Starting phenix.real_space_refine on Fri Sep 11 20:36:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.395 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.map" model { file = "/net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1d_0586/09_2026/6o1d_0586.cif" } resolution = 3.395 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 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 8 5.16 5 C 6664 2.51 5 N 2229 2.21 5 O 2791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11982 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} 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: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "F" 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: "G" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.39, per 1000 atoms: 0.20 Number of scatterers: 11982 At special positions: 0 Unit cell: (91.665, 117.127, 119.674, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 290 15.00 O 2791 8.00 N 2229 7.00 C 6664 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 272.7 milliseconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 67.4% alpha, 2.9% beta 120 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.707A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.571A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 94 through 101 removed outlier: 3.582A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.878A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.712A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.761A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.830A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (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 46 through 72 removed outlier: 3.514A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.642A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.696A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.960A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.728A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.875A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.525A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 removed outlier: 3.708A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 75 Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 89 through 116 removed outlier: 3.882A pdb=" N GLN E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.856A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.703A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.732A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.749A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.759A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.548A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.694A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.524A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.788A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 122 removed outlier: 3.932A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.325A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.371A 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: 7.699A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 removed outlier: 6.921A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.290A pdb=" N ASN E 85 " --> 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 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.754A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 299 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 288 hydrogen bonds 576 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1944 1.33 - 1.44: 4321 1.44 - 1.56: 5932 1.56 - 1.68: 578 1.68 - 1.80: 14 Bond restraints: 12789 Sorted by residual: bond pdb=" C3' DC J 100 " pdb=" O3' DC J 100 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C5' DG J 120 " pdb=" C4' DG J 120 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.48e+01 bond pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DT I 48 " pdb=" O3' DT I 48 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.41e+01 ... (remaining 12784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 16975 1.98 - 3.96: 1455 3.96 - 5.94: 62 5.94 - 7.92: 16 7.92 - 9.90: 4 Bond angle restraints: 18512 Sorted by residual: angle pdb=" O4' DT J 89 " pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.39e+01 angle pdb=" O5' DG J 120 " pdb=" C5' DG J 120 " pdb=" C4' DG J 120 " ideal model delta sigma weight residual 109.40 113.59 -4.19 8.00e-01 1.56e+00 2.74e+01 angle pdb=" O4' DT J 90 " pdb=" C4' DT J 90 " pdb=" C3' DT J 90 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O5' DT J 47 " pdb=" C5' DT J 47 " pdb=" C4' DT J 47 " ideal model delta sigma weight residual 109.40 113.17 -3.77 8.00e-01 1.56e+00 2.22e+01 angle pdb=" N3 DT J 70 " pdb=" C4 DT J 70 " pdb=" O4 DT J 70 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 ... (remaining 18507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 5509 35.47 - 70.94: 1473 70.94 - 106.42: 19 106.42 - 141.89: 1 141.89 - 177.36: 1 Dihedral angle restraints: 7003 sinusoidal: 4818 harmonic: 2185 Sorted by residual: dihedral pdb=" C SER H 32 " pdb=" N