Starting phenix.real_space_refine on Wed Jan 14 20:58:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.map" model { file = "/net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8caz_16536/01_2026/8caz_16536.cif" } resolution = 2.11 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= 0.001 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: 7 Type Number sf(0) Gaussians K 13 8.98 5 P 460 5.49 5 Mg 29 5.21 5 S 27 5.16 5 C 9853 2.51 5 N 3452 2.21 5 O 5359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19193 Number of models: 1 Model: "" Number of chains: 21 Chain: "4" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 107 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 9841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 9841 Classifications: {'RNA': 460} Modifications used: {'rna2p_pur': 39, 'rna2p_pyr': 36, 'rna3p': 3, 'rna3p_pur': 210, 'rna3p_pyr': 172} Link IDs: {'rna2p': 75, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1685 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 7, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1597 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 2 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Unusual residues: {' K': 12, ' MG': 29} Classifications: {'undetermined': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 503 Classifications: {'water': 503} Link IDs: {None: 502} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 3.83, per 1000 atoms: 0.20 Number of scatterers: 19193 At special positions: 0 Unit cell: (123.84, 120.24, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 13 19.00 S 27 16.00 P 460 15.00 Mg 29 11.99 O 5359 8.00 N 3452 7.00 C 9853 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: 1.43 Conformation dependent library (CDL) restraints added in 445.1 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 52.1% alpha, 18.5% beta 150 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain '4' and resid 55 through 64 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.521A pdb=" N LYS B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix removed outlier: 3.551A pdb=" N GLU B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 103 through 123 removed outlier: 4.098A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.506A pdb=" N LEU B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.551A pdb=" N LEU B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.724A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 4.392A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.675A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 51 Processing helix chain 'G' and resid 58 through 68 Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 149 through 152 removed outlier: 3.524A pdb=" N ALA G 152 " --> pdb=" O LYS G 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 149 through 152' Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 88 removed outlier: 3.754A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 19 Processing helix chain 'M' and resid 20 through 22 No H-bonds generated for 'chain 'M' and resid 20 through 22' Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 61 Processing helix chain 'M' and resid 65 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 33 removed outlier: 5.157A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.526A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'S' and resid 4 through 8 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.341A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 91 removed outlier: 5.982A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 164 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 70 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 161 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.558A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.092A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 79 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.073A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 35 through 52 removed outlier: 4.931A pdb=" N VAL J 36 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL J 77 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 35 through 52 removed outlier: 4.931A pdb=" N VAL J 36 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL J 77 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.542A pdb=" N LEU N 79 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 31 through 33 451 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 584 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3004 1.34 - 1.46: 7959 1.46 - 1.58: 7900 1.58 - 1.70: 919 1.70 - 1.82: 51 Bond restraints: 19833 Sorted by residual: bond pdb=" C ARG N 69 " pdb=" N PRO N 70 " ideal model delta sigma weight residual 1.331 1.358 -0.026 7.90e-03 1.60e+04 1.11e+01 bond pdb=" O5' G A1034 " pdb=" C5' G A1034 " ideal model delta sigma weight residual 1.420 1.465 -0.045 1.50e-02 4.44e+03 8.84e+00 bond pdb=" O5' A A1257 " pdb=" C5' A A1257 " ideal model delta sigma weight residual 1.424 1.465 -0.041 1.50e-02 