number of angles added : 24 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 14 sheets defined 60.7% alpha, 4.7% beta 122 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.959A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.712A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.059A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.552A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.462A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.961A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.562A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.647A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.046A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.579A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.919A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 16 Processing helix chain 'M' and resid 39 through 48 removed outlier: 3.698A pdb=" N ILE M 43 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 73 through 83 Processing helix chain 'M' and resid 85 through 101 removed outlier: 3.501A pdb=" N MET M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 26 removed outlier: 3.508A pdb=" N LEU N 24 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG N 26 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 removed outlier: 3.838A pdb=" N ASP N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 removed outlier: 3.649A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.557A pdb=" N ASP K 58 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.746A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.712A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.036A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.857A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.169A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.706A pdb=" N THR M 5 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 37 through 38 removed outlier: 3.798A pdb=" N THR M 30 " --> pdb=" O ARG M 70 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG M 70 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AB4, first strand: chain 'K' and resid 12 through 14 removed outlier: 7.227A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 25 through 26 460 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.46 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: 3325 1.34 - 1.46: 3925 1.46 - 1.57: 6707 1.57 - 1.69: 524 1.69 - 1.81: 53 Bond restraints: 14534 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 1.07e+01 bond pdb=" C3' DG I 44 " pdb=" C2' DG I 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG I 76 " pdb=" C2' DG I 76 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT J 88 " pdb=" C2' DT J 88 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC I 53 " pdb=" C2' DC I 53 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 14529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 19392 1.22 - 2.45: 1185 2.45 - 3.67: 157 3.67 - 4.89: 15 4.89 - 6.12: 5 Bond angle restraints: 20754 Sorted by residual: angle pdb=" O4' DA I 20 " pdb=" C4' DA I 20 " pdb=" C3' DA I 20 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.82e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 86 " pdb=" C4 DT I 86 " pdb=" O4 DT I 86 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 105 " pdb=" C4 DT I 105 " pdb=" O4 DT I 105 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 20749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6970 35.45 - 70.90: 1121 70.90 - 106.36: 20 106.36 - 141.81: 1 141.81 - 177.26: 1 Dihedral angle restraints: 8113 sinusoidal: 5048 harmonic: 3065 Sorted by residual: 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 37.26 -177.26 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 79.54 140.46 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CG ARG G 32 " pdb=" CD ARG G 32 " pdb=" NE ARG G 32 " pdb=" CZ ARG G 32 " ideal model delta sinusoidal sigma weight residual 180.00 -135.40 -44.60 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1229 0.027 - 0.054: 729 0.054 - 0.081: 243 0.081 - 0.109: 151 0.109 - 0.136: 27 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CA GLU H 68 " pdb=" N GLU H 68 " pdb=" C GLU H 68 " pdb=" CB GLU H 68 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-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 4.42e-01 chirality pdb=" C3' DT J 57 " pdb=" C4' DT J 57 " pdb=" O3' DT J 57 " pdb=" C2' DT J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 2376 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU H 68 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" CD GLU H 68 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU H 68 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU H 68 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 39 " 0.013 2.00e-02 2.50e+03 1.12e-02 2.52e+00 pdb=" CG TYR H 39 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR H 39 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR H 39 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR H 39 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 39 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.020 2.00e-02 2.50e+03 8.70e-03 2.08e+00 pdb=" N9 DA I 20 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.002 