Starting phenix.real_space_refine on Sat Oct 31 01:00:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xtc_67201/10_2026/9xtc_67201.map" } resolution = 2.1 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= 0.003 sd= 0.078 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: 6 Type Number sf(0) Gaussians P 1175 5.49 5 Mg 39 5.21 5 S 46 5.16 5 C 18341 2.51 5 N 6799 2.21 5 O 13457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39857 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 25261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 25261 Classifications: {'RNA': 1175, 'RNAv2': 1} Modifications used: {'rna2p': 1, 'rna2p_pur': 86, 'rna2p_pyr': 63, 'rna3p': 6, 'rna3p_pur': 586, 'rna3p_pyr': 434} Link IDs: {'rna2p': 150, 'rna3p': 1025} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2851, 2851 Unusual residues: {' MG': 39} Classifications: {'undetermined': 39, 'water': 2812} Link IDs: {None: 2850} Chain: "O" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Time building chain proxies: 7.86, per 1000 atoms: 0.20 Number of scatterers: 39857 At special positions: 0 Unit cell: (132.039, 173.463, 207.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 1175 15.00 Mg 39 11.99 O 13457 8.00 N 6799 7.00 C 18341 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: 2.88 Conformation dependent library (CDL) restraints added in 766.0 milliseconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 45.1% alpha, 21.1% beta 403 base pairs and 619 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'F' and resid 11 through 15 removed outlier: 3.844A pdb=" N SER F 15 " --> pdb=" O PRO F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 33 removed outlier: 4.362A pdb=" N GLY F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.799A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.948A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.652A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.525A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 153 through 165 removed outlier: 3.806A pdb=" N ALA D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.898A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.718A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 58 through 74 removed outlier: 3.579A pdb=" N VAL K 64 " --> pdb=" O PHE K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 89 through 92 Processing helix chain 'K' and resid 93 through 102 removed outlier: 3.531A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'R' and resid 25 through 33 removed outlier: 3.922A pdb=" N LYS R 30 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE R 33 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.509A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.501A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.732A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix removed outlier: 3.548A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.693A pdb=" N GLN B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 removed outlier: 3.751A pdb=" N ASP B 127 " --> pdb=" O GLY B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 removed outlier: 3.577A pdb=" N LEU B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing sheet with id=AA1, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.331A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.765A pdb=" N VAL F 7 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET F 88 " --> pdb=" O VAL F 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.893A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 12 through 24 removed outlier: 6.569A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER E 22 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE E 30 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.562A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.896A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'H' and resid 74 through 77 removed outlier: 5.773A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 40 through 45 removed outlier: 5.975A pdb=" N GLY K 18 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N MET K 84 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA K 20 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LYS K 86 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE K 22 " --> pdb=" O LYS K 86 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL K 83 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE K 109 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL K 85 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP K 111 " --> pdb=" O VAL K 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 29 through 40 removed outlier: 6.483A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.330A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 7 through 14 removed outlier: 17.098A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 13.268A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.815A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.968A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 