4.44e+03 7.37e+00 bond pdb=" O5' G A1033 " pdb=" C5' G A1033 " ideal model delta sigma weight residual 1.420 1.461 -0.041 1.50e-02 4.44e+03 7.37e+00 bond pdb=" O5' G A1026 " pdb=" C5' G A1026 " ideal model delta sigma weight residual 1.420 1.460 -0.040 1.50e-02 4.44e+03 7.29e+00 ... (remaining 19828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 25800 2.40 - 4.79: 2929 4.79 - 7.19: 243 7.19 - 9.58: 30 9.58 - 11.98: 3 Bond angle restraints: 29005 Sorted by residual: angle pdb=" O3' G A 976 " pdb=" P A A 977 " pdb=" O5' A A 977 " ideal model delta sigma weight residual 104.00 92.02 11.98 1.50e+00 4.44e-01 6.37e+01 angle pdb=" O3' G A1190 " pdb=" P A A1191 " pdb=" O5' A A1191 " ideal model delta sigma weight residual 104.00 93.42 10.58 1.50e+00 4.44e-01 4.97e+01 angle pdb=" O3' A A1377 " pdb=" P C A1378 " pdb=" O5' C A1378 " ideal model delta sigma weight residual 104.00 93.85 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" O3' G A1153 " pdb=" P G A1154 " pdb=" O5' G A1154 " ideal model delta sigma weight residual 104.00 94.75 9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" O3' A A1269 " pdb=" P G A1270 " pdb=" O5' G A1270 " ideal model delta sigma weight residual 104.00 94.90 9.10 1.50e+00 4.44e-01 3.68e+01 ... (remaining 29000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 11463 32.87 - 65.73: 1054 65.73 - 98.60: 149 98.60 - 131.47: 2 131.47 - 164.33: 2 Dihedral angle restraints: 12670 sinusoidal: 9535 harmonic: 3135 Sorted by residual: dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 64.94 135.06 1 1.50e+01 4.44e-03 7.29e+01 dihedral pdb=" O4' U A 960 " pdb=" C1' U A 960 " pdb=" N1 U A 960 " pdb=" C2 U A 960 " ideal model delta sinusoidal sigma weight residual 232.00 67.67 164.33 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" CA GLN B 89 " pdb=" C GLN B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 12667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2745 0.120 - 0.241: 850 0.241 - 0.361: 21 0.361 - 0.481: 1 0.481 - 0.601: 1 Chirality restraints: 3618 Sorted by residual: chirality pdb=" P C A 930 " pdb=" OP1 C A 930 " pdb=" OP2 C A 930 " pdb=" O5' C A 930 " both_signs ideal model delta sigma weight residual True 2.41 -3.01 -0.60 2.00e-01 2.50e+01 9.04e+00 chirality pdb=" P G A1221 " pdb=" OP1 G A1221 " pdb=" OP2 G A1221 " pdb=" O5' G A1221 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" P C A1059 " pdb=" OP1 C A1059 " pdb=" OP2 C A1059 " pdb=" O5' C A1059 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3615 not shown) Planarity restraints: 1984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1331 " 0.083 2.00e-02 2.50e+03 3.33e-02 3.33e+01 pdb=" N9 G A1331 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G A1331 " -0.025 2.00e-02 2.50e+03 pdb=" N7 G A1331 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1331 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A1331 " 0.031 2.00e-02 2.50e+03 pdb=" O6 G A1331 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G A1331 " 0.019 2.00e-02 2.50e+03 pdb=" C2 G A1331 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G A1331 " -0.007 2.00e-02 2.50e+03 pdb=" N3 G A1331 " -0.029 2.00e-02 2.50e+03 pdb=" C4 G A1331 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1316 " -0.082 2.00e-02 2.50e+03 3.22e-02 3.12e+01 pdb=" N9 G A1316 " 0.055 2.00e-02 2.50e+03 pdb=" C8 G A1316 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1316 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A1316 " 0.013 2.00e-02 2.50e+03 pdb=" C6 G A1316 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G A1316 " -0.026 2.00e-02 2.50e+03 pdb=" N1 G A1316 " -0.019 2.00e-02 2.50e+03 pdb=" C2 G A1316 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A1316 " 0.015 2.00e-02 2.50e+03 pdb=" N3 G A1316 " 0.018 2.00e-02 2.50e+03 pdb=" C4 G A1316 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1013 " -0.073 2.00e-02 2.50e+03 2.94e-02 2.60e+01 pdb=" N9 G A1013 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G A1013 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G A1013 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A1013 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A1013 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G A1013 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G A1013 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G A1013 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G A1013 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G A1013 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G A1013 " 0.019 2.00e-02 2.50e+03 ... (remaining 1981 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.51: 188 2.51 - 3.17: 16351 3.17 - 3.83: 46656 3.83 - 4.48: 66680 4.48 - 5.14: 90863 Nonbonded interactions: 220738 Sorted by model distance: nonbonded pdb=" OP1 C A 980 " pdb="MG MG A1610 " model vdw 1.855 2.170 nonbonded pdb=" OP1 C A 972 " pdb="MG MG A1627 " model vdw 1.873 2.170 nonbonded pdb=" O6 G A1108 " pdb="MG MG A1612 " model vdw 1.888 2.170 nonbonded pdb="MG MG A1620 " pdb=" O HOH A1980 " model vdw 1.895 2.170 nonbonded pdb="MG MG A1610 " pdb=" O HOH A2049 " model vdw 1.901 2.170 ... (remaining 220733 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 36.240 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 22.