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 251 2.66 - 3.22: 11505 3.22 - 3.78: 23678 3.78 - 4.34: 30470 4.34 - 4.90: 45595 Nonbonded interactions: 111499 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.102 2.496 nonbonded pdb=" O LYS K 27 " pdb=" NE2 GLN K 31 " model vdw 2.135 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I 51 " model vdw 2.288 3.120 ... (remaining 111494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 23 through 100) selection = (chain 'F' and resid 23 through 100) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 120) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.037 14554 Z= 0.452 Angle : 0.634 14.870 20778 Z= 0.559 Chirality : 0.042 0.136 2379 Planarity : 0.003 0.032 1712 Dihedral : 24.745 177.259 6125 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.27), residues: 1027 helix: 3.08 (0.21), residues: 608 sheet: -1.12 (0.90), residues: 39 loop : -0.42 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 45 TYR 0.027 0.001 TYR H 39 PHE 0.007 0.001 PHE N 106 TRP 0.001 0.000 TRP N 17 HIS 0.002 0.000 HIS M 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.45 (14534) covalent geometry : angle 0.62108 / 0.56 (20754) hydrogen bonds : bond 0.11143 / 7.38 ( 775) hydrogen bonds : angle 4.01740 / 2.90 ( 1973) metal coordination : bond 0.00899 / 0.52 ( 20) metal coordination : angle 3.73612 / 1.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.376 Fit side-chains REVERT: A 115 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7742 (mtmt) REVERT: N 86 GLU cc_start: 0.6418 (mm-30) cc_final: 0.5690 (mt-10) REVERT: K 31 GLN cc_start: 0.3678 (mp-120) cc_final: 0.2621 (mm-40) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1466 time to fit residues: 39.6307 Evaluate side-chains 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.0050 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 110 ASN D 46 HIS ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 HIS M 76 GLN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.170668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130906 restraints weight = 19672.619| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.49 r_work: 0.3195 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14554 Z= 0.175 Angle : 0.641 9.853 20778 Z= 0.369 Chirality : 0.045 0.307 2379 Planarity : 0.005 0.036 1712 Dihedral : 28.449 175.417 4022 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.66 % Allowed : 8.37 % Favored : 90.97 % 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: 2.11 (0.27), residues: 1027 helix: 2.71 (0.21), residues: 615 sheet: -0.71 (0.75), residues: 56 loop : -0.66 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.016 0.002 TYR N 22 PHE 0.014 0.002 PHE A 67 TRP 0.011 0.002 TRP L 25 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (14534) covalent geometry : angle 0.62610 / 0.37 (20754) hydrogen bonds : bond 0.06170 / 4.11 ( 775) hydrogen bonds : angle 2.95995 / 2.14 ( 1973) metal coordination : bond 0.01635 / 1.05 ( 20) metal coordination : angle 4.11199 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.406 Fit side-chains REVERT: C 35 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8014 (ttm-80) REVERT: H 68 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: M 16 LEU cc_start: 0.6925 (tt) cc_final: 0.6605 (mm) REVERT: N 86 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6411 (mt-10) REVERT: N 110 ILE cc_start: 0.8195 (mt) cc_final: 0.7797 (tp) REVERT: K 31 GLN cc_start: 0.2934 (mp10) cc_final: 0.2441 (tp-100) outliers start: 6 outliers final: 4 residues processed: 173 average time/residue: 0.1302 time to fit residues: 31.1069 Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN D 46 HIS H 60 ASN M 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.168018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129307 restraints weight = 19719.413| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.58 r_work: 0.3121 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14554 Z= 0.159 Angle : 0.593 10.260 20778 Z= 0.339 Chirality : 0.043 0.200 2379 Planarity : 0.004 0.045 1712 Dihedral : 28.912 176.573 4022 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 10.24 % Favored : 88.55 % 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: 2.04 (0.27), residues: 1027 helix: 2.69 (0.21), residues: 616 sheet: -0.51 (0.80), residues: 51 loop : -0.82 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 91 TYR 0.022 0.002 TYR N 22 PHE 0.008 0.001 PHE D 62 TRP 0.003 0.001 TRP N 17 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (14534) covalent geometry : angle 0.57442 / 0.34 (20754) hydrogen bonds : bond 0.06130 / 4.10 ( 775) hydrogen bonds : angle 2.89814 / 2.11 ( 1973) metal coordination : bond 0.01272 / 0.74 ( 20) metal coordination : angle 4.42160 / 2.