SER H 32 " pdb=" CA SER H 32 " pdb=" CB SER H 32 " ideal model delta harmonic sigma weight residual -122.60 -109.17 -13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" CA LYS H 46 " pdb=" C LYS H 46 " pdb=" N GLN H 47 " pdb=" CA GLN H 47 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ARG G 17 " pdb=" C ARG G 17 " pdb=" N SER G 18 " pdb=" CA SER G 18 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 7000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1578 0.066 - 0.131: 474 0.131 - 0.197: 45 0.197 - 0.263: 3 0.263 - 0.328: 1 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CA SER H 32 " pdb=" N SER H 32 " pdb=" C SER H 32 " pdb=" CB SER H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2098 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 78 " -0.036 2.00e-02 2.50e+03 1.84e-02 7.61e+00 pdb=" N1 DC J 78 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DC J 78 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DC J 78 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DC J 78 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 78 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 78 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DC J 78 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC J 78 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.016 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE G 25 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 130 " 0.032 2.00e-02 2.50e+03 1.37e-02 5.64e+00 pdb=" N9 DG J 130 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DG J 130 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG J 130 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG J 130 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG J 130 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 130 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 130 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 130 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 130 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG J 130 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 130 " -0.001 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3196 2.83 - 3.35: 9746 3.35 - 3.87: 23087 3.87 - 4.38: 27368 4.38 - 4.90: 37961 Nonbonded interactions: 101358 Sorted by model distance: nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.361 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH1 ARG D 92 " model vdw 2.371 3.120 ... (remaining 101353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.590 Find NCS groups from input model: 0.090 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 : 0.011 0.104 12789 Z= 0.742 Angle : 1.084 9.905 18512 Z= 0.866 Chirality : 0.058 0.328 2101 Planarity : 0.007 0.059 1335 Dihedral : 28.016 177.359 5597 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.14 % 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: -4.72 (0.21), residues: 745 helix: -3.19 (0.15), residues: 510 sheet: None (None), residues: 0 loop : -2.48 (0.30), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 118 TYR 0.023 0.003 TYR G 50 PHE 0.043 0.005 PHE G 25 TRP 0.026 0.004 TRP E 86 HIS 0.018 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.74 (12789) covalent geometry : angle 1.08406 / 0.87 (18512) hydrogen bonds : bond 0.13419 / 9.56 ( 587) hydrogen bonds : angle 4.64999 / 3.24 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.286 Fit side-chains REVERT: A 53 LYS cc_start: 0.8923 (ptmm) cc_final: 0.8626 (pttp) REVERT: D 113 GLU cc_start: 0.8391 (tp30) cc_final: 0.7952 (tp30) REVERT: D 120 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8660 (tttp) REVERT: E 96 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7837 (mm-30) REVERT: G 15 LYS cc_start: 0.8496 (mtmp) cc_final: 0.8252 (mttt) REVERT: G 61 GLU cc_start: 0.7900 (tp30) cc_final: 0.7483 (tp30) REVERT: G 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7915 (m-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1831 time to fit residues: 35.4573 Evaluate side-chains 119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110333 restraints weight = 15347.631| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.64 r_work: 0.3046 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12789 Z= 0.151 Angle : 0.685 7.120 18512 Z= 0.399 Chirality : 0.047 0.250 2101 Planarity : 0.005 0.051 1335 Dihedral : 31.462 179.207 4115 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.80 % Allowed : 7.38 % Favored : 91.81 % 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: -2.65 (0.26), residues: 745 helix: -1.61 (0.20), residues: 521 sheet: None (None), residues: 0 loop : -1.66 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.015 0.002 TYR H 83 PHE 0.011 0.001 PHE A 84 TRP 0.010 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12789) covalent geometry : angle 0.68451 / 0.40 (18512) hydrogen bonds : bond 0.05550 / 3.62 ( 587) hydrogen bonds : angle 3.19170 / 2.23 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.292 Fit side-chains REVERT: A 53 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8603 (pttp) REVERT: C 36 