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 19833 Z= 0.508 Angle : 1.502 11.975 29005 Z= 0.956 Chirality : 0.097 0.601 3618 Planarity : 0.017 0.157 1984 Dihedral : 21.038 164.331 10636 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 0.55 % Allowed : 3.60 % Favored : 95.85 % 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 (0.22), residues: 1069 helix: -0.99 (0.19), residues: 509 sheet: -0.35 (0.38), residues: 146 loop : -0.84 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG I 41 TYR 0.033 0.005 TYR I 7 PHE 0.037 0.004 PHE C 23 TRP 0.047 0.004 TRP C 201 HIS 0.011 0.003 HIS J 70 Details of bonding type rmsd covalent geometry : bond 0.00775 (19833) covalent geometry : angle 1.50232 (29005) hydrogen bonds : bond 0.17145 ( 820) hydrogen bonds : angle 6.68142 ( 1850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.555 Fit side-chains REVERT: B 21 ARG cc_start: 0.5252 (ptp-170) cc_final: 0.3871 (mmt-90) REVERT: B 23 TRP cc_start: 0.6692 (p-90) cc_final: 0.6345 (p-90) REVERT: B 27 MET cc_start: 0.6597 (mmm) cc_final: 0.6217 (mmm) REVERT: B 67 ILE cc_start: 0.6254 (mm) cc_final: 0.5530 (tp) REVERT: B 90 PHE cc_start: 0.6278 (m-80) cc_final: 0.6060 (m-80) REVERT: B 109 GLN cc_start: 0.6722 (mt0) cc_final: 0.5376 (tp40) REVERT: B 154 MET cc_start: 0.6431 (ttp) cc_final: 0.6154 (ttt) REVERT: B 169 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6686 (mm-30) REVERT: B 191 SER cc_start: 0.7073 (m) cc_final: 0.6592 (m) REVERT: C 45 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7579 (ttpt) REVERT: C 49 LYS cc_start: 0.7481 (mtpt) cc_final: 0.7024 (mppt) REVERT: C 72 ARG cc_start: 0.7277 (mtm-85) cc_final: 0.6951 (mtt-85) REVERT: C 83 ASP cc_start: 0.7332 (m-30) cc_final: 0.6933 (m-30) REVERT: C 100 GLN cc_start: 0.8046 (mt0) cc_final: 0.7458 (tt0) REVERT: C 129 MET cc_start: 0.7794 (mmm) cc_final: 0.7318 (mtm) REVERT: C 132 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7391 (ttm170) REVERT: C 139 GLN cc_start: 0.8005 (mt0) cc_final: 0.7797 (mt0) REVERT: G 48 GLU cc_start: 0.7358 (tt0) cc_final: 0.6819 (tp30) REVERT: G 60 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6160 (tp30) REVERT: G 63 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6681 (mm-30) REVERT: G 76 LYS cc_start: 0.5973 (mmtp) cc_final: 0.5609 (ttpp) REVERT: G 77 SER cc_start: 0.7656 (m) cc_final: 0.7307 (m) REVERT: G 78 ARG cc_start: 0.5807 (tpt90) cc_final: 0.5197 (mmp-170) REVERT: G 79 ARG cc_start: 0.5774 (ttt90) cc_final: 0.5386 (mtt-85) REVERT: G 86 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7203 (tp40) REVERT: G 136 LYS cc_start: 0.7233 (tttm) cc_final: 0.6762 (tttp) REVERT: G 144 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (tpp) REVERT: I 32 GLN cc_start: 0.7990 (mm110) cc_final: 0.7623 (mm-40) REVERT: I 33 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6878 (mtm-85) REVERT: I 37 GLN cc_start: 0.8104 (mt0) cc_final: 0.7873 (mt0) REVERT: I 41 ARG cc_start: 0.6641 (mtp85) cc_final: 0.5918 (ttm170) REVERT: I 49 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7424 (mtm180) REVERT: I 52 LEU cc_start: 0.8198 (mt) cc_final: 0.7947 (mm) REVERT: I 56 ASP cc_start: 0.7488 (t0) cc_final: 0.7257 (t0) REVERT: I 91 ASP cc_start: 0.7781 (t0) cc_final: 0.7518 (t0) REVERT: I 100 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8003 (tttt) REVERT: I 119 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7005 (mmt90) REVERT: J 16 ARG cc_start: 0.7266 (ttm-80) cc_final: 0.7017 (mtt90) REVERT: J 37 ARG cc_start: 0.6792 (mmm160) cc_final: 0.6408 (mmm-85) REVERT: J 46 LYS cc_start: 0.8143 (mttt) cc_final: 0.7580 (mppt) REVERT: J 88 MET cc_start: 0.6616 (mmt) cc_final: 0.4610 (tmm) REVERT: J 99 GLN cc_start: 0.7434 (tt0) cc_final: 0.6198 (mp10) REVERT: M 3 ARG cc_start: 0.7481 (tpt-90) cc_final: 0.7230 (tpt170) REVERT: M 12 HIS cc_start: 0.7836 (p-80) cc_final: 0.7530 (p-80) REVERT: M 27 LYS cc_start: 0.8197 (tttt) cc_final: 0.7734 (tppt) REVERT: M 43 VAL cc_start: 0.7559 (t) cc_final: 0.7342 (p) REVERT: M 75 MET cc_start: 0.7848 (mtp) cc_final: 0.7476 (mtm) REVERT: M 78 LYS cc_start: 0.8294 (tttm) cc_final: 0.7953 (ttpt) REVERT: M 93 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7232 (mtp-110) REVERT: N 23 LYS cc_start: 0.7917 (tppt) cc_final: 0.7616 (tptt) REVERT: N 26 GLU cc_start: 0.7479 (tt0) cc_final: 0.7274 (tm-30) REVERT: N 39 GLU cc_start: 0.7215 (tt0) cc_final: 0.6768 (mm-30) REVERT: N 41 ARG cc_start: 0.7381 (mtp180) cc_final: 0.7161 (mpp80) REVERT: N 47 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7435 (mtmt) REVERT: S 13 LEU cc_start: 0.8597 (tp) cc_final: 0.8380 (tm) REVERT: S 21 LYS cc_start: 0.7574 (ttmm) cc_final: 0.7104 (ttpp) outliers start: 5 outliers final: 2 residues processed: 211 average time/residue: 0.8349 time to fit residues: 192.0113 Evaluate side-chains 175 