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.385 Fit side-chains REVERT: A 115 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8155 (mtmt) REVERT: C 110 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6990 (m110) REVERT: H 68 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: M 90 GLU cc_start: 0.6322 (tm-30) cc_final: 0.6024 (tp30) REVERT: M 93 ARG cc_start: 0.5128 (ptm-80) cc_final: 0.4767 (ptm-80) REVERT: N 86 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7166 (mm-30) REVERT: K 31 GLN cc_start: 0.3059 (mp10) cc_final: 0.2550 (tp-100) REVERT: L 39 PHE cc_start: 0.7318 (m-80) cc_final: 0.7047 (m-10) outliers start: 11 outliers final: 5 residues processed: 171 average time/residue: 0.1251 time to fit residues: 30.0332 Evaluate side-chains 172 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 0.0270 chunk 85 optimal weight: 40.0000 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS D 81 ASN M 15 HIS ** M 76 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 = 0.4021 r_free = 0.4021 target = 0.164489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122253 restraints weight = 19508.142| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.45 r_work: 0.3072 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14554 Z= 0.207 Angle : 0.672 10.215 20778 Z= 0.372 Chirality : 0.047 0.301 2379 Planarity : 0.005 0.042 1712 Dihedral : 29.105 177.402 4022 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.09 % Allowed : 11.89 % Favored : 86.01 % 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 (0.26), residues: 1027 helix: 2.31 (0.21), residues: 610 sheet: -1.03 (0.78), residues: 50 loop : -1.21 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.014 0.002 TYR C 57 PHE 0.011 0.002 PHE N 106 TRP 0.004 0.001 TRP N 17 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (14534) covalent geometry : angle 0.65217 / 0.37 (20754) hydrogen bonds : bond 0.07166 / 4.81 ( 775) hydrogen bonds : angle 3.07128 / 2.25 ( 1973) metal coordination : bond 0.01275 / 0.70 ( 20) metal coordination : angle 4.83388 / 2.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.413 Fit side-chains REVERT: A 115 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8349 (mtmt) REVERT: A 131 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7840 (mtp85) REVERT: G 73 ASN cc_start: 0.7969 (t0) cc_final: 0.7682 (t0) REVERT: H 68 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: N 110 ILE cc_start: 0.8174 (mt) cc_final: 0.7809 (tp) REVERT: K 31 GLN cc_start: 0.3026 (mp10) cc_final: 0.2373 (tp-100) outliers start: 19 outliers final: 12 residues processed: 170 average time/residue: 0.1306 time to fit residues: 30.9175 Evaluate side-chains 172 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 77 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 110 ASN D 46 HIS M 15 HIS ** M 76 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 = 0.4049 r_free = 0.4049 target = 0.166868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125948 restraints weight = 19742.042| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.49 r_work: 0.3106 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14554 Z= 0.133 Angle : 0.585 9.257 20778 Z= 0.335 Chirality : 0.043 0.205 2379 Planarity : 0.004 0.075 1712 Dihedral : 29.090 175.824 4022 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.54 % Allowed : 13.77 % Favored : 84.69 % 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: 1.80 (0.27), residues: 1027 helix: 2.62 (0.21), residues: 612 sheet: -0.81 (0.73), residues: 56 loop : -1.09 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 93 TYR 0.017 0.001 TYR N 22 PHE 0.008 0.001 PHE N 106 TRP 0.003 0.001 TRP N 17 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 (14534) covalent geometry : angle 0.56893 / 0.33 (20754) hydrogen bonds : bond 0.05669 / 3.79 ( 775) hydrogen bonds : angle 2.89273 / 2.11 ( 1973) metal coordination : bond 0.00733 / 0.39 ( 20) metal coordination : angle 4.01244 / 2.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8162 (mtmt) REVERT: A 131 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7606 (mtp85) REVERT: C 35 ARG cc_start: 0.8466 (tpp80) cc_final: 0.7957 (ttm-80) REVERT: G 73 ASN cc_start: 0.7862 (t0) cc_final: 0.7529 (t0) REVERT: H 68 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: N 86 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6571 (mt-10) REVERT: N 106 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: N 110 ILE cc_start: 0.8135 (mt) cc_final: 0.7771 (tp) outliers start: 14 outliers final: 7 residues processed: 168 average time/residue: 0.1351 time to fit residues: 31.4567 Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 30.0000 chunk 22 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 46 HIS M 15 HIS ** M 76 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 = 0.4049 r_free = 0.4049 target = 0.166873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125325 restraints weight = 19644.034| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.46 r_work: 0.3119 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14554 Z= 0.132 Angle : 0.577 11.106 20778 Z= 0.327 Chirality : 0.042 0.193 2379 Planarity : 0.004 0.034 1712 Dihedral : 29.128 175.931 4022 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 14.65 % Favored : 83.81 % 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: 1.84 (0.27), residues: 1027 helix: 2.68 (0.21), residues: 613 sheet: -1.08 (0.90), residues: 34 loop : -1.11 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 91 TYR 0.007 0.001 TYR B 51 PHE 0.006 0.001 PHE N 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 0.00230 / 0.13 (14534) covalent geometry : angle 0.55259 / 0.33 (20754) hydrogen bonds : bond 0.05491 / 3.69 ( 775) hydrogen bonds : angle 2.82330 / 2.06 ( 1973) metal coordination : bond 0.00770 / 0.38 ( 20) metal coordination : angle 4.88588 / 2.