161 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1009 hydrogen bonds 1584 hydrogen bond angles 0 basepair planarities 403 basepair parallelities 619 stacking parallelities Total time for adding SS restraints: 55.49 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4229 1.32 - 1.45: 17221 1.45 - 1.57: 15882 1.57 - 1.70: 2347 1.70 - 1.82: 81 Bond restraints: 39760 Sorted by residual: bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.469 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" N9 A A 452 " pdb=" C4 A A 452 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.70e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.394 1.469 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3' G A 515 " pdb=" P PSU A 516 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.36e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.394 1.468 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 39755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 58726 2.64 - 5.28: 748 5.28 - 7.92: 38 7.92 - 10.56: 12 10.56 - 13.21: 3 Bond angle restraints: 59527 Sorted by residual: angle pdb=" O5' U A 252 " pdb=" C5' U A 252 " pdb=" C4' U A 252 " ideal model delta sigma weight residual 109.40 113.49 -4.09 8.00e-01 1.56e+00 2.61e+01 angle pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sigma weight residual 118.80 124.35 -5.55 1.10e+00 8.26e-01 2.55e+01 angle pdb=" O5' U A 89 " pdb=" C5' U A 89 " pdb=" C4' U A 89 " ideal model delta sigma weight residual 109.40 113.41 -4.01 8.00e-01 1.56e+00 2.51e+01 angle pdb=" C1' C A1096 " pdb=" N1 C A1096 " pdb=" C2 C A1096 " ideal model delta sigma weight residual 118.80 124.15 -5.35 1.10e+00 8.26e-01 2.37e+01 angle pdb=" C2' UR3 A1498 " pdb=" C1' UR3 A1498 " pdb=" N1 UR3 A1498 " ideal model delta sigma weight residual 114.00 106.71 7.29 1.50e+00 4.44e-01 2.36e+01 ... (remaining 59522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 22344 35.45 - 70.90: 2891 70.90 - 106.35: 312 106.35 - 141.80: 6 141.80 - 177.25: 2 Dihedral angle restraints: 25555 sinusoidal: 21416 harmonic: 4139 Sorted by residual: dihedral pdb=" O4' U A 610 " pdb=" C1' U A 610 " pdb=" N1 U A 610 " pdb=" C2 U A 610 " ideal model delta sinusoidal sigma weight residual -160.00 -5.86 -154.14 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 60.08 139.92 1 1.50e+01 4.44e-03 7.53e+01 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 61.78 138.22 1 1.50e+01 4.44e-03 7.45e+01 ... (remaining 25552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5899 0.066 - 0.132: 1263 0.132 - 0.197: 429 0.197 - 0.263: 7 0.263 - 0.329: 2 Chirality restraints: 7600 Sorted by residual: chirality pdb=" CG LEU B 54 " pdb=" CB LEU B 54 " pdb=" CD1 LEU B 54 " pdb=" CD2 LEU B 54 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C2' PSU A 516 " pdb=" C3' PSU A 516 " pdb=" O2' PSU A 516 " pdb=" C1' PSU A 516 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1' A A1446 " pdb=" O4' A A1446 " pdb=" C2' A A1446 " pdb=" N9 A A1446 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 7597 not shown) Planarity restraints: 3177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " -0.031 2.00e-02 2.50e+03 2.29e-01 1.71e+03 pdb=" N9 2MG A1516 " -0.033 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.142 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.130 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.017 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " 0.055 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " 0.016 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.172 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.228 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.330 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.160 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.043 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.651 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.126 2.00e-02 2.50e+03 2.10e-01 4.40e+02 pdb=" N6 MA6 A1519 " -0.363 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.118 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.125 2.00e-02 2.50e+03 2.08e-01 4.33e+02 pdb=" N6 MA6 A1518 " -0.360 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.118 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.118 2.00e-02 2.50e+03 ... (remaining 3174 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 591 2.44 - 3.05: 25642 3.05 - 3.67: 85089 3.67 - 4.28: 126961 4.28 - 4.90: 163427 Nonbonded interactions: 401710 Sorted by model distance: nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1604 " model vdw 1.822 2.170 nonbonded pdb=" OP1 A A 547 " pdb="MG MG A1623 " model vdw 1.901 2.170 nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1628 " model vdw 1.926 2.170 nonbonded pdb="MG MG A1629 " pdb=" O HOH A1808 " model vdw 1.934 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1614 " model vdw 1.942 2.170 ... (remaining 401705 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: 5.920 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 84.560 