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain J residue 84 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 177 ASN G 28 ASN G 68 ASN G 142 HIS I 5 GLN I 75 GLN I 81 HIS M 52 GLN S 14 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.124258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096985 restraints weight = 20667.722| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.74 r_work: 0.3117 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 0.027 19833 Z= 0.170 Angle : 0.613 5.455 29005 Z= 0.326 Chirality : 0.038 0.241 3618 Planarity : 0.006 0.090 1984 Dihedral : 22.213 163.600 8429 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % Rotamer: Outliers : 1.75 % Allowed : 8.41 % Favored : 89.85 % 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 (0.24), residues: 1069 helix: 0.99 (0.22), residues: 511 sheet: 0.26 (0.39), residues: 152 loop : 0.12 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 63 TYR 0.017 0.002 TYR I 6 PHE 0.024 0.002 PHE B 90 TRP 0.021 0.001 TRP C 201 HIS 0.006 0.001 HIS S 14 Details of bonding type rmsd covalent geometry : bond 0.00321 (19833) covalent geometry : angle 0.61268 (29005) hydrogen bonds : bond 0.05855 ( 820) hydrogen bonds : angle 4.08644 ( 1850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.374 Fit side-chains REVERT: B 23 TRP cc_start: 0.6944 (p-90) cc_final: 0.6660 (p-90) REVERT: B 27 MET cc_start: 0.6851 (mmm) cc_final: 0.6529 (mmm) REVERT: B 154 MET cc_start: 0.6534 (ttp) cc_final: 0.6269 (ttt) REVERT: B 169 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6510 (mm-30) REVERT: B 188 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.5791 (m-30) REVERT: C 49 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7488 (mmtt) REVERT: C 72 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7102 (mtt-85) REVERT: C 85 GLU cc_start: 0.7560 (tp30) cc_final: 0.7336 (tp30) REVERT: C 100 GLN cc_start: 0.7885 (mt0) cc_final: 0.7671 (tt0) REVERT: C 144 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8414 (mm) REVERT: G 60 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6445 (tp30) REVERT: G 79 ARG cc_start: 0.5735 (ttt90) cc_final: 0.5408 (mtt-85) REVERT: G 86 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7189 (tp40) REVERT: G 136 LYS cc_start: 0.7573 (tttm) cc_final: 0.7319 (ttpp) REVERT: I 59 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6682 (mp0) REVERT: J 16 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6817 (mtt-85) REVERT: J 19 ASP cc_start: 0.7469 (m-30) cc_final: 0.7205 (m-30) REVERT: J 20 GLN cc_start: 0.7470 (mt0) cc_final: 0.7190 (mp10) REVERT: J 99 GLN cc_start: 0.7485 (tt0) cc_final: 0.6994 (mp10) REVERT: M 113 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6268 (mtm180) REVERT: N 41 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7348 (ttp-110) REVERT: N 47 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7965 (mtmt) REVERT: S 21 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7546 (ttpp) outliers start: 16 outliers final: 4 residues processed: 187 average time/residue: 0.8253 time to fit residues: 168.4950 Evaluate side-chains 163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 128 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095665 restraints weight = 20702.951| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 0.73 r_work: 0.3085 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19833 Z= 0.223 Angle : 0.646 5.188 29005 Z= 0.340 Chirality : 0.040 0.236 3618 Planarity : 0.006 0.063 1984 Dihedral : 22.186 163.676 8426 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.78 % Favored : 98.13 % Rotamer: Outliers : 1.86 % Allowed : 10.48 % Favored : 87.66 % 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: 1.19 (0.25), residues: 1069 helix: 1.26 (0.22), residues: 512 sheet: 0.78 (0.39), residues: 159 loop : 0.35 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 4 TYR 0.015 0.002 TYR I 7 PHE 0.024 0.002 PHE B 90 TRP 0.020 0.002 TRP C 201 HIS 0.005 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00428 (19833) covalent geometry : angle 0.64617 (29005) hydrogen bonds : bond 0.06248 ( 820) hydrogen bonds : angle 4.06099 ( 1850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.499 Fit side-chains REVERT: B 21 ARG cc_start: 0.5778 (ptp-170) cc_final: 0.4128 (mmt90) REVERT: B 27 MET cc_start: 0.6837 (mmm) cc_final: 0.6488 (mmm) REVERT: B 109 GLN cc_start: 0.6742 (mt0) cc_final: 0.6525 (mt0) REVERT: B 154 MET cc_start: 0.6562 (ttp) cc_final: 0.6311 (ttm) REVERT: B 169 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6484 (mm-30) REVERT: C 72 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7168 (mtt-85) REVERT: C 144 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8264 (mm) REVERT: G 60 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6480 (tt0) REVERT: G 79 ARG cc_start: 0.5841 (ttt90) cc_final: 0.5370 (mtt-85) REVERT: G 86 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7137 (tp40) REVERT: G 136 LYS cc_start: 0.7595 (tttm) cc_final: 0.7343 (ttpp) REVERT: I 59 