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8190 (mtmt) REVERT: A 131 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7651 (mtp85) REVERT: G 73 ASN cc_start: 0.7815 (t0) cc_final: 0.7530 (t0) REVERT: H 68 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: H 110 GLU cc_start: 0.7881 (tt0) cc_final: 0.7614 (mt-10) REVERT: M 90 GLU cc_start: 0.6511 (tp30) cc_final: 0.5925 (pp20) REVERT: N 106 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: N 110 ILE cc_start: 0.8115 (mt) cc_final: 0.7776 (tp) outliers start: 14 outliers final: 7 residues processed: 167 average time/residue: 0.1226 time to fit residues: 28.4845 Evaluate side-chains 164 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 112 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 46 HIS M 15 HIS ** M 76 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 = 0.4032 r_free = 0.4032 target = 0.165422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124505 restraints weight = 19547.332| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.54 r_work: 0.3069 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14554 Z= 0.153 Angle : 0.605 10.496 20778 Z= 0.339 Chirality : 0.043 0.205 2379 Planarity : 0.004 0.039 1712 Dihedral : 29.213 177.196 4022 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.76 % Allowed : 14.65 % Favored : 83.59 % 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: 1.71 (0.27), residues: 1027 helix: 2.57 (0.21), residues: 611 sheet: -1.28 (0.88), residues: 39 loop : -1.10 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.014 0.001 TYR C 57 PHE 0.008 0.001 PHE D 62 TRP 0.004 0.001 TRP N 17 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (14534) covalent geometry : angle 0.58004 / 0.34 (20754) hydrogen bonds : bond 0.06011 / 4.04 ( 775) hydrogen bonds : angle 2.87816 / 2.11 ( 1973) metal coordination : bond 0.01034 / 0.55 ( 20) metal coordination : angle 5.10621 / 2.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.355 Fit side-chains REVERT: A 115 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8258 (mtmt) REVERT: A 131 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7708 (mtp85) REVERT: G 73 ASN cc_start: 0.7960 (t0) cc_final: 0.7719 (t0) REVERT: H 68 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: N 33 THR cc_start: 0.4599 (OUTLIER) cc_final: 0.4153 (m) REVERT: N 57 MET cc_start: 0.5095 (tpt) cc_final: 0.4477 (tmm) REVERT: N 59 LYS cc_start: 0.5533 (ptpp) cc_final: 0.5221 (ptpp) REVERT: N 86 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7295 (mm-30) REVERT: N 106 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: K 31 GLN cc_start: 0.2932 (mp10) cc_final: 0.2513 (tp-100) outliers start: 16 outliers final: 10 residues processed: 163 average time/residue: 0.1430 time to fit residues: 32.3860 Evaluate side-chains 164 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 88 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 HIS ** M 76 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 = 0.3995 r_free = 0.3995 target = 0.162437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121876 restraints weight = 19435.411| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.50 r_work: 0.3021 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14554 Z= 0.219 Angle : 0.705 13.145 20778 Z= 0.383 Chirality : 0.048 0.234 2379 Planarity : 0.006 0.054 1712 Dihedral : 29.365 178.713 4022 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.09 % Allowed : 15.31 % Favored : 82.60 % 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: 1.14 (0.26), residues: 1027 helix: 2.12 (0.21), residues: 615 sheet: -1.53 (0.88), residues: 39 loop : -1.39 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 40 TYR 0.017 0.002 TYR C 57 PHE 0.016 0.002 PHE N 106 TRP 0.006 0.001 TRP N 17 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (14534) covalent geometry : angle 0.67315 / 0.38 (20754) hydrogen bonds : bond 0.07524 / 5.04 ( 775) hydrogen bonds : angle 3.13502 / 2.30 ( 1973) metal coordination : bond 0.02030 / 1.43 ( 20) metal coordination : angle 6.23106 / 3.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8435 (mtmt) REVERT: A 131 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7894 (mtp85) REVERT: G 73 ASN cc_start: 0.8189 (t0) cc_final: 0.7951 (t0) REVERT: H 68 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: N 33 THR cc_start: 0.4300 (OUTLIER) cc_final: 0.3791 (m) REVERT: N 57 MET cc_start: 0.5200 (tpt) cc_final: 0.4926 (tmm) REVERT: N 106 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6775 (m-80) outliers start: 19 outliers final: 11 residues processed: 165 average time/residue: 0.1431 time to fit residues: 33.0390 Evaluate side-chains 169 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 120 optimal weight: 0.0030 chunk 112 optimal weight: 8.