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.004 0.087 39760 Z= 0.294 Angle : 0.811 13.205 59527 Z= 0.640 Chirality : 0.060 0.329 7600 Planarity : 0.008 0.229 3177 Dihedral : 23.111 177.248 22883 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1418 helix: 1.42 (0.22), residues: 571 sheet: -0.29 (0.33), residues: 243 loop : -0.32 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 74 TYR 0.029 0.002 TYR L 117 PHE 0.012 0.001 PHE F 78 TRP 0.013 0.001 TRP P 60 HIS 0.005 0.001 HIS F 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.29 (39760) covalent geometry : angle 0.81145 / 0.64 (59527) hydrogen bonds : bond 0.09921 / 10.52 ( 1580) hydrogen bonds : angle 4.49341 / 5.79 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 62 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7619 (mm-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.9825 time to fit residues: 242.9694 Evaluate side-chains 206 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 63 ASN E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS Q 51 ASN T 3 ASN T 48 GLN T 52 ASN T 61 GLN T 82 GLN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.190514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131898 restraints weight = 30749.939| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 0.61 r_work: 0.3314 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 39760 Z= 0.377 Angle : 0.905 10.870 59527 Z= 0.469 Chirality : 0.055 0.291 7600 Planarity : 0.008 0.087 3177 Dihedral : 23.451 178.510 20059 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.95 % Allowed : 14.73 % Favored : 82.32 % 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: 0.34 (0.22), residues: 1418 helix: 1.10 (0.21), residues: 576 sheet: -0.31 (0.33), residues: 235 loop : -0.29 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 74 TYR 0.049 0.004 TYR L 117 PHE 0.021 0.002 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.013 0.003 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.38 (39760) covalent geometry : angle 0.90490 / 0.47 (59527) hydrogen bonds : bond 0.08869 / 9.61 ( 1580) hydrogen bonds : angle 3.92939 / 4.93 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7080 (mttp) REVERT: D 128 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5580 (ptm160) REVERT: D 187 GLU cc_start: 0.5929 (tm-30) cc_final: 0.5580 (tm-30) REVERT: E 146 ASN cc_start: 0.7172 (m-40) cc_final: 0.6392 (p0) REVERT: H 90 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7464 (p0) REVERT: L 54 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7480 (ttm170) REVERT: B 72 THR cc_start: 0.6531 (m) cc_final: 0.6165 (p) outliers start: 35 outliers final: 10 residues processed: 224 average time/residue: 0.9421 time to fit residues: 246.6074 Evaluate side-chains 222 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 86 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [119, 18, 67, 151, 186, 214, 40, 20, 42, 159, 152] chunk 119 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 186 optimal weight: 30.0000 chunk 214 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 37 HIS E 19 ASN E 82 GLN P 79 ASN Q 51 ASN T 48 GLN T 82 GLN B 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.190844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130399 restraints weight = 30609.486| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.62 r_work: 0.3286 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 39760 Z= 0.347 Angle : 0.855 10.643 59527 Z= 0.446 Chirality : 0.052 0.289 7600 Planarity : 0.007 0.069 3177 Dihedral : 23.394 179.817 20059 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.20 % Allowed : 13.89 % Favored : 82.91 % 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: 0.25 (0.22), residues: 1418 helix: 0.96 (0.20), residues: 587 sheet: -0.29 (0.34), residues: 235 loop : -0.31 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 74 TYR 0.048 0.004 TYR L 117 PHE 0.019 0.002 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.015 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.35 (39760) covalent geometry : angle 0.85461 / 0.45 (59527) hydrogen bonds : bond 0.08389 / 9.13 ( 1580) hydrogen bonds : angle 3.79929 / 4.74 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7790 (mmtt) REVERT: D 77 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7565 (tmmt) REVERT: D 128 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.5459 (ptm160) REVERT: D 187 GLU cc_start: 0.5973 (tm-30) cc_final: 0.5336 (tm-30) REVERT: E 146 ASN cc_start: 0.7318 (m-40) cc_final: 0.6493 (p0) REVERT: H 90 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7410 (p0) REVERT: K 34 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6964 (t) REVERT: K 84 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.5968 (pmt) REVERT: L 54 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7903 (ttm170) REVERT: T 24 ARG cc_start: 0.8552 (mmp-170) cc_final: 0.8333 (mtp180) REVERT: B 72 THR cc_start: 0.6608 (m) cc_final: 0.6175 (p) outliers start: 38 outliers final: 16 residues processed: 224 average time/residue: 