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6666 (mp0) REVERT: J 16 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6857 (mtt-85) REVERT: J 19 ASP cc_start: 0.7485 (m-30) cc_final: 0.7232 (m-30) REVERT: J 20 GLN cc_start: 0.7430 (mt0) cc_final: 0.7140 (mp10) REVERT: J 99 GLN cc_start: 0.7459 (tt0) cc_final: 0.7027 (mp10) REVERT: M 113 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6327 (mtm180) REVERT: N 41 ARG cc_start: 0.7628 (mtp180) cc_final: 0.7351 (ttp-110) REVERT: N 47 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7980 (mtmt) REVERT: S 21 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7619 (ttpp) outliers start: 17 outliers final: 8 residues processed: 174 average time/residue: 0.8193 time to fit residues: 155.5927 Evaluate side-chains 173 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN C 139 GLN N 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093733 restraints weight = 20720.232| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.77 r_work: 0.3049 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 19833 Z= 0.353 Angle : 0.798 6.288 29005 Z= 0.408 Chirality : 0.046 0.217 3618 Planarity : 0.008 0.076 1984 Dihedral : 22.288 164.112 8426 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 2.18 % Allowed : 12.12 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1069 helix: 0.92 (0.22), residues: 514 sheet: 0.46 (0.36), residues: 169 loop : 0.29 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 4 TYR 0.018 0.003 TYR I 7 PHE 0.032 0.003 PHE B 90 TRP 0.023 0.003 TRP C 201 HIS 0.007 0.002 HIS S 83 Details of bonding type rmsd covalent geometry : bond 0.00689 (19833) covalent geometry : angle 0.79788 (29005) hydrogen bonds : bond 0.07180 ( 820) hydrogen bonds : angle 4.24861 ( 1850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.501 Fit side-chains REVERT: B 21 ARG cc_start: 0.5780 (ptp-170) cc_final: 0.4037 (mmt90) REVERT: B 27 MET cc_start: 0.6799 (mmm) cc_final: 0.6513 (mmm) REVERT: B 52 GLU cc_start: 0.5338 (pt0) cc_final: 0.4981 (tp30) REVERT: B 109 GLN cc_start: 0.6720 (mt0) cc_final: 0.6489 (mt0) REVERT: B 137 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4574 (ttp-170) REVERT: B 154 MET cc_start: 0.6505 (ttp) cc_final: 0.6294 (ttm) REVERT: B 169 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6577 (mm-30) REVERT: B 188 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.5813 (m-30) REVERT: C 144 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8213 (mm) REVERT: G 79 ARG cc_start: 0.5860 (ttt90) cc_final: 0.5481 (mtt-85) REVERT: G 136 LYS cc_start: 0.7685 (tttm) cc_final: 0.7446 (ttpp) REVERT: I 33 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6847 (mtt-85) REVERT: J 19 ASP cc_start: 0.7496 (m-30) cc_final: 0.7236 (m-30) REVERT: J 20 GLN cc_start: 0.7544 (mt0) cc_final: 0.7195 (mp10) REVERT: J 76 ILE cc_start: 0.7598 (mm) cc_final: 0.7388 (mm) REVERT: J 88 MET cc_start: 0.6700 (mmp) cc_final: 0.4980 (tmm) REVERT: M 113 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6603 (mtt180) REVERT: N 41 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7349 (ttp-110) REVERT: N 47 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7939 (mtmt) REVERT: S 21 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7643 (ttpp) outliers start: 20 outliers final: 10 residues processed: 177 average time/residue: 0.7943 time to fit residues: 153.9511 Evaluate side-chains 176 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN J 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096542 restraints weight = 20756.430| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 0.73 r_work: 0.3109 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 19833 Z= 0.187 Angle : 0.605 5.378 29005 Z= 0.321 Chirality : 0.039 0.229 3618 Planarity : 0.005 0.056 1984 Dihedral : 22.184 163.626 8426 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.94 % Rotamer: Outliers : 1.75 % Allowed : 12.55 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1069 helix: 1.40 (0.22), residues: 514 sheet: 0.81 (0.38), residues: 159 loop : 0.50 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 119 TYR 0.013 0.002 TYR I 7 PHE 0.020 0.002 PHE S 74 TRP 0.022 0.002 TRP C 201 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00357 (19833) covalent geometry : angle 0.60491 (29005) hydrogen bonds : bond 0.05793 ( 820) hydrogen bonds : angle 3.94059 ( 1850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.498 Fit side-chains REVERT: B 21 ARG cc_start: 0.5824 (ptp-170) cc_final: 0.4115 (mmt90) REVERT: B 27 MET cc_start: 0.6899 (mmm) cc_final: 0.6521 (mmm) REVERT: B 52 GLU cc_start: 0.5411 (pt0) cc_final: 0.5071 (tp30) REVERT: B 137 ARG cc_start: 0.5355 (OUTLIER) cc_final: 0.4708 (ttp-170) REVERT: B 154 MET cc_start: 0.6549 (ttp) cc_final: 0.6313 (ttm) REVERT: B 169 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6467 (mm-30) REVERT: B 188 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.5975 (m-30) REVERT: C 72 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7103 (mtt-85) REVERT: C 144 