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8417 (ttmm) REVERT: C 41 GLU cc_start: 0.8657 (tt0) cc_final: 0.8391 (tt0) REVERT: D 113 GLU cc_start: 0.8715 (tp30) cc_final: 0.8405 (tp30) REVERT: D 120 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8439 (tttp) REVERT: G 13 LYS cc_start: 0.9046 (ptmm) cc_final: 0.8803 (ttpp) REVERT: G 61 GLU cc_start: 0.8197 (tp30) cc_final: 0.7929 (tp30) REVERT: G 72 ASP cc_start: 0.8500 (m-30) cc_final: 0.7978 (m-30) REVERT: H 51 ASP cc_start: 0.7749 (p0) cc_final: 0.7524 (p0) REVERT: H 68 ASP cc_start: 0.8867 (t0) cc_final: 0.8509 (t0) REVERT: H 84 ASN cc_start: 0.9143 (m110) cc_final: 0.8908 (m-40) outliers start: 5 outliers final: 5 residues processed: 119 average time/residue: 0.1418 time to fit residues: 22.1865 Evaluate side-chains 115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN B 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 63 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.168270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102853 restraints weight = 15612.264| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.73 r_work: 0.2881 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.114 12789 Z= 0.443 Angle : 0.877 8.287 18512 Z= 0.467 Chirality : 0.057 0.243 2101 Planarity : 0.008 0.094 1335 Dihedral : 31.856 179.284 4115 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.05 % Allowed : 8.67 % Favored : 88.28 % 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: -2.73 (0.27), residues: 745 helix: -1.55 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 77 TYR 0.031 0.003 TYR C 50 PHE 0.027 0.004 PHE C 25 TRP 0.012 0.003 TRP E 86 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.44 (12789) covalent geometry : angle 0.87665 / 0.47 (18512) hydrogen bonds : bond 0.07290 / 4.74 ( 587) hydrogen bonds : angle 3.48819 / 2.40 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.288 Fit side-chains REVERT: A 53 LYS cc_start: 0.9121 (ptmm) cc_final: 0.8836 (pttp) REVERT: C 110 ASN cc_start: 0.8710 (t0) cc_final: 0.8406 (p0) REVERT: D 120 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8503 (tttp) REVERT: E 139 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6940 (mp) REVERT: G 61 GLU cc_start: 0.8274 (tp30) cc_final: 0.7891 (tp30) REVERT: G 72 ASP cc_start: 0.8655 (m-30) cc_final: 0.8129 (m-30) REVERT: H 51 ASP cc_start: 0.7876 (p0) cc_final: 0.7527 (p0) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 0.1425 time to fit residues: 22.4791 Evaluate side-chains 115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS D 84 ASN ** H 63 ASN ** 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 = 0.4086 r_free = 0.4086 target = 0.174100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108644 restraints weight = 15426.856| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.71 r_work: 0.2975 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12789 Z= 0.149 Angle : 0.632 7.423 18512 Z= 0.369 Chirality : 0.045 0.250 2101 Planarity : 0.004 0.041 1335 Dihedral : 31.240 178.992 4115 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 9.79 % Favored : 88.60 % 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: -1.46 (0.29), residues: 745 helix: -0.60 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 99 TYR 0.021 0.001 TYR H 40 PHE 0.009 0.001 PHE C 25 TRP 0.008 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (12789) covalent geometry : angle 0.63209 / 0.37 (18512) hydrogen bonds : bond 0.04887 / 3.17 ( 587) hydrogen bonds : angle 2.90919 / 2.02 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.295 Fit side-chains REVERT: A 53 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8760 (pttp) REVERT: C 110 ASN cc_start: 0.8649 (t0) cc_final: 0.8339 (p0) REVERT: D 120 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8474 (tttp) REVERT: E 139 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6857 (mp) REVERT: F 50 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (tt) REVERT: G 61 GLU cc_start: 0.8177 (tp30) cc_final: 0.7919 (tt0) REVERT: H 51 ASP cc_start: 0.7885 (p0) cc_final: 0.7588 (p0) REVERT: H 52 THR cc_start: 0.9014 (m) cc_final: 0.8718 (t) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.1444 time to fit residues: 22.2305 Evaluate side-chains 117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.173377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107246 restraints weight = 15426.853| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.65 r_work: 0.2982 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12789 Z= 0.166 Angle : 0.630 6.653 18512 Z= 0.363 Chirality : 0.044 0.248 2101 Planarity : 0.005 0.041 1335 Dihedral : 31.145 179.168 4115 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.41 % Allowed : 10.59 % Favored : 87.00 % 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: -0.98 (0.30), residues: 745 helix: -0.23 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.026 0.002 TYR H 40 PHE 0.009 0.001 PHE C 25 TRP 0.006 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (12789) covalent geometry : angle 0.63000 / 0.36 (18512) hydrogen bonds : bond 0.04884 / 3.18 ( 587) hydrogen bonds : angle 2.81141 / 1.95 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.221 Fit side-chains REVERT: A 53 LYS cc_start: 0.9074 (ptmm) cc_final: 0.8804 (pttp) REVERT: C 13 LYS cc_start: 0.8413 (tppt) cc_final: 0.8205 (tttp) REVERT: C 110 ASN cc_start: 0.8655 (t0) cc_final: 0.8342 (p0) REVERT: D 120 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8461 (tttp) REVERT: E 139 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6878 (mp) REVERT: F 50 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8588 (tt) REVERT: G 61 GLU cc_start: 0.8162 (tp30) cc_final: 0.7943 (tt0) REVERT: G 72 ASP cc_start: 0.8536 (m-30) cc_final: 0.8000 (m-30) REVERT: H 51 ASP cc_start: 0.7822 (p0) cc_final: 0.7498 (p0) REVERT: H 52 THR cc_start: 0.8989 (m) cc_final: 0.8672 (t) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.1353 time to fit residues: 21.3354 Evaluate side-chains 121 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.173657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107921 restraints weight = 15501.158| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.70 r_work: 0.2976 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12789 Z= 0.165 Angle : 0.621 6.784 18512 Z= 0.358 Chirality : 0.044 0.252 2101 Planarity : 0.004 0.049 1335 Dihedral : 31.101 177.946 4115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.25 % Allowed : 11.08 % Favored : 86.68 % 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: -0.73 (0.30), residues: 745 helix: -0.05 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.019 0.001 TYR H 40 PHE 0.009 0.001 PHE C 25 TRP 0.007 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (12789) covalent geometry : angle 0.62054 / 0.36 (18512) hydrogen bonds : bond 0.04679 / 3.06 ( 587) hydrogen bonds : angle 2.78517 / 1.92 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.288 Fit side-chains REVERT: C 13 LYS cc_start: 0.8440 (tppt) cc_final: 0.8235 (tttp) REVERT: C 110 ASN cc_start: 0.8657 (t0) cc_final: 0.8352 (p0) REVERT: D 120 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8470 (tttp) REVERT: E 139 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6885 (mp) REVERT: F 50 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8547 (tt) REVERT: H 34 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8712 (tttt) REVERT: H 51 ASP cc_start: 0.7783 (p0) cc_final: 0.7406 (p0) REVERT: H 52 THR cc_start: 0.8989 (m) cc_final: 0.8682 (t) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.1330 time to fit residues: 21.0335 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110904 restraints weight = 15741.784| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.73 r_work: 0.3022 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12789 Z= 0.128 Angle : 0.577 6.786 18512 Z= 0.342 Chirality : 0.041 0.252 2101 Planarity : 0.004 0.041 1335 Dihedral : 30.880 177.601 4115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.77 % Allowed : 11.88 % Favored : 86.36 % 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: -0.16 (0.31), residues: 745 helix: 0.35 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.025 0.001 TYR H 40 PHE 0.006 0.001 PHE D 70 TRP 0.005 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.13 (12789) covalent geometry : angle 0.57653 / 0.34 (18512) hydrogen bonds : bond 0.04151 / 2.71 ( 587) hydrogen bonds : angle 2.61204 / 1.81 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.295 Fit side-chains REVERT: C 110 ASN cc_start: 0.8652 (t0) cc_final: 0.8358 (p0) REVERT: D 120 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8510 (tttp) REVERT: E 139 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6887 (mp) REVERT: H 35 GLU cc_start: 0.8190 (pt0) cc_final: 0.7976 (pt0) REVERT: H 46 LYS cc_start: 0.8504 (mttm) cc_final: 0.8273 (mmtt) REVERT: H 51 ASP cc_start: 0.7717 (p0) cc_final: 0.7373 (p0) REVERT: H 52 THR cc_start: 0.8948 (m) cc_final: 0.8710 (t) REVERT: H 68 ASP cc_start: 0.8820 (t0) cc_final: 0.8514 (t0) outliers start: 11 outliers final: 10 residues processed: 124 average time/residue: 0.1380 time to fit residues: 22.7398 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.175682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111182 restraints weight = 15802.220| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.74 r_work: 0.3028 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 12789 Z= 0.123 Angle : 0.573 6.165 18512 Z= 0.339 Chirality : 0.041 0.253 2101 Planarity : 0.004 0.051 1335 Dihedral : 30.864 177.497 4115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.93 % Allowed : 11.56 % Favored : 86.52 % 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: 0.12 (0.31), residues: 745 helix: 0.56 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.013 0.001 TYR H 40 PHE 0.011 0.001 PHE H 65 TRP 0.004 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (12789) covalent geometry : angle 0.57321 / 0.34 (18512) hydrogen bonds : bond 0.04094 / 2.67 ( 587) hydrogen bonds : angle 2.58872 / 1.80 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.319 Fit side-chains REVERT: C 110 ASN