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 104 GLN M 15 HIS ** M 76 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 = 0.4036 r_free = 0.4036 target = 0.165886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124991 restraints weight = 19683.909| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.54 r_work: 0.3084 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14554 Z= 0.131 Angle : 0.621 13.246 20778 Z= 0.343 Chirality : 0.043 0.207 2379 Planarity : 0.004 0.036 1712 Dihedral : 29.281 175.085 4022 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.21 % Allowed : 16.41 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.27), residues: 1027 helix: 2.55 (0.21), residues: 615 sheet: -1.26 (0.85), residues: 44 loop : -1.17 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 35 TYR 0.019 0.001 TYR H 80 PHE 0.011 0.001 PHE N 106 TRP 0.006 0.001 TRP L 25 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.13 (14534) covalent geometry : angle 0.59494 / 0.34 (20754) hydrogen bonds : bond 0.05565 / 3.74 ( 775) hydrogen bonds : angle 2.87575 / 2.11 ( 1973) metal coordination : bond 0.00913 / 0.56 ( 20) metal coordination : angle 5.28044 / 2.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.398 Fit side-chains REVERT: A 115 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8232 (mtmt) REVERT: A 131 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7543 (mtp85) REVERT: G 73 ASN cc_start: 0.8055 (t0) cc_final: 0.7811 (t0) REVERT: H 68 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: N 33 THR cc_start: 0.4332 (OUTLIER) cc_final: 0.3826 (m) REVERT: N 57 MET cc_start: 0.5087 (tpt) cc_final: 0.4837 (tmm) REVERT: N 106 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: K 31 GLN cc_start: 0.2783 (mp10) cc_final: 0.2491 (tp-100) outliers start: 11 outliers final: 7 residues processed: 160 average time/residue: 0.1425 time to fit residues: 31.8619 Evaluate side-chains 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 74 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 19 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN M 15 HIS ** M 76 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 = 0.4016 r_free = 0.4016 target = 0.164184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124248 restraints weight = 19569.678| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.53 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14554 Z= 0.167 Angle : 0.638 13.050 20778 Z= 0.352 Chirality : 0.044 0.215 2379 Planarity : 0.005 0.037 1712 Dihedral : 29.305 177.037 4022 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.32 % Allowed : 16.08 % Favored : 82.60 % 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: 1.47 (0.27), residues: 1027 helix: 2.40 (0.21), residues: 616 sheet: -1.19 (0.85), residues: 39 loop : -1.33 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 93 TYR 0.014 0.001 TYR N 22 PHE 0.010 0.002 PHE N 106 TRP 0.007 0.001 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (14534) covalent geometry : angle 0.61013 / 0.35 (20754) hydrogen bonds : bond 0.06274 / 4.21 ( 775) hydrogen bonds : angle 2.95719 / 2.17 ( 1973) metal coordination : bond 0.01263 / 0.82 ( 20) metal coordination : angle 5.51830 / 3.10 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.406 Fit side-chains REVERT: A 115 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8291 (mtmt) REVERT: A 131 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7687 (mtp85) REVERT: G 73 ASN cc_start: 0.8147 (t0) cc_final: 0.7887 (t0) REVERT: H 68 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: N 33 THR cc_start: 0.4339 (OUTLIER) cc_final: 0.3834 (m) REVERT: N 57 MET cc_start: 0.5193 (tpt) cc_final: 0.4851 (tmm) REVERT: N 106 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6694 (m-80) REVERT: K 31 GLN cc_start: 0.3125 (mp10) cc_final: 0.2638 (tp-100) outliers start: 12 outliers final: 8 residues processed: 160 average time/residue: 0.1432 time to fit residues: 31.8278 Evaluate side-chains 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 106 PHE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 38 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 96 optimal weight: 40.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN M 15 HIS ** M 76 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 = 0.164712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123615 restraints weight = 19806.005| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.52 r_work: 0.3057 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14554 Z= 0.143 Angle : 0.618 12.820 20778 Z= 0.343 Chirality : 0.044 0.255 2379 Planarity : 0.004 0.035 1712 Dihedral : 29.296 177.182 4022 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.21 % Allowed : 16.30 % Favored : 82.49 % 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: 1.55 (0.27), residues: 1027 helix: 2.47 (0.21), residues: 616 sheet: -1.21 (0.85), residues: 39 loop : -1.31 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 93 TYR 0.009 0.001 TYR H 80 PHE 0.011 0.001 PHE N 106 TRP 0.006 0.001 TRP N 17 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (14534) covalent geometry : angle 0.59090 / 0.34 (20754) hydrogen bonds : bond 0.05865 / 3.94 ( 775) hydrogen bonds : angle 2.94240 / 2.16 ( 1973) metal coordination : bond 0.01159 / 0.75 ( 20) metal coordination : angle 5.33288 / 2.97 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.70 seconds wall clock time: 49 minutes 29.52 seconds (2969.52 seconds total)