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8227 (mm) REVERT: G 78 ARG cc_start: 0.6213 (mmp-170) cc_final: 0.5976 (mmp-170) REVERT: G 136 LYS cc_start: 0.7637 (tttm) cc_final: 0.7394 (ttpp) REVERT: I 33 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7577 (mtp180) REVERT: I 59 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6734 (mp0) REVERT: J 19 ASP cc_start: 0.7506 (m-30) cc_final: 0.7259 (m-30) REVERT: J 20 GLN cc_start: 0.7468 (mt0) cc_final: 0.7186 (mp10) REVERT: J 88 MET cc_start: 0.6744 (mmp) cc_final: 0.5065 (tmm) REVERT: M 93 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7807 (mmm160) REVERT: M 113 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6557 (mtt180) REVERT: N 41 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7391 (ttp-110) REVERT: S 21 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7640 (ttpp) outliers start: 16 outliers final: 7 residues processed: 174 average time/residue: 0.7680 time to fit residues: 146.9991 Evaluate side-chains 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN G 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094030 restraints weight = 20627.083| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.76 r_work: 0.3057 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19833 Z= 0.329 Angle : 0.765 6.260 29005 Z= 0.393 Chirality : 0.045 0.214 3618 Planarity : 0.007 0.073 1984 Dihedral : 22.243 163.939 8426 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 1.97 % Allowed : 13.21 % Favored : 84.83 % 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: 0.99 (0.25), residues: 1069 helix: 1.03 (0.22), residues: 519 sheet: 0.48 (0.36), residues: 164 loop : 0.46 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 3 TYR 0.017 0.003 TYR I 7 PHE 0.027 0.003 PHE S 74 TRP 0.023 0.003 TRP B 23 HIS 0.006 0.002 HIS S 83 Details of bonding type rmsd covalent geometry : bond 0.00641 (19833) covalent geometry : angle 0.76500 (29005) hydrogen bonds : bond 0.06943 ( 820) hydrogen bonds : angle 4.16166 ( 1850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.415 Fit side-chains REVERT: B 21 ARG cc_start: 0.5796 (ptp-170) cc_final: 0.4039 (mmt90) REVERT: B 27 MET cc_start: 0.6817 (mmm) cc_final: 0.6443 (mmm) REVERT: B 52 GLU cc_start: 0.5266 (pt0) cc_final: 0.5003 (tp30) REVERT: B 137 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.4520 (ttp-170) REVERT: B 169 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6564 (mm-30) REVERT: B 188 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.5792 (m-30) REVERT: C 144 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8190 (mm) REVERT: G 60 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: G 136 LYS cc_start: 0.7664 (tttm) cc_final: 0.7428 (ttpp) REVERT: I 33 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6795 (mtt-85) REVERT: J 19 ASP cc_start: 0.7519 (m-30) cc_final: 0.7268 (m-30) REVERT: J 20 GLN cc_start: 0.7525 (mt0) cc_final: 0.7154 (mp10) REVERT: J 88 MET cc_start: 0.6755 (mmp) cc_final: 0.4996 (tmm) REVERT: J 99 GLN cc_start: 0.7671 (mm-40) cc_final: 0.6809 (mp10) REVERT: M 93 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7774 (mmm160) REVERT: M 113 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6608 (mtt180) REVERT: N 41 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7328 (ttp-110) REVERT: S 21 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7638 (ttpp) outliers start: 18 outliers final: 9 residues processed: 168 average time/residue: 0.7653 time to fit residues: 141.5139 Evaluate side-chains 169 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.122064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095149 restraints weight = 20711.664| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 0.74 r_work: 0.3076 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19833 Z= 0.248 Angle : 0.681 6.041 29005 Z= 0.356 Chirality : 0.041 0.213 3618 Planarity : 0.006 0.063 1984 Dihedral : 22.226 163.719 8426 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 1.97 % Allowed : 13.43 % Favored : 84.61 % 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: 1.16 (0.25), residues: 1069 helix: 1.22 (0.22), residues: 514 sheet: 0.49 (0.37), residues: 164 loop : 0.50 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 16 TYR 0.015 0.002 TYR I 38 PHE 0.023 0.002 PHE S 74 TRP 0.027 0.002 TRP B 23 HIS 0.005 0.002 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00478 (19833) covalent geometry : angle 0.68124 (29005) hydrogen bonds : bond 0.06492 ( 820) hydrogen bonds : angle 4.07467 ( 1850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.458 Fit side-chains REVERT: B 21 ARG cc_start: 0.5821 (ptp-170) cc_final: 0.4062 (mmt90) REVERT: B 27 MET cc_start: 0.6842 (mmm) cc_final: 0.6499 (mmm) REVERT: B 52 GLU cc_start: 0.5325 (pt0) cc_final: 0.5070 (tp30) REVERT: B 137 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.4793 (ttp-170) REVERT: B 169 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6570 (mm-30) REVERT: B 188 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.5823 (m-30) REVERT: C 144 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8214 (mm) REVERT: G 136 LYS cc_start: 0.7677 (tttm) cc_final: 0.7438 (ttpp) REVERT: I 33 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6781 (mtt-85) REVERT: J 19 ASP cc_start: 0.7511 (m-30) cc_final: 0.7260 (m-30) REVERT: J 20 GLN cc_start: 0.7520 (mt0) cc_final: 0.7171 (mp10) REVERT: J 88 MET cc_start: 0.6823 (mmp) cc_final: 0.5091 (tmm) REVERT: J 99 GLN cc_start: 0.7701 (mm-40) cc_final: 0.6806 (mp10) REVERT: M 93 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7818 (mmm160) REVERT: M 113 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6584 (mtt180) REVERT: N 41 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7387 (ttp-110) REVERT: S 21 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7647 (ttpp) outliers start: 18 outliers final: 9 residues processed: 167 average time/residue: 0.7699 time to fit residues: 141.4315 Evaluate side-chains 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096481 restraints weight = 20851.865| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.72 r_work: 0.3105 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19833 Z= 0.190 Angle : 0.608 5.426 29005 Z= 0.322 Chirality : 0.039 0.224 3618 Planarity : 0.005 0.054 1984 Dihedral : 22.157 163.717 8426 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % Rotamer: Outliers : 1.86 % Allowed : 13.32 % Favored : 84.83 % 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: 1.50 (0.25), residues: 1069 helix: 1.51 (0.22), residues: 514 sheet: 0.81 (0.38), residues: 159 loop : 0.57 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 136 TYR 0.014 0.002 TYR I 38 PHE 0.020 0.002 PHE S 74 TRP 0.026 0.002 TRP B 23 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00364 (19833) covalent geometry : angle 0.60811 (29005) hydrogen bonds : bond 0.05794 ( 820) hydrogen bonds : angle 3.92776 ( 1850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.440 Fit side-chains REVERT: B 21 ARG cc_start: 0.5769 (ptp-170) cc_final: 0.4018 (mmt90) REVERT: B 27 MET cc_start: 0.6817 (mmm) cc_final: 0.6395 (mmm) REVERT: B 52 GLU cc_start: 0.5266 (pt0) cc_final: 0.4938 (tp30) REVERT: B 137 ARG cc_start: 0.5307 (OUTLIER) cc_final: 0.4660 (ttp-170) REVERT: B 169 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6522 (mm-30) REVERT: B 188 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: C 72 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.7065 (mtt-85) REVERT: C 144 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8200 (mm) REVERT: G 60 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6503 (tp30) REVERT: G 78 ARG cc_start: 0.6261 (mmp-170) cc_final: 0.6001 (mmp-170) REVERT: G 136 LYS cc_start: 0.7661 (tttm) cc_final: 0.7423 (ttpp) REVERT: G 144 MET cc_start: 0.7432 (tpp) cc_final: 0.7218 (tpp) REVERT: J 19 ASP cc_start: 0.7545 (m-30) cc_final: 0.7284 (m-30) REVERT: J 20 GLN cc_start: 0.7438 (mt0) cc_final: 0.7106 (mp10) REVERT: J 88 MET cc_start: 0.6863 (mmp) cc_final: 0.5150 (tmm) REVERT: J 99 GLN cc_start: 0.7650 (mm-40) cc_final: 0.6790 (mp10) REVERT: M 93 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7817 (mmm160) REVERT: M 113 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6570 (mtt180) REVERT: N 41 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7358 (ttp-110) REVERT: S 21 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7613 (ttpp) REVERT: S 32 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7856 (ttp-170) outliers start: 17 outliers final: 9 residues processed: 170 average time/residue: 0.7418 time to fit residues: 138.8959 Evaluate side-chains 169 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096172 restraints weight = 20672.143| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.72 r_work: 0.3096 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19833 Z= 0.206 Angle : 0.626 5.414 29005 Z= 0.330 Chirality : 0.039 0.223 3618 Planarity : 0.005 0.057 1984 Dihedral : 22.133 163.751 8426 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 13.86 % Favored : 84.39 % 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: 1.50 (0.25), residues: 1069 helix: 1.48 (0.22), residues: 519 sheet: 0.84 (0.38), residues: 159 loop : 0.59 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 136 TYR 0.014 0.002 TYR I 38 PHE 0.021 0.002 PHE S 74 TRP 0.031 0.002 TRP B 23 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00395 (19833) covalent geometry : angle 0.62589 (29005) hydrogen bonds : bond 0.05993 ( 820) hydrogen bonds : angle 3.95091 ( 1850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.397 Fit side-chains REVERT: B 21 ARG cc_start: 0.5791 (ptp-170) cc_final: 0.4053 (mmt90) REVERT: B 27 MET cc_start: 0.6867 (mmm) cc_final: 0.6456 (mmm) REVERT: B 52 GLU cc_start: 0.5286 (pt0) cc_final: 0.4995 (tp30) REVERT: B 137 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.4777 (ttp-170) REVERT: B 169 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 188 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.5841 (m-30) REVERT: C 