cc_start: 0.8647 (t0) cc_final: 0.8356 (p0) REVERT: D 82 HIS cc_start: 0.8201 (m-70) cc_final: 0.7969 (m-70) REVERT: D 120 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8570 (tttp) REVERT: E 139 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6813 (mp) REVERT: F 36 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7411 (mtp180) REVERT: H 46 LYS cc_start: 0.8507 (mttm) cc_final: 0.8250 (mmtt) REVERT: H 51 ASP cc_start: 0.7685 (p0) cc_final: 0.7333 (p0) REVERT: H 52 THR cc_start: 0.8961 (m) cc_final: 0.8698 (t) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.1553 time to fit residues: 24.7111 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112476 restraints weight = 15750.266| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.67 r_work: 0.3049 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12789 Z= 0.126 Angle : 0.571 6.141 18512 Z= 0.338 Chirality : 0.041 0.251 2101 Planarity : 0.004 0.043 1335 Dihedral : 30.841 177.564 4115 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.61 % Allowed : 11.72 % Favored : 86.68 % 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 (0.31), residues: 745 helix: 0.75 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.016 0.001 TYR H 40 PHE 0.009 0.001 PHE H 65 TRP 0.005 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (12789) covalent geometry : angle 0.57138 / 0.34 (18512) hydrogen bonds : bond 0.04086 / 2.68 ( 587) hydrogen bonds : angle 2.55446 / 1.77 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.304 Fit side-chains REVERT: C 110 ASN cc_start: 0.8665 (t0) cc_final: 0.8378 (p0) REVERT: D 82 HIS cc_start: 0.8159 (m-70) cc_final: 0.7941 (m-70) REVERT: D 120 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8537 (tttp) REVERT: E 139 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6873 (mp) REVERT: F 36 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7447 (mtp180) REVERT: H 51 ASP cc_start: 0.7652 (p0) cc_final: 0.7297 (p0) REVERT: H 52 THR cc_start: 0.8979 (m) cc_final: 0.8742 (t) outliers start: 10 outliers final: 8 residues processed: 124 average time/residue: 0.1494 time to fit residues: 24.3827 Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 71 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 99 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113494 restraints weight = 15917.746| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.73 r_work: 0.3036 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12789 Z= 0.123 Angle : 0.569 6.093 18512 Z= 0.336 Chirality : 0.040 0.253 2101 Planarity : 0.004 0.066 1335 Dihedral : 30.787 177.506 4115 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.44 % Allowed : 11.88 % Favored : 86.68 % 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: 0.42 (0.31), residues: 745 helix: 0.81 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.014 0.001 TYR H 40 PHE 0.006 0.001 PHE D 70 TRP 0.004 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.12 (12789) covalent geometry : angle 0.56850 / 0.34 (18512) hydrogen bonds : bond 0.04024 / 2.64 ( 587) hydrogen bonds : angle 2.53754 / 1.76 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.350 Fit side-chains REVERT: C 110 ASN cc_start: 0.8649 (t0) cc_final: 0.8352 (p0) REVERT: D 82 HIS cc_start: 0.8107 (m-70) cc_final: 0.7885 (m-70) REVERT: D 120 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8595 (tttp) REVERT: E 139 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6820 (mp) REVERT: F 36 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7421 (mtp180) REVERT: G 72 ASP cc_start: 0.8442 (m-30) cc_final: 0.7932 (m-30) REVERT: H 35 GLU cc_start: 0.7910 (pt0) cc_final: 0.7670 (pt0) REVERT: H 51 ASP cc_start: 0.7681 (p0) cc_final: 0.7295 (p0) REVERT: H 52 THR cc_start: 0.9020 (m) cc_final: 0.8714 (t) REVERT: H 68 ASP cc_start: 0.8773 (t0) cc_final: 0.8493 (t0) outliers start: 9 outliers final: 8 residues processed: 119 average time/residue: 0.1368 time to fit residues: 21.5401 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 4.9990 chunk 76 optimal weight: 40.0000 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 29 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113556 restraints weight = 15762.392| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.71 r_work: 0.3049 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12789 Z= 0.117 Angle : 0.558 8.359 18512 Z= 0.332 Chirality : 0.040 0.253 2101 Planarity : 0.003 0.040 1335 Dihedral : 30.674 177.338 4115 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.61 % Allowed : 11.72 % Favored : 86.68 % 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: 0.74 (0.31), residues: 745 helix: 1.05 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 44 TYR 0.014 0.001 TYR H 40 PHE 0.007 0.001 PHE H 65 TRP 0.005 0.001 TRP E 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.12 (12789) covalent geometry : angle 0.55780 / 0.33 (18512) hydrogen bonds : bond 0.03908 / 2.56 ( 587) hydrogen bonds : angle 2.50749 / 1.74 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.27 seconds wall clock time: 40 minutes 20.71 seconds (2420.71 seconds total)