0.9399 time to fit residues: 246.2911 Evaluate side-chains 221 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 136 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [134, 13, 163, 58, 95, 108, 50, 30, 190, 130, 200] chunk 134 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 37 ASN E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN B 146 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.192083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130527 restraints weight = 30521.958| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 0.63 r_work: 0.3329 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39760 Z= 0.239 Angle : 0.697 7.846 59527 Z= 0.380 Chirality : 0.044 0.291 7600 Planarity : 0.006 0.053 3177 Dihedral : 23.295 179.879 20059 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.28 % Allowed : 14.81 % Favored : 81.90 % 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: 0.50 (0.22), residues: 1418 helix: 1.27 (0.21), residues: 582 sheet: -0.19 (0.33), residues: 247 loop : -0.27 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 74 TYR 0.042 0.003 TYR L 117 PHE 0.015 0.002 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.006 0.002 HIS E 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.24 (39760) covalent geometry : angle 0.69742 / 0.38 (59527) hydrogen bonds : bond 0.07594 / 8.26 ( 1580) hydrogen bonds : angle 3.61990 / 4.52 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7753 (mmtt) REVERT: D 128 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.5484 (ptm160) REVERT: D 187 GLU cc_start: 0.6084 (tm-30) cc_final: 0.5477 (tm-30) REVERT: E 146 ASN cc_start: 0.7195 (m-40) cc_final: 0.6338 (p0) REVERT: H 67 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: H 90 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7353 (p0) REVERT: H 114 ARG cc_start: 0.7614 (ttp-110) cc_final: 0.7289 (ttp80) REVERT: K 84 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.5932 (pmt) REVERT: L 54 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7393 (ttm170) REVERT: P 76 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7780 (mtmt) REVERT: Q 11 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7307 (mtp-110) REVERT: T 24 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.8267 (mtp180) REVERT: B 72 THR cc_start: 0.6696 (m) cc_final: 0.6251 (p) REVERT: B 175 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6667 (tt0) outliers start: 39 outliers final: 15 residues processed: 226 average time/residue: 0.9530 time to fit residues: 252.3905 Evaluate side-chains 226 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [192, 1, 248, 242, 146, 238, 226, 156, 215, 19, 157] chunk 192 optimal weight: 0.0010 chunk 1 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 226 optimal weight: 0.0470 chunk 156 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 overall best weight: 2.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 GLN E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN B 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.192805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134340 restraints weight = 30857.600| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 0.57 r_work: 0.3341 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39760 Z= 0.182 Angle : 0.614 8.287 59527 Z= 0.345 Chirality : 0.041 0.317 7600 Planarity : 0.005 0.050 3177 Dihedral : 23.231 179.749 20059 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.86 % Allowed : 15.66 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1418 helix: 1.42 (0.21), residues: 582 sheet: -0.14 (0.33), residues: 247 loop : -0.20 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 74 TYR 0.038 0.002 TYR L 117 PHE 0.013 0.001 PHE Q 37 TRP 0.015 0.001 TRP P 60 HIS 0.006 0.001 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.18 (39760) covalent geometry : angle 0.61387 / 0.35 (59527) hydrogen bonds : bond 0.07097 / 7.72 ( 1580) hydrogen bonds : angle 3.53563 / 4.42 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7785 (mmtt) REVERT: D 128 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5550 (ptm160) REVERT: D 187 GLU cc_start: 0.6026 (tm-30) cc_final: 0.5422 (tm-30) REVERT: E 146 ASN cc_start: 0.7172 (m-40) cc_final: 0.6452 (p0) REVERT: H 67 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6941 (mm-40) REVERT: H 90 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7399 (p0) REVERT: H 114 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.7335 (ttp80) REVERT: K 84 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.5931 (pmt) REVERT: L 54 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: L 70 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: P 76 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7807 (mtmt) REVERT: Q 11 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7362 (mtp-110) REVERT: T 24 ARG cc_start: 0.8558 (mmp-170) cc_final: 0.8312 (mtp180) REVERT: B 72 THR cc_start: 0.6532 (m) cc_final: 0.6123 (p) REVERT: B 175 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6886 (tt0) outliers start: 34 outliers final: 14 residues processed: 219 average time/residue: 0.9279 time to fit residues: 238.1807 Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [206, 51, 48, 34, 114, 84, 96, 131, 30, 224, 216] chunk 206 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 114 optimal weight: 10.9990 chunk 84 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.189793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129572 restraints weight = 30577.413| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.65 r_work: 0.3267 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 39760 Z= 0.487 Angle : 1.061 13.282 59527 Z= 0.532 Chirality : 0.063 0.391 7600 Planarity : 0.009 0.093 3177 Dihedral : 23.418 179.505 20059 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 3.79 % Allowed : 15.40 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.17 (0.22), residues: 1418 helix: 0.86 (0.20), residues: 586 sheet: -0.33 (0.33), residues: 230 loop : -0.31 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG T 74 TYR 0.052 0.005 TYR L 117 PHE 0.024 0.003 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.013 0.003 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.49 (39760) covalent geometry : angle 1.06107 / 0.53 (59527) hydrogen bonds : bond 0.09308 / 10.07 ( 1580) hydrogen bonds : angle 3.93638 / 4.88 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7801 (mmtt) REVERT: D 33 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7224 (mttp) REVERT: D 77 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7594 (tmmt) REVERT: D 128 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5424 (ptm160) REVERT: E 146 ASN cc_start: 0.7414 (m-40) cc_final: 0.6509 (p0) REVERT: H 67 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7085 (mm-40) REVERT: H 90 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (p0) REVERT: H 114 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7324 (ttp80) REVERT: K 84 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.5868 (pmt) REVERT: L 54 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7222 (ttm-80) REVERT: L 56 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7874 (ttp-110) REVERT: P 76 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7843 (mtmt) REVERT: Q 11 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7385 (mtp-110) REVERT: T 24 ARG cc_start: 0.8613 (mmp-170) cc_final: 0.8312 (mtp180) REVERT: T 25 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (ttm110) REVERT: T 28 MET cc_start: 0.8849 (ttp) cc_final: 0.8590 (ttm) REVERT: B 72 THR cc_start: 0.6540 (m) cc_final: 0.6113 (p) REVERT: B 175 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6938 (tt0) outliers start: 45 outliers final: 21 residues processed: 228 average time/residue: 0.9734 time to fit residues: 259.2735 Evaluate side-chains 230 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 25 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 223 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [211, 244, 139, 237, 186, 183, 89, 205, 130, 248, 123] chunk 211 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.191586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131707 restraints weight = 30547.315| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 0.58 r_work: 0.3300 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39760 Z= 0.253 Angle : 0.734 11.324 59527 Z= 0.394 Chirality : 0.046 0.318 7600 Planarity : 0.006 0.057 3177 Dihedral : 23.284 179.509 20059 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.86 % Allowed : 17.09 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1418 helix: 1.18 (0.20), residues: 582 sheet: -0.23 (0.32), residues: 247 loop : -0.30 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 74 TYR 0.044 0.003 TYR L 117 PHE 0.016 0.002 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.008 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.25 (39760) covalent geometry : angle 0.73410 / 0.39 (59527) hydrogen bonds : bond 0.07754 / 8.45 ( 1580) hydrogen bonds : angle 3.64750 / 4.53 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7737 (mmtt) REVERT: D 128 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5492 (ptm160) REVERT: E 14 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7945 (mtmm) REVERT: E 146 ASN cc_start: 0.7346 (m-40) cc_final: 0.6372 (p0) REVERT: H 3 MET cc_start: 0.8397 (tpp) cc_final: 0.8190 (tpt) REVERT: H 67 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7485 (mm-40) REVERT: H 90 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7393 (p0) REVERT: H 114 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.7260 (ttp80) REVERT: K 84 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5915 (pmt) REVERT: L 54 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7424 (ttm170) REVERT: P 76 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7809 (mtmt) REVERT: Q 11 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7324 (mtp-110) REVERT: T 24 ARG cc_start: 0.8587 (mmp-170) cc_final: 0.8271 (mtp180) REVERT: T 