144 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8224 (mm) REVERT: G 60 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: G 136 LYS cc_start: 0.7612 (tttm) cc_final: 0.7377 (ttpp) REVERT: G 144 MET cc_start: 0.7438 (tpp) cc_final: 0.7223 (tpp) REVERT: I 33 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6814 (mtt-85) REVERT: J 19 ASP cc_start: 0.7537 (m-30) cc_final: 0.7280 (m-30) REVERT: J 20 GLN cc_start: 0.7453 (mt0) cc_final: 0.7113 (mp10) REVERT: J 88 MET cc_start: 0.6848 (mmp) cc_final: 0.5176 (tmm) REVERT: J 99 GLN cc_start: 0.7685 (mm-40) cc_final: 0.6784 (mp10) REVERT: M 41 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7794 (mt-10) REVERT: M 93 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7807 (mmm160) REVERT: M 113 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6341 (mtm180) REVERT: N 41 ARG cc_start: 0.7647 (mtp180) cc_final: 0.7398 (ttp-110) REVERT: S 21 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7642 (ttpp) REVERT: S 32 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7878 (ttp-170) outliers start: 16 outliers final: 9 residues processed: 168 average time/residue: 0.7648 time to fit residues: 141.4260 Evaluate side-chains 171 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096284 restraints weight = 20816.983| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.72 r_work: 0.3098 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19833 Z= 0.200 Angle : 0.623 5.693 29005 Z= 0.328 Chirality : 0.039 0.223 3618 Planarity : 0.005 0.056 1984 Dihedral : 22.134 163.746 8426 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 1.97 % Allowed : 13.76 % Favored : 84.28 % 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: 1.52 (0.25), residues: 1069 helix: 1.49 (0.22), residues: 519 sheet: 0.86 (0.38), residues: 159 loop : 0.60 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 136 TYR 0.014 0.002 TYR I 38 PHE 0.020 0.002 PHE S 74 TRP 0.037 0.002 TRP B 23 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00383 (19833) covalent geometry : angle 0.62264 (29005) hydrogen bonds : bond 0.05956 ( 820) hydrogen bonds : angle 3.94175 ( 1850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.474 Fit side-chains REVERT: B 21 ARG cc_start: 0.5751 (ptp-170) cc_final: 0.4003 (mmt90) REVERT: B 27 MET cc_start: 0.6810 (mmm) cc_final: 0.6386 (mmm) REVERT: B 52 GLU cc_start: 0.5259 (pt0) cc_final: 0.4919 (tp30) REVERT: B 137 ARG cc_start: 0.5368 (OUTLIER) cc_final: 0.4739 (ttp-170) REVERT: B 169 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6515 (mm-30) REVERT: B 188 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.5795 (m-30) REVERT: C 144 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8217 (mm) REVERT: G 60 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6510 (tp30) REVERT: G 136 LYS cc_start: 0.7614 (tttm) cc_final: 0.7376 (ttpp) REVERT: G 144 MET cc_start: 0.7403 (tpp) cc_final: 0.7201 (tpp) REVERT: I 33 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6816 (mtt-85) REVERT: J 19 ASP cc_start: 0.7532 (m-30) cc_final: 0.7283 (m-30) REVERT: J 20 GLN cc_start: 0.7439 (mt0) cc_final: 0.7100 (mp10) REVERT: J 88 MET cc_start: 0.6845 (mmp) cc_final: 0.5158 (tmm) REVERT: J 99 GLN cc_start: 0.7655 (mm-40) cc_final: 0.6779 (mp10) REVERT: M 93 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7794 (mmm160) REVERT: M 113 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6329 (mtm180) REVERT: N 41 ARG cc_start: 0.7620 (mtp180) cc_final: 0.7362 (ttp-110) REVERT: S 21 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7613 (ttpp) REVERT: S 32 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7876 (ttp-170) outliers start: 18 outliers final: 9 residues processed: 165 average time/residue: 0.7744 time to fit residues: 140.5509 Evaluate side-chains 170 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 154 TYR Chi-restraints excluded: chain I residue 33 ARG Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 137 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.096370 restraints weight = 20798.452| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 0.72 r_work: 0.3101 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19833 Z= 0.197 Angle : 0.619 5.416 29005 Z= 0.327 Chirality : 0.039 0.223 3618 Planarity : 0.005 0.055 1984 Dihedral : 22.131 163.734 8426 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 13.86 % Favored : 84.39 % 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: 1.53 (0.25), residues: 1069 helix: 1.50 (0.22), residues: 519 sheet: 0.86 (0.38), residues: 159 loop : 0.60 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 16 TYR 0.014 0.002 TYR I 38 PHE 0.020 0.002 PHE S 74 TRP 0.044 0.002 TRP B 23 HIS 0.004 0.001 HIS J 56 Details of bonding type rmsd covalent geometry : bond 0.00377 (19833) covalent geometry : angle 0.61934 (29005) hydrogen bonds : bond 0.05930 ( 820) hydrogen bonds : angle 3.93009 ( 1850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9590.58 seconds wall clock time: 163 minutes 56.53 seconds (9836.53 seconds total)