25 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8723 (ttm110) REVERT: T 28 MET cc_start: 0.8798 (ttp) cc_final: 0.8555 (ttm) REVERT: B 72 THR cc_start: 0.6479 (m) cc_final: 0.6063 (p) REVERT: B 175 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6900 (tt0) REVERT: B 220 THR cc_start: 0.6708 (t) cc_final: 0.6504 (p) outliers start: 34 outliers final: 17 residues processed: 221 average time/residue: 0.9473 time to fit residues: 244.5479 Evaluate side-chains 227 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 25 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [6, 207, 189, 250, 197, 3, 132, 143, 162, 78, 120] chunk 6 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN Q 51 ASN T 48 GLN T 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133619 restraints weight = 30627.141| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 0.58 r_work: 0.3326 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39760 Z= 0.226 Angle : 0.683 9.473 59527 Z= 0.372 Chirality : 0.044 0.341 7600 Planarity : 0.006 0.055 3177 Dihedral : 23.215 179.291 20059 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.86 % Allowed : 17.59 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1418 helix: 1.36 (0.21), residues: 581 sheet: -0.23 (0.32), residues: 247 loop : -0.20 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 54 TYR 0.041 0.003 TYR L 117 PHE 0.016 0.002 PHE Q 37 TRP 0.017 0.002 TRP P 60 HIS 0.007 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.23 (39760) covalent geometry : angle 0.68304 / 0.37 (59527) hydrogen bonds : bond 0.07363 / 7.99 ( 1580) hydrogen bonds : angle 3.59355 / 4.47 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7773 (mmtt) REVERT: D 77 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7599 (tmmt) REVERT: D 128 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5524 (ptm160) REVERT: E 14 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7984 (mtmm) REVERT: E 146 ASN cc_start: 0.7219 (m-40) cc_final: 0.6487 (p0) REVERT: H 90 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7406 (p0) REVERT: H 114 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7312 (ttp80) REVERT: K 84 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6009 (pmt) REVERT: L 54 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7397 (ttm170) REVERT: P 76 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7824 (mtmt) REVERT: Q 11 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7320 (mtp-110) REVERT: T 24 ARG cc_start: 0.8596 (mmp-170) cc_final: 0.8301 (mtp180) REVERT: T 25 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8747 (ttm110) REVERT: T 28 MET cc_start: 0.8852 (ttp) cc_final: 0.8618 (ttm) REVERT: B 72 THR cc_start: 0.6599 (m) cc_final: 0.6155 (p) REVERT: B 175 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7188 (tt0) outliers start: 34 outliers final: 16 residues processed: 221 average time/residue: 0.9482 time to fit residues: 244.4296 Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 25 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [3, 23, 20, 164, 77, 137, 151, 9, 161, 0, 191] chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 137 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 0.2980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 GLN E 19 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.191232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130717 restraints weight = 30610.621| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.60 r_work: 0.3301 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 39760 Z= 0.278 Angle : 0.766 12.759 59527 Z= 0.407 Chirality : 0.048 0.273 7600 Planarity : 0.007 0.055 3177 Dihedral : 23.263 179.152 20059 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.53 % Allowed : 18.01 % Favored : 79.46 % 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: 0.50 (0.22), residues: 1418 helix: 1.25 (0.21), residues: 581 sheet: -0.27 (0.33), residues: 235 loop : -0.21 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 74 TYR 0.044 0.003 TYR L 117 PHE 0.023 0.002 PHE F 80 TRP 0.016 0.002 TRP P 60 HIS 0.008 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.28 (39760) covalent geometry : angle 0.76623 / 0.41 (59527) hydrogen bonds : bond 0.07876 / 8.53 ( 1580) hydrogen bonds : angle 3.66091 / 4.56 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7769 (mmtt) REVERT: D 77 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7574 (tmmt) REVERT: D 128 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5444 (ptm160) REVERT: E 14 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7981 (mtmm) REVERT: E 146 ASN cc_start: 0.7229 (m-40) cc_final: 0.6468 (p0) REVERT: H 90 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7405 (p0) REVERT: H 114 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7264 (ttp80) REVERT: K 84 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.5898 (pmt) REVERT: L 54 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7175 (ttm-80) REVERT: P 76 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7822 (mtmt) REVERT: Q 11 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (mtp-110) REVERT: T 24 ARG cc_start: 0.8598 (mmp-170) cc_final: 0.8277 (mtp180) REVERT: T 25 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8719 (ttm110) REVERT: T 28 MET cc_start: 0.8812 (ttp) cc_final: 0.8552 (ttm) REVERT: B 72 THR cc_start: 0.6533 (m) cc_final: 0.6183 (p) REVERT: B 169 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6369 (mm-30) REVERT: B 175 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7006 (tt0) outliers start: 30 outliers final: 16 residues processed: 219 average time/residue: 0.9771 time to fit residues: 249.4380 Evaluate side-chains 229 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 25 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 223 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [18, 108, 163, 75, 113, 16, 144, 106, 104, 176, 73] chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.189857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129672 restraints weight = 30296.162| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.65 r_work: 0.3264 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 39760 Z= 0.440 Angle : 1.007 13.081 59527 Z= 0.508 Chirality : 0.059 0.356 7600 Planarity : 0.009 0.085 3177 Dihedral : 23.362 179.008 20059 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 2.78 % Allowed : 17.93 % Favored : 79.29 % 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: 0.25 (0.22), residues: 1418 helix: 0.93 (0.20), residues: 585 sheet: -0.36 (0.33), residues: 230 loop : -0.25 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 74 TYR 0.051 0.005 TYR L 117 PHE 0.024 0.003 PHE Q 37 TRP 0.018 0.003 TRP P 60 HIS 0.013 0.003 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.44 (39760) covalent geometry : angle 1.00668 / 0.51 (59527) hydrogen bonds : bond 0.08980 / 9.71 ( 1580) hydrogen bonds : angle 3.89603 / 4.82 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 48 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7760 (mmtt) REVERT: D 33 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7149 (mttp) REVERT: D 77 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7545 (tmmt) REVERT: D 128 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5457 (ptm160) REVERT: E 14 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7948 (mtmm) REVERT: E 146 ASN cc_start: 0.7385 (m-40) cc_final: 0.6458 (p0) REVERT: H 67 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7579 (mm-40) REVERT: H 90 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7445 (p0) REVERT: H 114 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7239 (ttp80) REVERT: K 84 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.5885 (pmt) REVERT: L 54 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7459 (ttm170) REVERT: P 76 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: Q 11 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7345 (mtp-110) REVERT: T 24 ARG cc_start: 0.8628 (mmp-170) cc_final: 0.8282 (mtp180) REVERT: T 25 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8661 (ttm110) REVERT: T 28 MET cc_start: 0.8835 (ttp) cc_final: 0.8569 (ttm) REVERT: B 27 MET cc_start: 0.5999 (mmp) cc_final: 0.5784 (mmm) REVERT: B 72 THR cc_start: 0.6630 (m) cc_final: 0.6272 (p) REVERT: B 169 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6418 (mm-30) REVERT: B 175 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7046 (tt0) outliers start: 33 outliers final: 15 residues processed: 218 average time/residue: 0.9973 time to fit residues: 253.3366 Evaluate side-chains 225 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 25 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [72, 182, 28, 19, 179, 29, 121, 30, 90, 136, 243] chunk 72 optimal weight: 9.9990 chunk 182 optimal weight: 50.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 48 GLN T 82 GLN B 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.190794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130035 restraints weight = 30536.027| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 0.61 r_work: 0.3294 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 39760 Z= 0.322 Angle : 0.826 13.077 59527 Z= 0.432 Chirality : 0.050 0.284 7600 Planarity : 0.007 0.056 3177 Dihedral : 23.293 178.991 20059 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.61 % Allowed : 18.10 % Favored : 79.29 % 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: 0.39 (0.22), residues: 1418 helix: 1.13 (0.21), residues: 580 sheet: -0.33 (0.33), residues: 235 loop : -0.23 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 74 TYR 0.047 0.004 TYR L 117 PHE 0.020 0.002 PHE F 80 TRP 0.017 0.002 TRP P 60 HIS 0.011 0.002 HIS P 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.32 (39760) covalent geometry : angle 0.82603 / 0.43 (59527) hydrogen bonds : bond 0.08168 / 8.86 ( 1580) hydrogen bonds : angle 3.73092 / 4.63 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20203.54 seconds wall clock time: 343 minutes 9.13 seconds (20589.13 seconds total)